Bacterial cytochrome c maturation system I

A reusable bacterial module for covalent attachment of heme to exported c-type cytochrome apoproteins by cytochrome c maturation system I. The canonical CcmABCDEFGH machinery combines CcmCDE-dependent heme trafficking and holo-CcmE formation, downstream CcmAB-dependent energy coupling, CcmG/CcmH thiol reduction, and CcmF/CcmH-dependent heme ligation. Lineage-dependent CcmI/CycH-family factors can support the ligation stage. Sec-dependent apocytochrome export, upstream DsbD electron delivery, and heme biosynthesis are external dependencies.

MODULE:bacterial_cytochrome_c_maturation_system_iDRAFTABSTRACTBiological Processmodules/bacterial_cytochrome_c_maturation_system_i.yaml
cytochrome c-heme linkageGO:0018063
GO:0018063
cytochrome c-heme linkage
GO:0018063 defines the process boundary as covalent linkage of heme to cytochrome c.
GO:0004408
holocytochrome-c synthase activity
GO:0004408 defines the terminal molecular function as conversion of apocytochrome c and heme to holocytochrome c.
PMID:10339610
Heme transfer to the heme chaperone CcmE during cytochrome c maturation requires the CcmC protein, which may function independently of the ABC-transporter CcmAB.
Direct experiments distinguish the CcmAB energy-coupling subcomplex from the CcmC-dependent heme-transfer step and place CcmD in stabilization of membrane-associated CcmE.
PMID:17419738
Loss of ATP hydrolysis activity by CcmAB results in loss of c-type cytochrome synthesis and incomplete processing of CcmE.
CcmAB ATP hydrolysis is required for efficient processing and release of holo-CcmE rather than an established heme-export reaction.
PMID:19721088
Cytochrome c biogenesis: mechanisms for covalent modifications and trafficking of heme and for heme-iron redox control.
The system I framework separates CcmABCD/CcmE heme handling from CcmF/CcmH-dependent heme-iron reduction and ligation.
PMID:18753134
The cytochrome c maturation components CcmF, CcmH, and CcmI form a membrane-integral multisubunit heme ligation complex.
Biochemical evidence supports a membrane-integral CcmF/CcmH ligation complex with a lineage-dependent CcmI-family accessory.
PMID:20544959
Structural and functional characterization of CcmG from Pseudomonas aeruginosa, a key component of the bacterial cytochrome c maturation apparatus.
Structural analysis supports CcmG thiol-disulfide reductase activity and proposes a CcmH-apocytochrome mixed disulfide as a physiological substrate.
PMID:28634234
The thioreduction component CcmG confers efficiency and the heme ligation component CcmH ensures stereo-specificity during cytochrome c maturation.
Reconstituted biochemistry separates the efficiency contribution of CcmG from the stereospecific ligation role of CcmH.
PMID:8231805
Formation of several bacterial c-type cytochromes requires a novel membrane-anchored protein that faces the periplasm.
Disruption of a characterized CycH-family ortholog causes broad loss of c-type cytochromes.
file:projects/P_PUTIDA/deep-research/PSEPK__bacterial_cytochrome_c_maturation_system_i__ppu02010-deep-research-openscientist.md
PSEPK cytochrome c maturation system I module/pathway/taxon research
The report confirms that the nine selected PSEPK proteins cover the internal module and distinguishes PP_5748 CcmH from PP_4320 CcmI/CycH. Its recommendation to assign heme transport to CcmABC is rejected because it conflicts with direct experimental evidence.
file:modules/bacterial_cytochrome_c_maturation_system_i-deep-research-openscientist.md
Generic bacterial cytochrome c maturation system I research
The report supports CcmABCD physical assembly, CcmE heme chaperoning, the CcmG/CcmH redox relay, and CcmF/CcmH ligation. Its membrane-trafficking language is interpreted as intramachinery heme handling, not a literal CcmAB heme-export function.

This module represents the canonical bacterial system I boundary. CcmAB is modeled as an ATP-dependent energy-coupling subcomplex, not as a literal heme exporter. CcmCDE performs heme transfer and holo-CcmE formation, while CcmG and CcmH provide the thiol-redox dependency that converges with holo-CcmE at the CcmF/CcmH ligation complex. CcmH therefore appears in both the redox and ligation roles. CcmI/CycH-family accessories are lineage dependent. General Sec export, DsbD electron supply, and heme biosynthesis remain outside the module.

