NprE (bacillolysin) is a secreted zinc metalloendopeptidase of the peptidase M4 (thermolysin-like) family. It is one of the two dominant extracellular proteases in stationary-phase B. subtilis culture supernatants, along with AprE (subtilisin). NprE is synthesized as a preproenzyme with an N-terminal Sec signal peptide (residues 1-27), a large propeptide (residues 28-221) that assists folding and transiently inhibits activity, and a mature catalytic domain (residues 222-521). The active site contains the conserved HExxH zinc-binding motif characteristic of M4 family proteases. The enzyme binds one catalytic Zn2+ ion and four structural Ca2+ ions that provide stability. NprE expression is tightly regulated and restricted to post-exponential/ stationary phase through the integrated action of repressors CodY, ScoC, and AbrB, and activator DegU~P. Together with AprE, deletion of nprE accounts for approximately 95% reduction in bulk extracellular protease activity, indicating its major contribution to extracellular proteolysis for nutrient scavenging during stationary phase.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0006508
proteolysis
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: IBA annotation of proteolysis based on phylogenetic inference from PANTHER (PTN002138658) and thermolysin (UniProtKB:P14756). NprE is a well-characterized metalloendopeptidase that catalyzes hydrolysis of peptide bonds, directly contributing to proteolysis in the extracellular milieu.
Reason: This is a core function of NprE. The enzyme is a secreted zinc metalloprotease that hydrolyzes peptide bonds, directly performing proteolysis. The phylogenetic inference from thermolysin (a closely related M4 family member) is appropriate. Multiple reviews confirm NprE as one of the two dominant extracellular proteases in B. subtilis stationary phase cultures.
Supporting Evidence:
file:BACSU/nprE/nprE-deep-research-falcon.md
NprE is a secreted zinc metallopeptidase of the peptidase M4 family (thermolysin-like proteases) and is one of the two dominant extracellular proteases in stationary phase culture supernatants (the other is AprE/subtilisin)
|
|
GO:0004222
metalloendopeptidase activity
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: IEA annotation from InterPro domain mapping (IPR001570, IPR013856, IPR023612). NprE contains the Peptidase_M4 domain and related domains characteristic of thermolysin-like metalloendopeptidases.
Reason: This is the most specific and accurate molecular function term for NprE. The enzyme is a zinc-dependent metalloendopeptidase that hydrolyzes internal peptide bonds using a catalytic mechanism involving Zn2+-activated water. The HExxH motif characteristic of M4 metalloproteases is present, and the catalytic mechanism is well-established for this enzyme family.
Supporting Evidence:
file:BACSU/nprE/nprE-deep-research-falcon.md
Thermolysin-like M4 metalloproteases are "Glu-zincins," using the conserved HExxH motif to bind Zn2+ (His-His) and a downstream Glu as the third zinc ligand; catalysis proceeds via activation of a zinc-bound water/hydroxide for peptide bond hydrolysis
|
|
GO:0005576
extracellular region
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: IEA annotation from UniProtKB subcellular location vocabulary mapping. UniProt records NprE as secreted (ECO:0000250). The protein has an N-terminal signal peptide for Sec-dependent export.
Reason: This is a core localization for NprE. The enzyme is secreted via the Sec pathway and functions in the extracellular milieu. The signal peptide (residues 1-27) directs export, and the mature protease accumulates in stationary-phase culture supernatants.
Supporting Evidence:
file:BACSU/nprE/nprE-deep-research-falcon.md
Mature NprE is extracellular/secreted, accumulating in stationary-phase culture supernatants
UniProt:P68736
SUBCELLULAR LOCATION: Secreted
|
|
GO:0006508
proteolysis
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: IEA annotation from combined automated methods (InterPro:IPR023612 Peptidase_M4 and UniProtKB-KW:KW-0645 Protease). This is a duplicate of the IBA annotation for proteolysis.
Reason: Duplicate annotation with different evidence source is acceptable. The IEA annotation reinforces the IBA annotation and is based on valid domain and keyword mappings. Both evidence lines correctly identify proteolysis as a core biological process for this enzyme.
