3VTI

Crystal structure of HypE-HypF complex

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	YrdC/RibB-like	8004431	3000166	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HypF zinc finger	8019806	3002027	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Actin-like ATPases	8092407	3000092	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Acylphosphatase/BLUF domain-like	8004422	3000165	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HypF zinc finger	8019805	3002027	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Actin-like ATPases	8004425	3000092	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Acylphosphatase/BLUF domain-like	8004422	3000165	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Actin-like ATPases	8004425	3000092	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Actin-like ATPases	8092407	3000092	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HypF zinc finger	8019806	3002027	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HypF zinc finger	8019805	3002027	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	YrdC/RibB-like	8004431	3000166	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)
B	Acylphosphatase	e3vtiB15	A: a+b two layers	X: Alpha-beta plaits	H: Acylphosphatase-like (From Topology)	T: Acylphosphatase-like	F: Acylphosphatase	ECOD (1.6)
B	Sua5_yciO_yrdC	e3vtiB14	A: a+b complex topology	X: YrdC/RibB (From Topology)	H: YrdC/RibB (From Topology)	T: YrdC/RibB	F: Sua5_yciO_yrdC	ECOD (1.6)
B	Peptidase_M22_C_1	e3vtiB16	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Peptidase_M22_C_1	ECOD (1.6)
B	HypF_1	e3vtiB17	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: HypF_1	ECOD (1.6)
B	zf-HYPF	e3vtiB13	A: few secondary structure elements	X: Zinc finger domain in hydrogenase maturation protein HypF (From Topology)	H: Zinc finger domain in hydrogenase maturation protein HypF (From Topology)	T: Zinc finger domain in hydrogenase maturation protein HypF	F: zf-HYPF	ECOD (1.6)
A	Acylphosphatase	e3vtiA15	A: a+b two layers	X: Alpha-beta plaits	H: Acylphosphatase-like (From Topology)	T: Acylphosphatase-like	F: Acylphosphatase	ECOD (1.6)
A	Sua5_yciO_yrdC	e3vtiA14	A: a+b complex topology	X: YrdC/RibB (From Topology)	H: YrdC/RibB (From Topology)	T: YrdC/RibB	F: Sua5_yciO_yrdC	ECOD (1.6)
A	Peptidase_M22_C_1	e3vtiA16	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Peptidase_M22_C_1	ECOD (1.6)
A	HypF_1	e3vtiA17	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: HypF_1	ECOD (1.6)
A	zf-HYPF	e3vtiA13	A: few secondary structure elements	X: Zinc finger domain in hydrogenase maturation protein HypF (From Topology)	H: Zinc finger domain in hydrogenase maturation protein HypF (From Topology)	T: Zinc finger domain in hydrogenase maturation protein HypF	F: zf-HYPF	ECOD (1.6)
C	AIRS_C	e3vtiC3	A: a+b two layers	X: Alpha-beta plaits	H: PurM C-terminal domain-like (From Topology)	T: PurM C-terminal domain-like	F: AIRS_C	ECOD (1.6)
C	AIRS	e3vtiC4	A: a+b three layers	X: Bacillus chorismate mutase-like	H: PurM N-terminal domain-like (From Topology)	T: PurM N-terminal domain-like	F: AIRS	ECOD (1.6)
D	AIRS_C	e3vtiD3	A: a+b two layers	X: Alpha-beta plaits	H: PurM C-terminal domain-like (From Topology)	T: PurM C-terminal domain-like	F: AIRS_C	ECOD (1.6)
D	AIRS	e3vtiD4	A: a+b three layers	X: Bacillus chorismate mutase-like	H: PurM N-terminal domain-like (From Topology)	T: PurM N-terminal domain-like	F: AIRS	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.70.100	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
B	3.90.870.40	Alpha Beta	Alpha-Beta Complex	DHBP synthase		CATH (4.3.0)
B	3.30.110.120	Alpha Beta	2-Layer Sandwich	Translation Initiation Factor IF3		CATH (4.3.0)
B	3.30.420.360	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	3.30.420.560	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	1.10.357.160	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	CATH (4.3.0)
A	3.30.70.100	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
A	3.90.870.40	Alpha Beta	Alpha-Beta Complex	DHBP synthase		CATH (4.3.0)
A	3.30.110.120	Alpha Beta	2-Layer Sandwich	Translation Initiation Factor IF3		CATH (4.3.0)
A	3.30.420.360	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	3.30.420.560	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	1.10.357.160	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	CATH (4.3.0)
C	3.30.1330.10	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
C	3.90.650.10	Alpha Beta	Alpha-Beta Complex	Phosphoribosyl-aminoimidazole Synthetase	Chain A, domain 2	CATH (4.3.0)
D	3.30.1330.10	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
