3SHD | pdb_00003shd

Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
L	d3shdl_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli APEC O1 ) [TaxId: 405955 ],	SCOPe (2.08)
K	d3shdk_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli APEC O1 ) [TaxId: 405955 ],	SCOPe (2.08)
J	d3shdj_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli APEC O1 ) [TaxId: 405955 ],	SCOPe (2.08)
I	d3shdi_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli APEC O1 ) [TaxId: 405955 ],	SCOPe (2.08)
H	d3shdh_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli APEC O1 ) [TaxId: 405955 ],	SCOPe (2.08)
G	d3shdg_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli APEC O1 ) [TaxId: 405955 ],	SCOPe (2.08)
F	d3shdf_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli APEC O1 ) [TaxId: 405955 ],	SCOPe (2.08)
E	d3shde_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli APEC O1 ) [TaxId: 405955 ],	SCOPe (2.08)
D	d3shdd_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli APEC O1 ) [TaxId: 405955 ],	SCOPe (2.08)
C	d3shdc_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli APEC O1 ) [TaxId: 405955 ],	SCOPe (2.08)
B	d3shdb_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli APEC O1 ) [TaxId: 405955 ],	SCOPe (2.08)
A	d3shda_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	(Escherichia coli APEC O1 ) [TaxId: 405955 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L	SCOP2B Superfamily	Nudix	8081766	3000098	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Nudix	8081766	3000098	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Nudix	8081766	3000098	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Nudix	8081766	3000098	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Nudix	8081766	3000098	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Nudix	8081766	3000098	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Nudix	8081766	3000098	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Nudix	8081766	3000098	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nudix	8081766	3000098	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nudix	8081766	3000098	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nudix	8081766	3000098	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nudix	8081766	3000098	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
L	NUDIX_1	e3shdL1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_1	ECOD (1.6)
K	NUDIX_1	e3shdK1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_1	ECOD (1.6)
J	NUDIX_1	e3shdJ1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_1	ECOD (1.6)
I	NUDIX_1	e3shdI1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_1	ECOD (1.6)
H	NUDIX_1	e3shdH1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_1	ECOD (1.6)
G	NUDIX_1	e3shdG1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_1	ECOD (1.6)
F	NUDIX_1	e3shdF1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_1	ECOD (1.6)
E	NUDIX_1	e3shdE1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_1	ECOD (1.6)
D	NUDIX_1	e3shdD1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_1	ECOD (1.6)
C	NUDIX_1	e3shdC1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_1	ECOD (1.6)
B	NUDIX_1	e3shdB1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_1	ECOD (1.6)
A	NUDIX_1	e3shdA1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_1	ECOD (1.6)

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	Phosphatase nudJ	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 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

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
I	Nudix hydrolase (YmfB) M-CSA #988	Nudix hydrolases are enzymes that turn triphosphate nucleotides into monophosphate nucleotides in a stepwise manner which is crucial for the metabolism of thiamine pyrophosphate and important for several metabolic processes. In addition, they hydrolyse a wide range of organic pyrophosphates, including nucleotide sugars, dinucleoside polyphosphates, dinucleotide coenzymes and capped RNAs. They do this with a highly conserved 23-amino acid sequence called the Nudix motif. These proteins are present across the natural world from bacteria to humans.	Defined by 4 residues: GLU:I-23GLU:I-51GLU:I-55ARG:I-119 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.6.1 (PDB Primary Data) Search M-CSA Motif + EC 3.6.1

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.