2PMB | pdb_00002pmb

Crystal structure of predicted nucleotide-binding protein from Vibrio cholerae

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d2pmbd2	Alpha and beta proteins (a/b)	MCP/YpsA-like	MCP/YpsA-like	MoCo carrier protein-like	Nucleosidase PpnN	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
D	d2pmbd1	Alpha and beta proteins (a+b)	Ferredoxin-like	DUF4478 domain-like	DUF4478 domain	Nucleosidase PpnN	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
D	d2pmbd3	Membrane and cell surface proteins and peptides	Anoctamin (TMEM16)-like	DUF3412 domain	DUF3412 domain	Nucleosidase PpnN	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
D	d2pmbd4	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
C	d2pmbc2	Alpha and beta proteins (a/b)	MCP/YpsA-like	MCP/YpsA-like	MoCo carrier protein-like	Nucleosidase PpnN	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
C	d2pmbc1	Alpha and beta proteins (a+b)	Ferredoxin-like	DUF4478 domain-like	DUF4478 domain	Nucleosidase PpnN	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
C	d2pmbc3	Membrane and cell surface proteins and peptides	Anoctamin (TMEM16)-like	DUF3412 domain	DUF3412 domain	Nucleosidase PpnN	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
C	d2pmbc4	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
B	d2pmbb2	Alpha and beta proteins (a/b)	MCP/YpsA-like	MCP/YpsA-like	MoCo carrier protein-like	Nucleosidase PpnN	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
B	d2pmbb1	Alpha and beta proteins (a+b)	Ferredoxin-like	DUF4478 domain-like	DUF4478 domain	Nucleosidase PpnN	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
B	d2pmbb3	Membrane and cell surface proteins and peptides	Anoctamin (TMEM16)-like	DUF3412 domain	DUF3412 domain	Nucleosidase PpnN	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
B	d2pmbb4	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
A	d2pmba1	Alpha and beta proteins (a/b)	MCP/YpsA-like	MCP/YpsA-like	MoCo carrier protein-like	Nucleosidase PpnN	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
A	d2pmba2	Alpha and beta proteins (a+b)	Ferredoxin-like	DUF4478 domain-like	DUF4478 domain	Nucleosidase PpnN	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
A	d2pmba3	Membrane and cell surface proteins and peptides	Anoctamin (TMEM16)-like	DUF3412 domain	DUF3412 domain	Nucleosidase PpnN	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
A	d2pmba4	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D		e2pmbD1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: DAO, NAD_binding_8	F:	ECOD (20:10:01)
C		e2pmbC1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: DAO, NAD_binding_8	F:	ECOD (20:10:01)
B		e2pmbB1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: DAO, NAD_binding_8	F:	ECOD (20:10:01)
A		e2pmbA1	A: Cysteine proteinases-like	X: Immunoglobulin-related	H: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	T: DUF4478	F:	ECOD (20:10:01)
A		e2pmbA2	A: Cysteine proteinases-like	X: Immunoglobulin-related	H: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	T: Topo-VIb_trans	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.1850.10	Alpha Beta	2-Layer Sandwich	MCP/YpsA-like	MoCo carrier protein-like	CATH (4.3.0)
D	3.40.50.450	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
C	3.30.1850.10	Alpha Beta	2-Layer Sandwich	MCP/YpsA-like	MoCo carrier protein-like	CATH (4.3.0)
C	3.40.50.450	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	3.30.1850.10	Alpha Beta	2-Layer Sandwich	MCP/YpsA-like	MoCo carrier protein-like	CATH (4.3.0)
B	3.40.50.450	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.30.1850.10	Alpha Beta	2-Layer Sandwich	MCP/YpsA-like	MoCo carrier protein-like	CATH (4.3.0)
A	3.40.50.450	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF11892	Pyrimidine/purine nucleotide monophosphate nucleosidase, C-terminal (PpnN_C)	Pyrimidine/purine nucleotide monophosphate nucleosidase, C-terminal	-	Family
A, B, C, D	PF14793	Pyrimidine/purine nucleotide 5'-monophosphate nucleosidases (DUF4478)	Pyrimidine/purine nucleotide 5'-monophosphate nucleosidases	This is an N-terminal domain found in pyrimidine/purine nucleotide 5'-monophosphate nucleosidases (PpnN) in bacteria. PpnN catalyzes the hydrolysis of the N-glycosidic bond of diverse pyrimidine and purine nucleotide 5'-monophosphates, to form ribose ...	This is an N-terminal domain found in pyrimidine/purine nucleotide 5'-monophosphate nucleosidases (PpnN) in bacteria. PpnN catalyzes the hydrolysis of the N-glycosidic bond of diverse pyrimidine and purine nucleotide 5'-monophosphates, to form ribose 5-phosphate and the corresponding free base. It can use AMP, GMP, IMP, CMP, dTMP and UMP as substrates [1]. It is found in association with Pfam:PF03641 and Pfam:PF11892.	Domain
A, B, C, D	PF03641	Possible lysine decarboxylase (Lysine_decarbox)	Possible lysine decarboxylase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Uncharacterized protein	hydrolase activity, acting on glycosyl bonds pyrimidine-5'-nucleotide nucleosidase activity hydrolase activity hydrolase activity, hydrolyzing N-glycosyl compounds catalytic activity AMP nucleosidase activity	-	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR037153	Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase PpnN-like superfamily	Homologous Superfamily
A, B, C, D	IPR049788	Nucleotide 5'-monophosphate nucleosidase PpnN	Family
A, B, C, D	IPR031100	LOG family	Family
A, B, C, D	IPR052341	LOG family pyrimidine/purine nucleotide 5'-monophosphatases	Family
A, B, C, D	IPR021826	Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase, C-terminal domain	Domain
A, B, C, D	IPR027820	Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase, N-terminal	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.