5YXY

Crystal structure of the HyhL-HypA complex (form I)

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)
D	SCOP2B Superfamily	HypA-like	8057059	3002385	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	HypA-like	8057059	3002385	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	HypA-like	8057059	3002385	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)
A	F_UNCLASSIFIED	e5yxyA5	A: alpha complex topology	X: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)	H: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)	T: alpha-helical domain in nickel-iron hydrogenase, large subunit	F: F_UNCLASSIFIED	ECOD (1.6)
B	F_UNCLASSIFIED	e5yxyB4	A: beta meanders	X: all-beta domain in nickel-iron hydrogenase large subunit (From Topology)	H: all-beta domain in nickel-iron hydrogenase large subunit (From Topology)	T: all-beta domain in nickel-iron hydrogenase large subunit	F: F_UNCLASSIFIED	ECOD (1.6)
B	F_UNCLASSIFIED	e5yxyB1	A: alpha complex topology	X: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)	H: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)	T: alpha-helical domain in nickel-iron hydrogenase, large subunit	F: F_UNCLASSIFIED	ECOD (1.6)
B	F_UNCLASSIFIED	e5yxyB2	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)	T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e5yxyC1	A: beta meanders	X: all-beta domain in nickel-iron hydrogenase large subunit (From Topology)	H: all-beta domain in nickel-iron hydrogenase large subunit (From Topology)	T: all-beta domain in nickel-iron hydrogenase large subunit	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e5yxyC3	A: alpha complex topology	X: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)	H: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)	T: alpha-helical domain in nickel-iron hydrogenase, large subunit	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e5yxyC2	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)	T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit	F: F_UNCLASSIFIED	ECOD (1.6)
D	PF01155	e5yxyD2	A: a+b three layers	X: Bacillus chorismate mutase-like	H: HypA Ni-binding domain (From Topology)	T: HypA Ni-binding domain	F: PF01155	ECOD (1.6)
D	F_UNCLASSIFIED	e5yxyD1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: F_UNCLASSIFIED	ECOD (1.6)
E	PF01155	e5yxyE2	A: a+b three layers	X: Bacillus chorismate mutase-like	H: HypA Ni-binding domain (From Topology)	T: HypA Ni-binding domain	F: PF01155	ECOD (1.6)
E	F_UNCLASSIFIED	e5yxyE1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: F_UNCLASSIFIED	ECOD (1.6)
F	PF01155	e5yxyF1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: HypA Ni-binding domain (From Topology)	T: HypA Ni-binding domain	F: PF01155	ECOD (1.6)
F	F_UNCLASSIFIED	e5yxyF2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: F_UNCLASSIFIED	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.2320.50	Alpha Beta	2-Layer Sandwich	hypothetical protein PF0899 fold		CATH (4.3.0)
E	3.30.2320.50	Alpha Beta	2-Layer Sandwich	hypothetical protein PF0899 fold		CATH (4.3.0)
F	3.30.2320.50	Alpha Beta	2-Layer Sandwich	hypothetical protein PF0899 fold		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF00374	Nickel-dependent hydrogenase (NiFeSe_Hases)	Nickel-dependent hydrogenase	-	Family
D, E, F	PF01155	Hydrogenase/urease nickel incorporation, metallochaperone, hypA (HypA)	Hydrogenase/urease nickel incorporation, metallochaperone, hypA	HypA is a metallochaperone that binds nickel to bring it safely to its target. The targets for Hypa are the nickel-containing enzymes [Ni,Fe]-hydrogenase and urease. The nickel coordinates with four nitrogens within the protein. The four conserved cy ...	HypA is a metallochaperone that binds nickel to bring it safely to its target. The targets for Hypa are the nickel-containing enzymes [Ni,Fe]-hydrogenase and urease. The nickel coordinates with four nitrogens within the protein. The four conserved cysteines towards the C-terminus bind one zinc moiety probably to stabilise the protein fold [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Cytosolic NiFe-hydrogenase, alpha subunit	cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor oxidoreductase activity, acting on hydrogen as donor ferredoxin hydrogenase activity catalytic activity	-	-
D, E, F	Probable hydrogenase nickel incorporation protein HypA	cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding zinc ion binding	organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process biosynthetic process organic substance biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process biosynthetic process organic substance biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process macromolecule modification protein modification process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR001501	Nickel-dependent hydrogenase, large subunit	Family
A, B, C	IPR029014	[NiFe]-hydrogenase, large subunit	Homologous Superfamily
A, B, C	IPR018194	Nickel-dependent hydrogenase, large subunit, nickel binding site	Binding Site
D, E, F	IPR020538	Hydrogenase nickel incorporation protein HypA/HybF, conserved site	Conserved Site
D, E, F	IPR000688	Hydrogenase maturation factor HypA/HybF	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 R01GM133198.