Supporting Evidence:
file:BACSU/nprE/nprE-deep-research-falcon.md
Deletion of nprE and aprE together reduces culture supernatant protease activity by ~95% in stationary phase
|
|
GO:0008233
peptidase activity
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: IEA annotation from UniProtKB keyword mapping (KW-0645 Protease). GO:0008233 peptidase activity is a parent term of GO:0004222 metalloendopeptidase activity.
Reason: While this is a more general term than GO:0004222, it is not incorrect. The IEA annotation is based on a valid keyword mapping. Since the more specific term GO:0004222 (metalloendopeptidase activity) is also annotated, this broader term is acceptable as it provides a different evidence lineage and could be useful for hierarchical queries.
Supporting Evidence:
UniProt:P68736
RecName: Full=Bacillolysin; EC=3.4.24.28
|
|
GO:0008237
metallopeptidase activity
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: IEA annotation from UniProtKB keyword mapping (KW-0482 Metalloprotease). GO:0008237 metallopeptidase activity is a parent term of GO:0004222 metalloendopeptidase activity.
Reason: This term accurately describes NprE as a metal-dependent peptidase. While more general than GO:0004222, it correctly captures the metallopeptidase nature of the enzyme. The zinc dependence of the catalytic mechanism is well-established.
Supporting Evidence:
file:BACSU/nprE/nprE-deep-research-falcon.md
Activity is abolished by chelators (e.g., EDTA), and Ca2+ enhances stability/activity
|
|
GO:0016787
hydrolase activity
|
IEA
GO_REF:0000043 |
MARK AS OVER ANNOTATED |
Summary: IEA annotation from UniProtKB keyword mapping (KW-0378 Hydrolase). GO:0016787 hydrolase activity is a high-level parent term in the GO hierarchy.
Reason: While technically correct (metalloendopeptidases are hydrolases that use water as a nucleophile), this term is too general to be informative. The more specific terms GO:0004222 (metalloendopeptidase activity) and GO:0008237 (metallopeptidase activity) are already annotated and provide much more useful functional information. Retaining this very broad term adds little value.
Supporting Evidence:
file:BACSU/nprE/nprE-deep-research-falcon.md
catalysis proceeds via activation of a zinc-bound water/hydroxide for peptide bond hydrolysis
|
|
GO:0046872
metal ion binding
|
IEA
GO_REF:0000043 |
MODIFY |
Summary: IEA annotation from UniProtKB keyword mapping (KW-0479 Metal-binding). NprE binds one catalytic Zn2+ ion and four structural Ca2+ ions.
Reason: While NprE does bind metal ions, this generic term does not capture the specific and functionally important metal binding. The enzyme specifically binds zinc (essential for catalysis) and calcium (essential for structural stability). More specific terms GO:0008270 (zinc ion binding) and GO:0005509 (calcium ion binding) would be more informative and accurately represent the documented metal binding properties.
Proposed replacements:
zinc ion binding
calcium ion binding
Supporting Evidence:
UniProt:P68736
Binds 4 Ca(2+) ions per subunit
UniProt:P68736
Binds 1 zinc ion per subunit
file:BACSU/nprE/nprE-deep-research-falcon.md
Ca2+ ions stabilize structure and thermal resistance
|
provider: falcon
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start_time: '2025-12-18T08:26:45.687084'
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template_file: templates/gene_research_go_focused.md
template_variables:
organism: BACSU
gene_id: nprE
gene_symbol: nprE
uniprot_accession: P68736
protein_description: 'RecName: Full=Bacillolysin; EC=3.4.24.28; AltName: Full=Neutral
protease NprE; Flags: Precursor;'
gene_info: Name=nprE; OrderedLocusNames=BSU14700;
organism_full: Bacillus subtilis (strain 168).
protein_family: Belongs to the peptidase M4 family. .
protein_domains: FTP_domain. (IPR011096); PepSY. (IPR025711); Peptidase_M4. (IPR023612);
Peptidase_M4/M1_CTD_sf. (IPR027268); Peptidase_M4_C_domain. (IPR001570)
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citation_count: 30
BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'nprE' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information
Please provide a comprehensive research report on the gene nprE (gene ID: nprE, UniProt: P68736) in BACSU.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
Question: You are an expert researcher providing comprehensive, well-cited information.