D	3.90.650.10	Alpha Beta	Alpha-Beta Complex	Phosphoribosyl-aminoimidazole Synthetase	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF22521	Carbamoyltransferase, Kae1-like Domain, second subdomain (HypF_C_2)	Carbamoyltransferase, Kae1-like Domain, second subdomain	This domain is found at the C-terminal end of Carbamoyltransferase from Caldanaerobacter subterraneus (HypF, Swiss:Q8RDB0) and similar prokaryotic sequences. HypF is involved in the biosynthesis of the nitrile group as a precursor of the cyano groups ...	This domain is found at the C-terminal end of Carbamoyltransferase from Caldanaerobacter subterraneus (HypF, Swiss:Q8RDB0) and similar prokaryotic sequences. HypF is involved in the biosynthesis of the nitrile group as a precursor of the cyano groups of hydrogenases. HypF consists of four domains: the acylphosphatase domain (Pfam:PF00708), the Zn finger-like domain (Pfam:PF07503), the YrdC-like domain (Pfam:PF01300) and the Kae1 (kinase-associated endopeptidase 1)-like domain, which is composed of two alpha-beta subdomains (Pfam:PF17788 and this entry) [5].	Domain
A, B	PF07503	HypF finger (zf-HYPF)	HypF finger	The HypF family of proteins are involved in the maturation and regulation of hydrogenase ([1]). In the N-terminus they appear to have two Zinc finger domains, as modelled by this family.	Domain
A, B	PF17788	HypF Kae1-like domain (HypF_C)	HypF Kae1-like domain	This domain is found in the HypF protein. In the structure it is one of the two subdomains of the Kae1 domain [1].	Domain
A, B	PF00708	Acylphosphatase (Acylphosphatase)	Acylphosphatase	-	Domain
A, B	PF01300	Telomere recombination (Sua5_yciO_yrdC)	Telomere recombination	-	Family
C, D	PF02769	AIR synthase related protein, C-terminal domain (AIRS_C)	AIR synthase related protein, C-terminal domain	This family includes Hydrogen expression/formation protein HypE Swiss:P24193, AIR synthases Swiss:P08178 EC:6.3.3.1, FGAM synthase Swiss:P35852 EC:6.3.5.3 and selenide, water dikinase Swiss:P16456 EC:2.7.9.3. The function of the C-terminal domain of ...	This family includes Hydrogen expression/formation protein HypE Swiss:P24193, AIR synthases Swiss:P08178 EC:6.3.3.1, FGAM synthase Swiss:P35852 EC:6.3.5.3 and selenide, water dikinase Swiss:P16456 EC:2.7.9.3. The function of the C-terminal domain of AIR synthase is unclear, but the cleft formed between N and C domains is postulated as a sulphate binding site [1].	Domain
C, D	PF00586	AIR synthase related protein, N-terminal domain (AIRS)	AIR synthase related protein, N-terminal domain	This family includes Hydrogen expression/formation protein HypE Swiss:P24193, AIR synthases Swiss:P08178 EC:6.3.3.1, FGAM synthase Swiss:P35852 EC:6.3.5.3 and selenide, water dikinase Swiss:P16456 EC:2.7.9.3. The N-terminal domain of AIR synthase fo ...	This family includes Hydrogen expression/formation protein HypE Swiss:P24193, AIR synthases Swiss:P08178 EC:6.3.3.1, FGAM synthase Swiss:P35852 EC:6.3.5.3 and selenide, water dikinase Swiss:P16456 EC:2.7.9.3. The N-terminal domain of AIR synthase forms the dimer interface of the protein, and is suggested as a putative ATP binding domain [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Hydrogenase maturation factor	RNA binding double-stranded RNA binding binding organic cyclic compound binding nucleic acid binding carboxyl- or carbamoyltransferase activity transferase activity, transferring one-carbon groups transferase activity catalytic activity pyrophosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides acylphosphatase activity hydrolase activity hydrolase activity, acting on acid anhydrides RNA binding double-stranded RNA binding binding organic cyclic compound binding nucleic acid binding carboxyl- or carbamoyltransferase activity transferase activity, transferring one-carbon groups transferase activity catalytic activity pyrophosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides acylphosphatase activity hydrolase activity hydrolase activity, acting on acid anhydrides ligase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation	-
C, D	Hydrogenase maturation factor	cation binding ion binding binding metal ion binding small molecule binding	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR041440	HypF, Kae1-like domain	Domain
A, B	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
A, B	IPR051060	Carbamoyltransferase HypF-like	Family
A, B	IPR036046	Acylphosphatase-like domain superfamily	Homologous Superfamily
A, B	IPR004421	Carbamoyltransferase, HypF-type	Family
A, B	IPR017945	DHBP synthase RibB-like alpha/beta domain superfamily	Homologous Superfamily
A, B	IPR006070	Threonylcarbamoyl-AMP synthase-like domain	Domain
A, B	IPR011125	Zinc finger, HypF-type	Domain
A, B	IPR017968	Acylphosphatase, conserved site	Conserved Site
A, B	IPR001792	Acylphosphatase-like domain	Domain
C, D	IPR036676	PurM-like, C-terminal domain superfamily	Homologous Superfamily
C, D	IPR010918	PurM-like, C-terminal domain	Domain
C, D	IPR016188	PurM-like, N-terminal domain	Domain
C, D	IPR036921	PurM-like, N-terminal domain superfamily	Homologous Superfamily
C, D	IPR011854	Carbamoyl dehydratase HypE	Family

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.