NANP

Gene Description

NANP is the human N-acylneuraminate-9-phosphatase (EC 3.1.3.29; also known as N-acetylneuraminate-9-phosphate phosphatase / Neu5Ac-9-Pase / HDHD4), a Mg2+-dependent member of the HAD-like (haloacid dehalogenase) hydrolase superfamily. It catalyzes the third step of the de novo sialic acid biosynthetic pathway, hydrolyzing N-acetylneuraminate-9-phosphate (Neu5Ac-9-P) to free N-acetylneuraminate (sialic acid) plus inorganic phosphate; it can also dephosphorylate N-glycoloylneuraminate 9-phosphate. In the pathway the enzyme acts downstream of the Neu5Ac-9-P synthase NANS and upstream of the CMP-sialic acid synthetase CMAS, providing the free sialic acid that is subsequently activated to CMP-sialic acid for sialyltransferase reactions. The protein is a soluble cytosolic enzyme with a HAD Rossmann-like catalytic core; crystal structures show a Mg2+ ion and phosphate bound in the active site, with Mg2+-coordinating aspartates (Asp12, Asp14, Asp189). Genetic knockout studies in human cell lines indicate that although Neu5Ac-9-P accumulates when NANP is lost, cell-surface sialylation and CMP-sialic acid levels are largely preserved, implying that an alternative phosphatase can bypass NANP in de novo sialic acid production.