8Nodes
7Parts
0Variant Sets
0Variants
9Annotons
6Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✓ present

  • bacterial_cytochrome_c_maturation_system_i-deep-research-openscientist.md (openscientist)

Leaf nodes lacking representative members

✓ representative grounding skipped for abstract module.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Gene-review completeness (9/9 grounded genes reviewed)

9 complete review(s) · 0 with deep research · 0 missing review · 9 reviewed but lacking deep research

Gene Review Complete Deep research
ccmA Q88EX5 ✓ ✓ ✗
ccmB Q88EX6 ✓ ✓ ✗
ccmC Q88EX7 ✓ ✓ ✗
ccmD Q88EX8 ✓ ✓ ✗
ccmE Q88EX9 ✓ ✓ ✗
ccmF Q88EY0 ✓ ✓ ✗
ccmG Q88EY1 ✓ ✓ ✗
ccmH A0A140FWM4 ✓ ✓ ✗
cycH A0A140FWM3 ✓ ✓ ✗

Details

Context
bacteriaNCBITaxon:2
Bacterial cytochrome c maturation system IBiological Processbacterial_cytochrome_c_maturation_system_i
cytochrome c-heme linkageGO:0018063
Context
bacteriaNCBITaxon:2

Connections

Part 1: heme trafficking and holo-CcmE formation
CcmABCDE heme trafficking and holo-CcmE formationBiological Processccmabcde_heme_trafficking

CcmC binds heme and loads it covalently onto CcmE with support from CcmD, after which CcmAB supplies ATP-dependent energy coupling for holo-CcmE processing and release. CcmA-D can associate in a larger membrane complex, while the CcmAB energy-coupling and CcmCDE heme-loading roles remain functionally distinguishable. The transported substrate or coupled transition of CcmAB remains unresolved.

Connections

Part 1: heme transfer and covalent loading of CcmE
CcmCDE holo-CcmE-forming assemblyProtein Complexccmcde_holo_ccme_formation

Annotons

CcmC heme-handling subunit
ccmc_heme_handling_subunit
Participant: Family: CcmC cytochrome-c-biogenesis family
Family:
CcmC cytochrome-c-biogenesis familyInterPro:IPR003557
Representative Members: CcmC (Pseudomonas putida KT2440)UniProtKB:Q88EX7

Function

heme bindingGO:0020037

Binds membrane-associated heme and supports covalent heme transfer to CcmE; literal heme transmembrane transport is not asserted.

CcmD accessory subunit
ccmd_accessory_subunit
Participant: Family: CcmD cytochrome-c-maturation family
Family:
CcmD cytochrome-c-maturation familyPANTHER:PTHR37531:SF1
Representative Members: CcmD (Pseudomonas putida KT2440)UniProtKB:Q88EX8

Stabilizes membrane-associated CcmE and supports accumulation of holo-CcmE.

CcmE heme chaperone
ccme_heme_chaperone
Participant: Family: CcmE heme-chaperone family
Family:
CcmE heme-chaperone familyInterPro:IPR004329
Representative Members: CcmE (Pseudomonas putida KT2440)UniProtKB:Q88EX9

Function

heme bindingGO:0020037

Processes

cytochrome c-heme linkageGO:0018063

Transiently carries covalently bound heme from the CcmCDE assembly to the downstream ligation machinery.

Connections

Part 2: ATP-dependent holo-CcmE processing
CcmAB energy-coupling subcomplexProtein Complexccmab_energy_coupling

Annotons

CcmA ATPase
ccma_atpase
Participant: Family: CcmA cytochrome-c-maturation ATPase family
Family:
CcmA cytochrome-c-maturation ATPase familyInterPro:IPR005895
Representative Members: CcmA (Pseudomonas putida KT2440)UniProtKB:Q88EX5

Function

ATP hydrolysis activityGO:0016887

Hydrolyzes ATP to support processing and release of holo-CcmE; no substrate-specific transporter activity is asserted.

