3A44 | pdb_00003a44

Crystal structure of HypA in the dimeric 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
Protein Modification Annotation

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)
C	SCOP2B Superfamily	HypA-like	8057059	3002385	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HypA-like	8057059	3002385	SCOP2B (2022-06-29)
A	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)
D	GTP_EFTU_D2	e3a44D4	A: a/b three-layered sandwiches	X: POZ domain	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: GTP_EFTU_D2	ECOD (v294.1)
D	HypA	e3a44D2	A: a/b three-layered sandwiches	X: Ribosomal protein S7	H: HypA Ni-binding domain	T: HypA Ni-binding domain	F: HypA	ECOD (v294.1)
C	Pept_tRNA_hydro	e3a44C2	A: a/b three-layered sandwiches	X: Tautomerase/MIF-like	H: Tautomerase/MIF	T: Tautomerase/MIF	F: Pept_tRNA_hydro	ECOD (v294.1)
C	HypA	e3a44C3	A: a/b three-layered sandwiches	X: Ribosomal protein S7	H: HypA Ni-binding domain	T: HypA Ni-binding domain	F: HypA	ECOD (v294.1)
B	PDEase_I	e3a44B2	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: PDEase_I	ECOD (v294.1)
B	HypA	e3a44B3	A: a/b three-layered sandwiches	X: Ribosomal protein S7	H: HypA Ni-binding domain	T: HypA Ni-binding domain	F: HypA	ECOD (v294.1)
A	HypA	e3a44A1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: HypA	ECOD (v294.1)
A	DNA_pol_B	e3a44A2	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: DNA_pol_B	ECOD (v294.1)

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)
C	3.30.2320.50	Alpha Beta	2-Layer Sandwich	hypothetical protein PF0899 fold		CATH (4.3.0)
C	4.10.80.120	Few Secondary Structures	Irregular	Rhinovirus 14, subunit 4		CATH (4.3.0)
B	3.30.2320.50	Alpha Beta	2-Layer Sandwich	hypothetical protein PF0899 fold		CATH (4.3.0)
A	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, D	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, D	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	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	IPR020538	Hydrogenase nickel incorporation protein HypA/HybF, conserved site	Conserved Site
A, B, C, D	IPR000688	Hydrogenase maturation factor HypA/HybF	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D	FME	Parent Component: MET RESID: AA0021 , AA0566 PSI-MOD : N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891

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.