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0046380 N-acetylneuraminate biosynthetic process	IBA GO_REF:0000033	ACCEPT	Summary: Phylogenetic (IBA) propagation of NANP's role in sialic acid (Neu5Ac) biosynthesis. This is correct and matches the direct experimental IDA annotation to the same term. The free Neu5Ac produced by NANP is the immediate product of this dephosphorylation step. Accept as a core BP. Supporting Evidence: file:human/NANP/NANP-uniprot.txt PATHWAY: Amino-sugar metabolism; N-acetylneuraminate biosynthesis.
GO:0050124 N-acylneuraminate-9-phosphatase activity	IBA GO_REF:0000033	ACCEPT	Summary: Phylogenetic (IBA) propagation of the characterized catalytic activity. This is the defining molecular function of NANP and agrees with the experimental IDA annotations to the same term. Accept as the core molecular function. Supporting Evidence: file:human/NANP/NANP-uniprot.txt Catalyzes the dephosphorylation of N-acylneuraminate 9-
GO:0006054 N-acetylneuraminate metabolic process	IEA GO_REF:0000117	KEEP AS NON CORE	Summary: ARBA electronic annotation to the generic metabolic-process parent. This is correct but less informative than, and a parent of, the specific GO:0046380 (N-acetylneuraminate biosynthetic process) already annotated with experimental evidence. Keep as non-core (redundant generalization). Supporting Evidence: file:human/NANP/NANP-uniprot.txt PATHWAY: Amino-sugar metabolism; N-acetylneuraminate biosynthesis.
GO:0016787 hydrolase activity	IEA GO_REF:0000002	MARK AS OVER ANNOTATED	Summary: InterPro2GO (IPR011950, HAD-SF hydrolase subfamily IA) electronic annotation to the root hydrolase term. NANP is indeed a hydrolase, but this is a maximally generic ancestor of the specific and informative GO:0050124 (N-acylneuraminate-9-phosphatase activity). Over-annotation relative to the characterized function. Supporting Evidence: file:human/NANP/NANP-uniprot.txt Belongs to the HAD-like hydrolase superfamily. NANP family.
GO:0050124 N-acylneuraminate-9-phosphatase activity	IEA GO_REF:0000120	ACCEPT	Summary: Electronic annotation from RHEA/EC (RHEA:80839\|RHEA:83303\|EC:3.1.3.29) mapping to the enzyme's molecular function. Correct and consistent with the experimental IDA annotations to the same term; redundant with them but accurate. Accept. Supporting Evidence: file:human/NANP/NANP-uniprot.txt Reaction=N-acetylneuraminate 9-phosphate + H2O = N-acetylneuraminate +
GO:0006045 N-acetylglucosamine biosynthetic process	IEA GO_REF:0000041	MODIFY	Summary: Electronic annotation derived from UniPathway UPA00630. However, UPA00630 is the N-acetylneuraminate (sialic acid) biosynthesis pathway, not GlcNAc biosynthesis; NANP does not synthesize N-acetylglucosamine (GlcNAc is an upstream substrate of the sialic acid pathway, not a product of NANP). This is a UniPathway-to-GO mapping artifact. The intended biological process is N-acetylneuraminate biosynthesis (already captured by GO:0046380), so modify to that term rather than retaining an incorrect GlcNAc-biosynthesis process. Proposed replacements: N-acetylneuraminate biosynthetic process Supporting Evidence: file:human/NANP/NANP-uniprot.txt PATHWAY: Amino-sugar metabolism; N-acetylneuraminate biosynthesis.
GO:0050124 N-acylneuraminate-9-phosphatase activity	IDA PMID:23747226 Design, synthesis, functional and structural characterizatio...	ACCEPT	Summary: Direct experimental (IDA) annotation of the N-acylneuraminate-9-phosphatase activity. Kim et al. 2013 biochemically and structurally characterized HDHD4 (NANP), reporting inhibition by a designed phosphonate mimicking the native substrate Neu5Ac-9-P (Km ~47 uM) and solving Mg2+/phosphate-bound structures (PDB 4KNV/4KNW). This is the core molecular function; accept. Supporting Evidence: PMID:23747226 in the range of the native substrate
GO:0006055 CMP-N-acetylneuraminate biosynthetic process	IMP PMID:31121216 Activity of N-acylneuraminate-9-phosphatase (NANP) is not es...	KEEP AS NON CORE	Summary: Experimental (IMP) annotation from the NANP-knockout study of Willems et al. 2019, which read out CMP-sialic acid levels and cell-surface sialylation. NANP acts upstream of CMP-Neu5Ac formation, but its direct product is free Neu5Ac, and the study concluded that NANP activity is not essential for de novo sialic acid production (CMP-sialic acid levels in NANP KO were comparable to WT because an alternative phosphatase bypasses NANP). The annotation reflects the pathway/assay context but is one step removed from NANP's direct product; keep as non-core rather than core. As an experimental annotation it is not removed. Supporting Evidence: PMID:31121216 NANP is the third enzyme in sialic acid biosynthesis PMID:31121216 CMP-sialic acid levels in NANP KO were comparable to
GO:0005829 cytosol	TAS Reactome:R-HSA-4084989	ACCEPT	Summary: Cytosolic localization asserted by Reactome (TAS). Consistent with NANP being a soluble HAD-superfamily phosphatase with no transmembrane segment or signal peptide, acting on cytosolic sialic-acid pathway intermediates. Accept as the core cellular location. Supporting Evidence: Reactome:R-HSA-4084989 NANP dephosphorylates Neu5Ac-9-P to Neu5Ac
GO:0046380 N-acetylneuraminate biosynthetic process	IDA PMID:16237198 Identification of the sequence encoding N-acetylneuraminate-...	ACCEPT	Summary: Direct experimental (IDA) annotation. Maliekal et al. 2006 identified the gene encoding Neu5Ac-9-phosphatase and characterized the recombinant human enzyme, establishing its role in the dephosphorylation step of N-acetylneuraminate (sialic acid) biosynthesis. Accept as a core biological process. Supporting Evidence: PMID:16237198 dephosphorylation of the latter by a specific phosphatase
GO:0050124 N-acylneuraminate-9-phosphatase activity	IDA PMID:16237198 Identification of the sequence encoding N-acetylneuraminate-...	ACCEPT	Summary: Direct experimental (IDA) annotation of the defining catalytic activity. Maliekal et al. 2006 purified and identified the enzyme, showing the recombinant human protein had >230-fold higher catalytic efficiency on Neu5Ac-9-phosphate than on its next-best substrate, confirming substrate specificity for N-acylneuraminate 9-phosphate. This is the core molecular function; accept. Supporting Evidence: PMID:16237198 >230-fold higher catalytic efficiency on Neu5Ac-9-phosphate than on its second

Gene Description

Existing Annotations Review

Core Functions

Magnesium ion binding: NANP requires Mg2+ as an obligate cofactor, coordinated at the HAD active site (aspartates Asp12, Asp14, Asp189) together with the substrate phosphate.

References

📚 Additional Documentation

Notes

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