4HI0 | pdb_00004hi0

Crystal Structure of Helicobacter pylori Urease Accessory Protein UreF/H/G 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)
E	SCOP2 Family	CobW/HypB/UreG nucleotide-binding domain-like	8058223	4003988	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	Simibi-like P-loop NTPases	8058224	3002018	SCOP2 (2022-06-29)
F	SCOP2B Superfamily	Simibi-like P-loop NTPases	8058224	3002018	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)
E		e4hi0E1	A: Flavodoxin-like	X: Class I glutamine amidotransferase-like	H: Phosphofructokinase N-terminal domain	T: PK_Tyr_Ser-Thr	F:	ECOD (20:10:01)
F		e4hi0F1	A: Flavodoxin-like	X: Class I glutamine amidotransferase-like	H: Phosphofructokinase N-terminal domain	T: PK_Tyr_Ser-Thr	F:	ECOD (20:10:01)
D		e4hi0D1	A: Flavodoxin-like	X: Class I glutamine amidotransferase-like	H: Phosphofructokinase N-terminal domain	T: PK_Tyr_Ser-Thr	F:	ECOD (20:10:01)
B		e4hi0B1	A: Flavodoxin-like	X: Class I glutamine amidotransferase-like	H: Phosphofructokinase N-terminal domain	T: PK_Tyr_Ser-Thr	F:	ECOD (20:10:01)
C		e4hi0C1	A: Flavodoxin-like	X: Class I glutamine amidotransferase-like	H: Phosphofructokinase N-terminal domain	T: PK_Tyr_Ser-Thr	F:	ECOD (20:10:01)
A		e4hi0A1	A: Flavodoxin-like	X: Class I glutamine amidotransferase-like	H: Phosphofructokinase N-terminal domain	T: PK_Tyr_Ser-Thr	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
F	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	1.10.4190.10	Mainly Alpha	Orthogonal Bundle	Urease accessory protein UreF	Urease accessory protein UreF	CATH (4.3.0)
A	1.10.4190.10	Mainly Alpha	Orthogonal Bundle	Urease accessory protein UreF	Urease accessory protein UreF	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E, F	PF02492	CobW/HypB/UreG, nucleotide-binding domain (cobW)	CobW/HypB/UreG, nucleotide-binding domain	This domain is found in HypB, a hydrogenase expression / formation protein, and UreG a urease accessory protein. Both these proteins contain a P-loop nucleotide binding motif [2,3]. HypB has GTPase activity and is a guanine nucleotide binding prot ...	This domain is found in HypB, a hydrogenase expression / formation protein, and UreG a urease accessory protein. Both these proteins contain a P-loop nucleotide binding motif [2,3]. HypB has GTPase activity and is a guanine nucleotide binding protein [3]. It is not known whether UreG binds GTP or some other nucleotide. Both enzymes are involved in nickel binding. HypB can store nickel and is required for nickel dependent hydrogenase expression [1]. UreG is required for functional incorporation of the urease nickel metallocenter.[4] GTP hydrolysis may required by these proteins for nickel incorporation into other nickel proteins [1]. This family of domains also contains P47K (Swiss:P31521), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression, and the cobW gene product (Swiss:P29937), which may be involved in cobalamin biosynthesis in Pseudomonas denitrificans [5].	Domain
B, D	PF01774	UreD urease accessory protein (UreD)	UreD urease accessory protein	-	Family
A, C	PF01730	UreF (UreF)	UreF	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F	Urease accessory protein UreG	cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity identical protein binding protein binding enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity urease activator activity	nitrogen cycle metabolic process small molecule metabolic process metabolic process cellular process urea metabolic process catabolic process urea catabolic process small molecule catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm
B, D	Urease accessory protein UreH	cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity urease activator activity	nitrogen cycle metabolic process small molecule metabolic process metabolic process cellular process urea metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm
A, C	Urease accessory protein UreF	cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity urease activator activity	nitrogen cycle metabolic process small molecule metabolic process metabolic process cellular process urea metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F	IPR004400	Urease accessory protein UreG	Family
E, F	IPR003495	CobW/HypB/UreG, nucleotide-binding domain	Domain
E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B, D	IPR002669	Urease accessory protein UreD	Family
A, C	IPR002639	Urease accessory protein UreF	Family
A, C	IPR038277	UreF domain superfamily	Homologous Superfamily

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.