CcmB membrane subunit
ccmb_membrane_subunit
Participant: Family: CcmB cytochrome-c-maturation family
Family:
CcmB cytochrome-c-maturation familyPANTHER:PTHR30070:SF1
Representative Members: CcmB (Pseudomonas putida KT2440)UniProtKB:Q88EX6

Forms the integral membrane partner of the CcmA ATPase; the coupled molecular substrate or conformational transition is unresolved.

Part 2: reductive preparation of apocytochrome CXXCH motifs
CcmG/CcmH apocytochrome thiol-redox preparationBiological Processccmgh_redox_preparation

CcmG and the redox-active region of CcmH maintain apocytochrome CXXCH cysteines in a ligation-competent state. Electrons ultimately supplied by DsbD enter this relay upstream of the modeled boundary.

Annotons

CcmG thiol-disulfide oxidoreductase
ccmg_disulfide_reductase
Participant: Family: CcmG/DsbE thioredoxin family
Family:
CcmG/DsbE thioredoxin familyInterPro:IPR004799
Representative Members: CcmG (Pseudomonas putida KT2440)UniProtKB:Q88EY1

Function

protein-disulfide reductase activityGO:0015035

Supplies thiol-reducing activity by reducing apocytochrome disulfides and/or resolving CcmH-apocytochrome mixed-disulfide intermediates, depending on system architecture.

CcmH redox component
ccmh_redox_component
Participant: Family: CcmH cytochrome-c-maturation family
Family:
CcmH cytochrome-c-maturation familyPANTHER:PTHR47870:SF1
Representative Members: CcmH (Pseudomonas putida KT2440)UniProtKB:A0A140FWM4

Forms and resolves redox intermediates with apocytochrome and also contributes to stereospecific heme ligation; no unsupported standalone molecular function is assigned.

Connections

Part 3: covalent heme ligation to reduced apocytochrome
CcmF/CcmH heme-ligation machineryBiological Processccmfh_heme_ligation

The CcmF/CcmH membrane assembly receives holo-CcmE and reduced apocytochrome and catalyzes stereospecific covalent attachment of heme to the CXXCH motif. Some lineages add a CcmI/CycH-family maturation factor to this stage.

Part 1: holocytochrome-c synthase complex
CcmF/CcmH holocytochrome-c synthase complexProtein Complexccmfh_ligation_complex

Annotons

CcmF/CcmH holocytochrome-c synthase activity
ccmfh_synthetase_activity
Participant: Protein Complex: bacterial CcmF/CcmH heme-ligation complex
Protein Complex:
bacterial CcmF/CcmH heme-ligation complex
Active units:
CcmF catalytic subunit
Participant: Family: CcmF cytochrome-c-maturation family
Family:
CcmF cytochrome-c-maturation familyPANTHER:PTHR43653:SF1
Representative Members: CcmF (Pseudomonas putida KT2440)UniProtKB:Q88EY0
Role: Binds heme and forms the membrane catalytic core of the ligation machinery.
CcmH ligation subunit
Participant: Family: CcmH cytochrome-c-maturation family
Family:
CcmH cytochrome-c-maturation familyPANTHER:PTHR47870:SF1
Representative Members: CcmH (Pseudomonas putida KT2440)UniProtKB:A0A140FWM4
Role: Couples apocytochrome redox state and orientation to stereospecific heme attachment.
Required Function:
holocytochrome-c synthase activityGO:0004408

Function

holocytochrome-c synthase activityGO:0004408
Substrates: apocytochrome c with a reduced CXXCH motif heme supplied by holo-CcmE
Products: holocytochrome c

Processes

cytochrome c-heme linkageGO:0018063

Represents the complex-level ligase function without assigning holocytochrome-c synthase activity to CcmF or CcmH alone.

Part 2: lineage-dependent maturation accessory (optional)
CcmI/CycH-family accessory factorBiological Processccmi_cych_accessory

Annotons

CycH-family maturation accessory
cych_accessory_component
Participant: Family: CycH cytochrome-c-maturation family
Family:
CycH cytochrome-c-maturation familyPANTHER:PTHR47870:SF4
Representative Members: CycH (Pseudomonas putida KT2440)UniProtKB:A0A140FWM3

Processes

cytochrome c biosynthetic processGO:1903607

Supports c-type cytochrome maturation in lineages that encode this accessory family; its direct molecular activity and substrate range remain unresolved.