Provide detailed information focusing on:
1. Key concepts and definitions with current understanding
2. Recent developments and latest research (prioritize 2023-2024 sources)
3. Current applications and real-world implementations
4. Expert opinions and analysis from authoritative sources
5. Relevant statistics and data from recent studies
Format as a comprehensive research report with proper citations. Include URLs and publication dates where available.
Always prioritize recent, authoritative sources and provide specific citations for all major claims.
BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'nprE' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information
Please provide a comprehensive research report on the gene nprE (gene ID: nprE, UniProt: P68736) in BACSU.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
Plan status: Objective 1 (identity verification) completed; objectives 2–7 addressed below with sourced evidence; final objective (write report) submitted here.
Comprehensive research report: Bacillus subtilis nprE (UniProt P68736)
1) Key concepts and definitions
2) Recent developments and latest research (2023–2024 priority)
3) Current applications and real-world implementations
4) Expert opinions and analysis from authoritative sources
5) Relevant statistics and data from recent studies
Functional detail: enzymology, localization, maturation, regulation, and physiology
Notes on substrate preferences and optima
Ambiguity check and symbol verification
Gaps and future directions (data needs)
References with URLs and dates
References
(harwood2022theinsand pages 12-13): Colin R Harwood and Yoshimi Kikuchi. The ins and outs of bacillus proteases: activities, functions and commercial significance. FEMS Microbiology Reviews, Aug 2022. URL: https://doi.org/10.1093/femsre/fuab046, doi:10.1093/femsre/fuab046. This article has 100 citations and is from a domain leading peer-reviewed journal.
(harwood2022theinsand pages 13-14): Colin R Harwood and Yoshimi Kikuchi. The ins and outs of bacillus proteases: activities, functions and commercial significance. FEMS Microbiology Reviews, Aug 2022. URL: https://doi.org/10.1093/femsre/fuab046, doi:10.1093/femsre/fuab046. This article has 100 citations and is from a domain leading peer-reviewed journal.
(harwood2022theinsand pages 14-15): Colin R Harwood and Yoshimi Kikuchi. The ins and outs of bacillus proteases: activities, functions and commercial significance. FEMS Microbiology Reviews, Aug 2022. URL: https://doi.org/10.1093/femsre/fuab046, doi:10.1093/femsre/fuab046. This article has 100 citations and is from a domain leading peer-reviewed journal.
(hase1993bacterialextracellularzinccontaining pages 2-3): C. Hase and Richard A. Finkelstein. Bacterial extracellular zinc-containing metalloproteases. Microbiological Reviews, 57:823-837, Dec 1993. URL: https://doi.org/10.1128/mr.57.4.823-837.1993, doi:10.1128/mr.57.4.823-837.1993. This article has 425 citations.
(adekoya2009thethermolysinfamily pages 3-4): Olayiwola A. Adekoya and Ingebrigt Sylte. The thermolysin family (m4) of enzymes: therapeutic and biotechnological potential. Chemical Biology & Drug Design, 73:7-16, Jan 2009. URL: https://doi.org/10.1111/j.1747-0285.2008.00757.x, doi:10.1111/j.1747-0285.2008.00757.x. This article has 225 citations and is from a peer-reviewed journal.
(hase1993bacterialextracellularzinccontaining pages 3-4): C. Hase and Richard A. Finkelstein. Bacterial extracellular zinc-containing metalloproteases. Microbiological Reviews, 57:823-837, Dec 1993. URL: https://doi.org/10.1128/mr.57.4.823-837.1993, doi:10.1128/mr.57.4.823-837.1993. This article has 425 citations.
