4G9I | pdb_00004g9i

Crystal structure of T.kodakarensis HypF

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
F	SCOP2B Superfamily	HypF zinc finger	8092449	3002027	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Acylphosphatase/BLUF domain-like	8092446	3000165	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	HypF zinc finger	8092450	3002027	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Actin-like ATPases	8092454	3000092	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Actin-like ATPases	8092455	3000092	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	YrdC/RibB-like	8092452	3000166	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Acylphosphatase/BLUF domain-like	8092446	3000165	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	HypF zinc finger	8092449	3002027	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Actin-like ATPases	8092454	3000092	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	YrdC/RibB-like	8092452	3000166	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Actin-like ATPases	8092455	3000092	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	HypF zinc finger	8092450	3002027	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Actin-like ATPases	8092455	3000092	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Actin-like ATPases	8092454	3000092	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Acylphosphatase/BLUF domain-like	8092446	3000165	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	HypF zinc finger	8092450	3002027	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	YrdC/RibB-like	8092452	3000166	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	HypF zinc finger	8092449	3002027	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Actin-like ATPases	8092455	3000092	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Acylphosphatase/BLUF domain-like	8092446	3000165	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	HypF zinc finger	8092449	3002027	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	HypF zinc finger	8092450	3002027	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	YrdC/RibB-like	8092452	3000166	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Actin-like ATPases	8092454	3000092	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Actin-like ATPases	8092454	3000092	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HypF zinc finger	8092449	3002027	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Actin-like ATPases	8092455	3000092	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	YrdC/RibB-like	8092452	3000166	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Acylphosphatase/BLUF domain-like	8092446	3000165	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HypF zinc finger	8092450	3002027	SCOP2B (2022-06-29)
A	SCOP2 Family	Acylphosphatase-like	8049601	4000382	SCOP2 (2022-06-29)
A	SCOP2 Family	HypF zinc finger	8092447	4000385	SCOP2 (2022-06-29)
A	SCOP2 Family	HypF zinc finger	8092448	4000385	SCOP2 (2022-06-29)
A	SCOP2 Family	YrdC/Sua5-like	8092451	4000384	SCOP2 (2022-06-29)
A	SCOP2 Family	YgjD/Kae1-like	8092453	4000383	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Acylphosphatase/BLUF domain-like	8092446	3000165	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	HypF zinc finger	8092449	3002027	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	HypF zinc finger	8092450	3002027	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	YrdC/RibB-like	8092452	3000166	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Actin-like ATPases	8092455	3000092	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Actin-like ATPases	8092454	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)
F	Acylphosphatase	e4g9iF6	A: a+b two layers	X: Alpha-beta plaits	H: Acylphosphatase-like (From Topology)	T: Acylphosphatase-like	F: Acylphosphatase	ECOD (1.6)
F	Sua5_yciO_yrdC	e4g9iF8	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)
F	HypF	e4g9iF10	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: HypF	ECOD (1.6)
F	Peptidase_M22_C_1	e4g9iF9	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)
F	zf-HYPF	e4g9iF7	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)
E	Acylphosphatase	e4g9iE6	A: a+b two layers	X: Alpha-beta plaits	H: Acylphosphatase-like (From Topology)	T: Acylphosphatase-like	F: Acylphosphatase	ECOD (1.6)
E	Sua5_yciO_yrdC	e4g9iE8	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)
E	HypF	e4g9iE10	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: HypF	ECOD (1.6)
E	Peptidase_M22_C_1	e4g9iE9	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)
E	zf-HYPF	e4g9iE7	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)
D	Acylphosphatase	e4g9iD6	A: a+b two layers	X: Alpha-beta plaits	H: Acylphosphatase-like (From Topology)	T: Acylphosphatase-like	F: Acylphosphatase	ECOD (1.6)
D	Sua5_yciO_yrdC	e4g9iD8	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)
D	HypF	e4g9iD10	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: HypF	ECOD (1.6)
D	Peptidase_M22_C_1	e4g9iD9	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)
D	zf-HYPF	e4g9iD7	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	Acylphosphatase	e4g9iC12	A: a+b two layers	X: Alpha-beta plaits	H: Acylphosphatase-like (From Topology)	T: Acylphosphatase-like	F: Acylphosphatase	ECOD (1.6)
C	Sua5_yciO_yrdC	e4g9iC14	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)
C	HypF	e4g9iC16	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: HypF	ECOD (1.6)
C	Peptidase_M22_C_1	e4g9iC15	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)
C	zf-HYPF	e4g9iC13	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)
B	Acylphosphatase	e4g9iB6	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	e4g9iB8	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	HypF	e4g9iB14	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: HypF	ECOD (1.6)
B	Peptidase_M22_C_1	e4g9iB13	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	zf-HYPF	e4g9iB7	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	e4g9iA5	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	e4g9iA7	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	HypF	e4g9iA9	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: HypF	ECOD (1.6)
A	Peptidase_M22_C_1	e4g9iA8	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	zf-HYPF	e4g9iA6	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	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, C, D, E A, B, C, D, E, F	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, C, D, E A, B, C, D, E, F	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, C, D, E A, B, C, D, E, F	PF00708	Acylphosphatase (Acylphosphatase)	Acylphosphatase		Domain
A, B, C, D, E A, B, C, D, E, F	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, C, D, E A, B, C, D, E, F	Hydrogenase maturation protein HypF	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, C, D, E A, B, C, D, E, F	IPR041440	HypF, Kae1-like domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR051060	Carbamoyltransferase HypF-like	Family
A, B, C, D, E A, B, C, D, E, F	IPR036046	Acylphosphatase-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR004421	Carbamoyltransferase, HypF-type	Family
A, B, C, D, E A, B, C, D, E, F	IPR055128	Carbamoyltransferase, Kae1-like domain, second subdomain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR017945	DHBP synthase RibB-like alpha/beta domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR006070	Threonylcarbamoyl-AMP synthase-like domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR011125	Zinc finger, HypF-type	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001792	Acylphosphatase-like domain	Domain