3VTH | pdb_00003vth

Crystal structure of full-length HypF in the phosphate- and nucleotide-bound form

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	Actin-like ATPases	8092407	3000092	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	YrdC/RibB-like	8004431	3000166	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Actin-like ATPases	8004425	3000092	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HypF zinc finger	8019805	3002027	SCOP2B (2022-06-29)
A	SCOP2 Family	Acylphosphatase-like	8004421	4000382	SCOP2 (2022-06-29)
A	SCOP2 Family	YgjD/Kae1-like	8004424	4000383	SCOP2 (2022-06-29)
A	SCOP2 Family	YrdC/Sua5-like	8004430	4000384	SCOP2 (2022-06-29)
A	SCOP2 Family	HypF zinc finger	8004433	4000385	SCOP2 (2022-06-29)
A	SCOP2 Family	HypF zinc finger	8004434	4000385	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Acylphosphatase/BLUF domain-like	8004422	3000165	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Actin-like ATPases	8092407	3000092	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	YrdC/RibB-like	8004431	3000166	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	HypF zinc finger	8019805	3002027	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	HypF zinc finger	8019806	3002027	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Actin-like ATPases	8004425	3000092	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)
B		e3vthB1	A: MHC antigen-recognition domain	X: MHC antigen-recognition domain	H: MHC antigen-recognition domain	T: Sua5_yciO_yrdC	F:	ECOD (20:10:01)
B		e3vthB4	A: MHC antigen-recognition domain	X: MHC antigen-recognition domain	H: MHC antigen-recognition domain	T: HypF_C_2	F:	ECOD (20:10:01)
B		e3vthB5	A: MHC antigen-recognition domain	X: MHC antigen-recognition domain	H: MHC antigen-recognition domain	T: Glypican	F:	ECOD (20:10:01)
A		e3vthA2	A: Glutamine synthetase-like	X: Glutamine synthetase/guanido kinase	H: Glutamine synthetase/guanido kinase	T: Peptidase_S8	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.90.870.30	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	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	3.90.870.50	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	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	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	PF00708	Acylphosphatase (Acylphosphatase)	Acylphosphatase		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	PF01300	Telomere recombination (Sua5_yciO_yrdC)	Telomere recombination	This domain has been shown to bind preferentially to dsRNA [1]. The domain is found in SUA5 Swiss:P32579 as well as HypF and YrdC Swiss:P45748. It has also been shown to be required for telomere recombniation in yeast.	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 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 RNA binding double-stranded RNA binding 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	-

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	IPR055128	Carbamoyltransferase, Kae1-like domain, second subdomain	Domain
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

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.