(adekoya2009thethermolysinfamily pages 7-8): Olayiwola A. Adekoya and Ingebrigt Sylte. The thermolysin family (m4) of enzymes: therapeutic and biotechnological potential. Chemical Biology & Drug Design, 73:7-16, Jan 2009. URL: https://doi.org/10.1111/j.1747-0285.2008.00757.x, doi:10.1111/j.1747-0285.2008.00757.x. This article has 225 citations and is from a peer-reviewed journal.
(astles2024novelextremophilicmetalloproteases pages 56-60): Benjamin Michael Astles. Novel extremophilic metalloproteases for consumer product application. Unknown, Jul 2024. URL: https://doi.org/10.7488/era/4696, doi:10.7488/era/4696. This article has 0 citations.
(liu2018efficientproductionof pages 6-9): Xin Liu, Hai Wang, Bin Wang, and Li Pan. Efficient production of extracellular pullulanase in bacillus subtilis atcc6051 using the host strain construction and promoter optimization expression system. Microbial Cell Factories, Oct 2018. URL: https://doi.org/10.1186/s12934-018-1011-y, doi:10.1186/s12934-018-1011-y. This article has 59 citations and is from a peer-reviewed journal.
(harwood2022theinsand pages 11-12): Colin R Harwood and Yoshimi Kikuchi. The ins and outs of bacillus proteases: activities, functions and commercial significance. FEMS Microbiology Reviews, Aug 2022. URL: https://doi.org/10.1093/femsre/fuab046, doi:10.1093/femsre/fuab046. This article has 100 citations and is from a domain leading peer-reviewed journal.
(barbieri2016interplayofcody pages 1-6): Giulia Barbieri, Alessandra M. Albertini, Eugenio Ferrari, Abraham L. Sonenshein, and Boris R. Belitsky. Interplay of cody and scoc in the regulation of major extracellular protease genes of bacillus subtilis. Journal of Bacteriology, 198:907-920, Mar 2016. URL: https://doi.org/10.1128/jb.00894-15, doi:10.1128/jb.00894-15. This article has 83 citations and is from a peer-reviewed journal.
(manni2008biochemicalandmolecular pages 5-8): Laila Manni, Kemel Jellouli, Rym Agrebi, Ahmed Bayoudh, and Moncef Nasri. Biochemical and molecular characterization of a novel calcium-dependent metalloprotease from bacillus cereus sv1. Process Biochemistry, 43:522-530, May 2008. URL: https://doi.org/10.1016/j.procbio.2008.01.016, doi:10.1016/j.procbio.2008.01.016. This article has 34 citations and is from a peer-reviewed journal.
(manni2008biochemicalandmolecular pages 9-9): Laila Manni, Kemel Jellouli, Rym Agrebi, Ahmed Bayoudh, and Moncef Nasri. Biochemical and molecular characterization of a novel calcium-dependent metalloprotease from bacillus cereus sv1. Process Biochemistry, 43:522-530, May 2008. URL: https://doi.org/10.1016/j.procbio.2008.01.016, doi:10.1016/j.procbio.2008.01.016. This article has 34 citations and is from a peer-reviewed journal.
id: P68736
gene_symbol: nprE
product_type: PROTEIN
status: DRAFT
taxon:
id: NCBITaxon:224308
label: Bacillus subtilis (strain 168)
description: >-
NprE (bacillolysin) is a secreted zinc metalloendopeptidase of the peptidase M4 (thermolysin-like) family.
It is one of the two dominant extracellular proteases in stationary-phase B. subtilis culture supernatants,
along with AprE (subtilisin). NprE is synthesized as a preproenzyme with an N-terminal Sec signal peptide
(residues 1-27), a large propeptide (residues 28-221) that assists folding and transiently inhibits activity,
and a mature catalytic domain (residues 222-521). The active site contains the conserved HExxH zinc-binding
motif characteristic of M4 family proteases. The enzyme binds one catalytic Zn2+ ion and four structural
Ca2+ ions that provide stability. NprE expression is tightly regulated and restricted to post-exponential/
stationary phase through the integrated action of repressors CodY, ScoC, and AbrB, and activator DegU~P.
