4NFW | pdb_00004nfw

Structure and atypical hydrolysis mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli

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)
L	d4nfwl_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli str. 'clone D i14 ) [TaxId: 885275 ],	SCOPe (2.08)
K	d4nfwk_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli str. 'clone D i14 ) [TaxId: 885275 ],	SCOPe (2.08)
J	d4nfwj_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli str. 'clone D i14 ) [TaxId: 885275 ],	SCOPe (2.08)
I	d4nfwi_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli str. 'clone D i14 ) [TaxId: 885275 ],	SCOPe (2.08)
H	d4nfwh_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli str. 'clone D i14 ) [TaxId: 885275 ],	SCOPe (2.08)
G	d4nfwg_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli str. 'clone D i14 ) [TaxId: 885275 ],	SCOPe (2.08)
F	d4nfwf_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli str. 'clone D i14 ) [TaxId: 885275 ],	SCOPe (2.08)
E	d4nfwe_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli str. 'clone D i14 ) [TaxId: 885275 ],	SCOPe (2.08)
D	d4nfwd_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli str. 'clone D i14 ) [TaxId: 885275 ],	SCOPe (2.08)
C	d4nfwc_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli str. 'clone D i14 ) [TaxId: 885275 ],	SCOPe (2.08)
B	d4nfwb_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli str. 'clone D i14 ) [TaxId: 885275 ],	SCOPe (2.08)
A	d4nfwa_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli str. 'clone D i14 ) [TaxId: 885275 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
L	RBM39linker	e4nfwL1	A: alpha arrays	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: RBM39linker	ECOD (v295.2)
K	RBM39linker	e4nfwK1	A: alpha arrays	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: RBM39linker	ECOD (v295.2)
J	RBM39linker	e4nfwJ1	A: alpha arrays	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: RBM39linker	ECOD (v295.2)
I	RBM39linker	e4nfwI1	A: alpha arrays	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: RBM39linker	ECOD (v295.2)
H	RBM39linker	e4nfwH1	A: alpha arrays	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: RBM39linker	ECOD (v295.2)
G	RBM39linker	e4nfwG1	A: alpha arrays	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: RBM39linker	ECOD (v295.2)
F	RBM39linker	e4nfwF1	A: alpha arrays	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: RBM39linker	ECOD (v295.2)
E	RBM39linker	e4nfwE1	A: alpha arrays	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: RBM39linker	ECOD (v295.2)
D	RBM39linker	e4nfwD1	A: alpha arrays	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: RBM39linker	ECOD (v295.2)
C	RBM39linker	e4nfwC1	A: alpha arrays	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: RBM39linker	ECOD (v295.2)
B	RBM39linker	e4nfwB1	A: alpha arrays	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: RBM39linker	ECOD (v295.2)
A	RBM39linker	e4nfwA1	A: alpha arrays	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: RBM39linker	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
K	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
J	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
I	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
H	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
G	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
F	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
E	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
D	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
C	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
B	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
A	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	PF00293	NUDIX domain (NUDIX)	NUDIX domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	Putative Nudix hydrolase ymfB	pyrophosphatase activity nucleoside diphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity 4-amino-5-hydroxymethyl-2-methylpyrimidine diphosphatase activity ribonucleoside triphosphate phosphatase activity thiamine diphosphate phosphatase activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR000086	NUDIX hydrolase domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR015797	NUDIX hydrolase-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR020084	NUDIX hydrolase, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR020476	NUDIX hydrolase	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR033713	Phosphatase NudJ	Family

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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.