4DU6 | pdb_00004du6

Crystal structure of GTP cyclohydrolase I from Yersinia pestis complexed with GTP

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)
E	d4du6e_	Alpha and beta proteins (a+b)	T-fold	Tetrahydrobiopterin biosynthesis enzymes-like	GTP cyclohydrolase I	automated matches	(Yersinia pestis CO92 ) [TaxId: 214092 ],	SCOPe (2.08)
D	d4du6d_	Alpha and beta proteins (a+b)	T-fold	Tetrahydrobiopterin biosynthesis enzymes-like	GTP cyclohydrolase I	automated matches	(Yersinia pestis CO92 ) [TaxId: 214092 ],	SCOPe (2.08)
C	d4du6c_	Alpha and beta proteins (a+b)	T-fold	Tetrahydrobiopterin biosynthesis enzymes-like	GTP cyclohydrolase I	automated matches	(Yersinia pestis CO92 ) [TaxId: 214092 ],	SCOPe (2.08)
B	d4du6b_	Alpha and beta proteins (a+b)	T-fold	Tetrahydrobiopterin biosynthesis enzymes-like	GTP cyclohydrolase I	automated matches	(Yersinia pestis CO92 ) [TaxId: 214092 ],	SCOPe (2.08)
A	d4du6a_	Alpha and beta proteins (a+b)	T-fold	Tetrahydrobiopterin biosynthesis enzymes-like	GTP cyclohydrolase I	automated matches	(Yersinia pestis CO92 ) [TaxId: 214092 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	Tetrahydrobiopterin biosynthesis enzymes-like	8074808	3000283	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Tetrahydrobiopterin biosynthesis enzymes-like	8074808	3000283	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Tetrahydrobiopterin biosynthesis enzymes-like	8074808	3000283	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Tetrahydrobiopterin biosynthesis enzymes-like	8074808	3000283	SCOP2B (2022-06-29)
A	SCOP2 Family	GTP cyclohydrolase I	8074807	4001710	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Tetrahydrobiopterin biosynthesis enzymes-like	8074808	3000283	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)
E	ABC_tran	e4du6E1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (develop294)
D	ABC_tran	e4du6D1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (develop294)
C	ABC_tran	e4du6C1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (develop294)
B	ABC_tran	e4du6B1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (develop294)
A	p450	e4du6A1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: p450	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	1.10.286.10	Mainly Alpha	Orthogonal Bundle	GTP Cyclohydrolase I	Chain A, domain 1	CATH (4.3.0)
E	3.30.1130.10	Alpha Beta	2-Layer Sandwich	GTP Cyclohydrolase I, domain 2	GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain	CATH (4.3.0)
D	1.10.286.10	Mainly Alpha	Orthogonal Bundle	GTP Cyclohydrolase I	Chain A, domain 1	CATH (4.3.0)
D	3.30.1130.10	Alpha Beta	2-Layer Sandwich	GTP Cyclohydrolase I, domain 2	GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain	CATH (4.3.0)
C	1.10.286.10	Mainly Alpha	Orthogonal Bundle	GTP Cyclohydrolase I	Chain A, domain 1	CATH (4.3.0)
C	3.30.1130.10	Alpha Beta	2-Layer Sandwich	GTP Cyclohydrolase I, domain 2	GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain	CATH (4.3.0)
B	1.10.286.10	Mainly Alpha	Orthogonal Bundle	GTP Cyclohydrolase I	Chain A, domain 1	CATH (4.3.0)
B	3.30.1130.10	Alpha Beta	2-Layer Sandwich	GTP Cyclohydrolase I, domain 2	GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain	CATH (4.3.0)
A	1.10.286.10	Mainly Alpha	Orthogonal Bundle	GTP Cyclohydrolase I	Chain A, domain 1	CATH (4.3.0)
A	3.30.1130.10	Alpha Beta	2-Layer Sandwich	GTP Cyclohydrolase I, domain 2	GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E	PF01227	GTP cyclohydrolase I (GTP_cyclohydroI)	GTP cyclohydrolase I	This family includes GTP cyclohydrolase enzymes and a family of related bacterial proteins including Swiss:Q46920.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E	GTP cyclohydrolase 1	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines GTP cyclohydrolase activity cyclohydrolase activity hydrolase activity GTP cyclohydrolase I activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines GTP cyclohydrolase activity cyclohydrolase activity hydrolase activity GTP cyclohydrolase I activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding	polyol metabolic process small molecule biosynthetic process alcohol metabolic process diol biosynthetic process diol metabolic process biosynthetic process tetrahydrobiopterin biosynthetic process tetrahydrobiopterin metabolic process pteridine-containing compound biosynthetic process polyol biosynthetic process alcohol biosynthetic process metabolic process cellular process small molecule metabolic process polyol metabolic process small molecule biosynthetic process alcohol metabolic process diol biosynthetic process diol metabolic process biosynthetic process tetrahydrobiopterin biosynthetic process tetrahydrobiopterin metabolic process pteridine-containing compound biosynthetic process polyol biosynthetic process alcohol biosynthetic process metabolic process cellular process small molecule metabolic process pteridine-containing compound metabolic process one-carbon metabolic process folic acid-containing compound biosynthetic process modified amino acid biosynthetic process modified amino acid metabolic process folic acid-containing compound metabolic process tetrahydrofolate biosynthetic process tetrahydrofolate metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E	IPR020602	GTP cyclohydrolase I domain	Domain
A, B, C, D, E	IPR018234	GTP cyclohydrolase I, conserved site	Conserved Site
A, B, C, D, E	IPR001474	GTP cyclohydrolase I	Family
A, B, C, D, E	IPR043133	GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase	Homologous Superfamily
A, B, C, D, E	IPR043134	GTP cyclohydrolase I, N-terminal domain	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.