Together with AprE, deletion of nprE accounts for approximately 95% reduction in bulk extracellular protease
activity, indicating its major contribution to extracellular proteolysis for nutrient scavenging during
stationary phase.
existing_annotations:
- term:
id: GO:0006508
label: proteolysis
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
IBA annotation of proteolysis based on phylogenetic inference from PANTHER (PTN002138658) and
thermolysin (UniProtKB:P14756). NprE is a well-characterized metalloendopeptidase that catalyzes
hydrolysis of peptide bonds, directly contributing to proteolysis in the extracellular milieu.
action: ACCEPT
reason: >-
This is a core function of NprE. The enzyme is a secreted zinc metalloprotease that hydrolyzes
peptide bonds, directly performing proteolysis. The phylogenetic inference from thermolysin
(a closely related M4 family member) is appropriate. Multiple reviews confirm NprE as one of
the two dominant extracellular proteases in B. subtilis stationary phase cultures.
supported_by:
- reference_id: file:BACSU/nprE/nprE-deep-research-falcon.md
supporting_text: >-
NprE is a secreted zinc metallopeptidase of the peptidase M4 family (thermolysin-like proteases)
and is one of the two dominant extracellular proteases in stationary phase culture supernatants
(the other is AprE/subtilisin)
- term:
id: GO:0004222
label: metalloendopeptidase activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
IEA annotation from InterPro domain mapping (IPR001570, IPR013856, IPR023612). NprE contains
the Peptidase_M4 domain and related domains characteristic of thermolysin-like metalloendopeptidases.
action: ACCEPT
reason: >-
This is the most specific and accurate molecular function term for NprE. The enzyme is a
zinc-dependent metalloendopeptidase that hydrolyzes internal peptide bonds using a catalytic
mechanism involving Zn2+-activated water. The HExxH motif characteristic of M4 metalloproteases
is present, and the catalytic mechanism is well-established for this enzyme family.
supported_by:
- reference_id: file:BACSU/nprE/nprE-deep-research-falcon.md
supporting_text: >-
Thermolysin-like M4 metalloproteases are "Glu-zincins," using the conserved HExxH motif to bind
Zn2+ (His-His) and a downstream Glu as the third zinc ligand; catalysis proceeds via activation
of a zinc-bound water/hydroxide for peptide bond hydrolysis
- term:
id: GO:0005576
label: extracellular region
evidence_type: IEA
original_reference_id: GO_REF:0000044
review:
summary: >-
IEA annotation from UniProtKB subcellular location vocabulary mapping. UniProt records NprE
as secreted (ECO:0000250). The protein has an N-terminal signal peptide for Sec-dependent export.
action: ACCEPT
reason: >-
This is a core localization for NprE. The enzyme is secreted via the Sec pathway and functions
in the extracellular milieu. The signal peptide (residues 1-27) directs export, and the mature
protease accumulates in stationary-phase culture supernatants.
supported_by:
- reference_id: file:BACSU/nprE/nprE-deep-research-falcon.md
supporting_text: >-
Mature NprE is extracellular/secreted, accumulating in stationary-phase culture supernatants
- reference_id: UniProt:P68736
supporting_text: >-
SUBCELLULAR LOCATION: Secreted
- term:
id: GO:0006508
label: proteolysis
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
IEA annotation from combined automated methods (InterPro:IPR023612 Peptidase_M4 and
UniProtKB-KW:KW-0645 Protease). This is a duplicate of the IBA annotation for proteolysis.
action: ACCEPT
reason: >-
Duplicate annotation with different evidence source is acceptable. The IEA annotation reinforces
the IBA annotation and is based on valid domain and keyword mappings. Both evidence lines
correctly identify proteolysis as a core biological process for this enzyme.
