2NTK | pdb_00002ntk

Crystal structure of PurO/IMP from Methanothermobacter thermoautotrophicus

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d2ntkd_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	Archaeal IMP cyclohydrolase PurO	Archaeal IMP cyclohydrolase PurO	Hypothetical protein MTH1020	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
C	d2ntkc_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	Archaeal IMP cyclohydrolase PurO	Archaeal IMP cyclohydrolase PurO	Hypothetical protein MTH1020	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
B	d2ntkb_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	Archaeal IMP cyclohydrolase PurO	Archaeal IMP cyclohydrolase PurO	Hypothetical protein MTH1020	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
A	d2ntka2	Alpha and beta proteins (a+b)	Ntn hydrolase-like	Archaeal IMP cyclohydrolase PurO	Archaeal IMP cyclohydrolase PurO	Hypothetical protein MTH1020	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
A	d2ntka3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Archaeal IMP cyclohydrolase PurO	8043260	3001783	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Archaeal IMP cyclohydrolase PurO	8043260	3001783	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Archaeal IMP cyclohydrolase PurO	8043260	3001783	SCOP2B (2022-06-29)
A	SCOP2 Family	Archaeal IMP cyclohydrolase PurO	8030881	4002811	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Archaeal IMP cyclohydrolase PurO	8043260	3001783	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	IMP_cyclohyd	e2ntkD1	A: a+b four layers	X: Ntn/PP2C	H: Ntn	T: Proteasome subunits	F: IMP_cyclohyd	ECOD (1.6)
C	IMP_cyclohyd	e2ntkC1	A: a+b four layers	X: Ntn/PP2C	H: Ntn	T: Proteasome subunits	F: IMP_cyclohyd	ECOD (1.6)
B	IMP_cyclohyd	e2ntkB1	A: a+b four layers	X: Ntn/PP2C	H: Ntn	T: Proteasome subunits	F: IMP_cyclohyd	ECOD (1.6)
A	IMP_cyclohyd	e2ntkA1	A: a+b four layers	X: Ntn/PP2C	H: Ntn	T: Proteasome subunits	F: IMP_cyclohyd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.60.20.20	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Inosine monophosphate cyclohydrolase-like	CATH (4.3.0)
C	3.60.20.20	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Inosine monophosphate cyclohydrolase-like	CATH (4.3.0)
B	3.60.20.20	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Inosine monophosphate cyclohydrolase-like	CATH (4.3.0)
A	3.60.20.20	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Inosine monophosphate cyclohydrolase-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF07826	IMP cyclohydrolase-like protein (IMP_cyclohyd)	IMP cyclohydrolase-like protein	This enzyme (Swiss:O27099) is may catalyse the cyclization of 5-formylamidoimidazole-4-carboxamide ribonucleotide to inosine monophosphate (IMP), a reaction which is important in de novo purine biosynthesis in archaeal species. This single domain pro ...	This enzyme (Swiss:O27099) is may catalyse the cyclization of 5-formylamidoimidazole-4-carboxamide ribonucleotide to inosine monophosphate (IMP), a reaction which is important in de novo purine biosynthesis in archaeal species. This single domain protein is arranged to form an overall fold that consists of a four-layered alpha-beta-beta-alpha core structure. The two antiparallel beta-sheets pack against each other and are covered by alpha-helices on one face of the molecule. The protein is structurally similar to members of the N-terminal nucleophile (NTN) hydrolase superfamily. A deep pocket was in fact found on the surface of IMP cyclohydrolase in a position equivalent to that of active sites of NTN-hydrolases, but an N-terminal nucleophile could not be found. Therefore, it is thought that this enzyme is structurally but not functionally similar to members of the NTN-hydrolase family [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	IMP cyclohydrolase	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines IMP cyclohydrolase activity cyclohydrolase activity hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	ribose phosphate metabolic process IMP metabolic process purine ribonucleoside monophosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleoside monophosphate biosynthetic process purine ribonucleoside monophosphate metabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process purine nucleoside monophosphate metabolic process ribose phosphate metabolic process IMP metabolic process purine ribonucleoside monophosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleoside monophosphate biosynthetic process purine ribonucleoside monophosphate metabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process purine nucleoside monophosphate metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside monophosphate metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process nucleoside monophosphate biosynthetic process purine-containing compound metabolic process IMP biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process 'de novo' IMP biosynthetic process purine ribonucleotide metabolic process ribonucleoside monophosphate biosynthetic process purine nucleotide biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR020600	Inosine monophosphate cyclohydrolase-like	Domain
A, B, C, D	IPR010191	IMP cyclohydrolase	Family
A, B, C, D	IPR036795	Inosine monophosphate cyclohydrolase-like superfamily	Homologous Superfamily

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.