supported_by:
- reference_id: file:BACSU/nprE/nprE-deep-research-falcon.md
supporting_text: >-
Deletion of nprE and aprE together reduces culture supernatant protease activity by ~95%
in stationary phase
- term:
id: GO:0008233
label: peptidase activity
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
IEA annotation from UniProtKB keyword mapping (KW-0645 Protease). GO:0008233 peptidase activity
is a parent term of GO:0004222 metalloendopeptidase activity.
action: ACCEPT
reason: >-
While this is a more general term than GO:0004222, it is not incorrect. The IEA annotation
is based on a valid keyword mapping. Since the more specific term GO:0004222 (metalloendopeptidase
activity) is also annotated, this broader term is acceptable as it provides a different evidence
lineage and could be useful for hierarchical queries.
supported_by:
- reference_id: UniProt:P68736
supporting_text: >-
RecName: Full=Bacillolysin; EC=3.4.24.28
- term:
id: GO:0008237
label: metallopeptidase activity
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
IEA annotation from UniProtKB keyword mapping (KW-0482 Metalloprotease). GO:0008237 metallopeptidase
activity is a parent term of GO:0004222 metalloendopeptidase activity.
action: ACCEPT
reason: >-
This term accurately describes NprE as a metal-dependent peptidase. While more general than
GO:0004222, it correctly captures the metallopeptidase nature of the enzyme. The zinc dependence
of the catalytic mechanism is well-established.
supported_by:
- reference_id: file:BACSU/nprE/nprE-deep-research-falcon.md
supporting_text: >-
Activity is abolished by chelators (e.g., EDTA), and Ca2+ enhances stability/activity
- term:
id: GO:0016787
label: hydrolase activity
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
IEA annotation from UniProtKB keyword mapping (KW-0378 Hydrolase). GO:0016787 hydrolase activity
is a high-level parent term in the GO hierarchy.
action: MARK_AS_OVER_ANNOTATED
reason: >-
While technically correct (metalloendopeptidases are hydrolases that use water as a nucleophile),
this term is too general to be informative. The more specific terms GO:0004222 (metalloendopeptidase
activity) and GO:0008237 (metallopeptidase activity) are already annotated and provide much more
useful functional information. Retaining this very broad term adds little value.
supported_by:
- reference_id: file:BACSU/nprE/nprE-deep-research-falcon.md
supporting_text: >-
catalysis proceeds via activation of a zinc-bound water/hydroxide for peptide bond hydrolysis
- term:
id: GO:0046872
label: metal ion binding
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
IEA annotation from UniProtKB keyword mapping (KW-0479 Metal-binding). NprE binds one catalytic
Zn2+ ion and four structural Ca2+ ions.
action: MODIFY
reason: >-
While NprE does bind metal ions, this generic term does not capture the specific and functionally
important metal binding. The enzyme specifically binds zinc (essential for catalysis) and calcium
(essential for structural stability). More specific terms GO:0008270 (zinc ion binding) and
GO:0005509 (calcium ion binding) would be more informative and accurately represent the
documented metal binding properties.
proposed_replacement_terms:
- id: GO:0008270
label: zinc ion binding
- id: GO:0005509
label: calcium ion binding
supported_by:
- reference_id: UniProt:P68736
supporting_text: >-
Binds 4 Ca(2+) ions per subunit
- reference_id: UniProt:P68736
supporting_text: >-
Binds 1 zinc ion per subunit
- reference_id: file:BACSU/nprE/nprE-deep-research-falcon.md
supporting_text: >-
Ca2+ ions stabilize structure and thermal resistance
core_functions:
- molecular_function:
id: GO:0004222
label: metalloendopeptidase activity
directly_involved_in:
- id: GO:0006508
label: proteolysis
locations:
- id: GO:0005576
label: extracellular region
description: >-
Core enzymatic function. NprE is a zinc-dependent metalloendopeptidase with thermolysin-like
catalytic activity (EC 3.4.24.28). Uses HExxH motif for zinc binding and catalysis.
Along with AprE, NprE accounts for approximately 95% of extracellular proteolytic activity
in stationary-phase B. subtilis cultures. Secreted via Sec pathway with N-terminal signal
peptide. Mature enzyme accumulates in culture supernatant during stationary phase.
supported_by:
- reference_id: file:BACSU/nprE/nprE-deep-research-falcon.md
supporting_text: >-
NprE is a secreted zinc metallopeptidase of the peptidase M4 family (thermolysin-like proteases)
and is one of the two dominant extracellular proteases in stationary phase culture supernatants
(the other is AprE/subtilisin)
- reference_id: file:BACSU/nprE/nprE-deep-research-falcon.md
supporting_text: >-
Thermolysin-like M4 metalloproteases are "Glu-zincins," using the conserved HExxH motif
to bind Zn2+ (His-His) and a downstream Glu as the third zinc ligand; catalysis proceeds
via activation of a zinc-bound water/hydroxide for peptide bond hydrolysis
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO terms
findings:
- statement: InterPro domains IPR001570, IPR013856, IPR023612 identify Peptidase_M4 family membership
- id: GO_REF:0000033
title: Annotation inferences using phylogenetic trees
findings:
- statement: Phylogenetic relationship to thermolysin (P14756) supports proteolysis annotation
- id: GO_REF:0000043
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
findings:
- statement: Keywords Protease, Metalloprotease, Hydrolase, Metal-binding map to corresponding GO terms
- id: GO_REF:0000044
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping
findings:
- statement: Secreted subcellular location maps to extracellular region
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings:
- statement: Combined InterPro and keyword evidence for proteolysis
- id: UniProt:P68736
title: UniProt entry for Bacillus subtilis bacillolysin (NprE)
findings:
- statement: Extracellular zinc metalloprotease with thermolysin-like activity
supporting_text: >-
FUNCTION: Extracellular zinc metalloprotease
- statement: Binds calcium ions for structural stability
supporting_text: >-
Binds 4 Ca(2+) ions per subunit
- statement: Binds zinc for catalytic activity
supporting_text: >-
Binds 1 zinc ion per subunit
- statement: Secreted protein
supporting_text: >-
SUBCELLULAR LOCATION: Secreted
- statement: Member of peptidase M4 family
supporting_text: >-
Belongs to the peptidase M4 family
- id: file:BACSU/nprE/nprE-deep-research-falcon.md
title: Deep research review of nprE gene function
findings:
- statement: NprE is one of two dominant extracellular proteases in B. subtilis stationary phase
supporting_text: >-
NprE is a secreted zinc metallopeptidase of the peptidase M4 family (thermolysin-like proteases)
and is one of the two dominant extracellular proteases in stationary phase culture supernatants
(the other is AprE/subtilisin)
- statement: M4 family proteases contain HExxH zinc-binding motif and use Glu-zincin mechanism
supporting_text: >-
Thermolysin-like M4 metalloproteases are "Glu-zincins," using the conserved HExxH motif to bind
Zn2+ (His-His) and a downstream Glu as the third zinc ligand; catalysis proceeds via activation
of a zinc-bound water/hydroxide for peptide bond hydrolysis
- statement: Deletion of nprE and aprE reduces extracellular protease activity by approximately 95%
supporting_text: >-
Deletion of nprE and aprE together reduces culture supernatant protease activity by ~95%
in stationary phase
- statement: NprE is secreted and accumulates extracellularly
supporting_text: >-
Mature NprE is extracellular/secreted, accumulating in stationary-phase culture supernatants
- statement: Activity abolished by chelators, enhanced by Ca2+
supporting_text: >-
Activity is abolished by chelators (e.g., EDTA), and Ca2+ enhances stability/activity
- statement: Ca2+ provides structural stability
supporting_text: >-
Ca2+ ions stabilize structure and thermal resistance
- statement: Expression regulated by CodY, ScoC, AbrB, and DegU~P
supporting_text: >-
nprE expression is strongly expressed only post-exponentially/late log-to-stationary phase.
Regulation involves: (i) direct repression by CodY under nutrient-replete conditions