4UPE

Structure of the unready Ni-A state of the S499C mutant of D. fructosovorans NiFe-hydrogenase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4upea_	Multi-domain proteins (alpha and beta)	HydA/Nqo6-like	HydA/Nqo6-like	Nickel-iron hydrogenase, small subunit	automated matches	(Solidesulfovibrio fructosivorans ) [TaxId: 878 ],	SCOPe (2.08)
B	d4upeb_	Multi-domain proteins (alpha and beta)	HydA/Nqo6-like	HydA/Nqo6-like	Nickel-iron hydrogenase, small subunit	automated matches	(Solidesulfovibrio fructosivorans ) [TaxId: 878 ],	SCOPe (2.08)
C	d4upec_	Multi-domain proteins (alpha and beta)	HydA/Nqo6-like	HydA/Nqo6-like	Nickel-iron hydrogenase, small subunit	automated matches	(Solidesulfovibrio fructosivorans ) [TaxId: 878 ],	SCOPe (2.08)
D [auth Q]	d4upeq_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	Nickel-iron hydrogenase, large subunit	automated matches	(Solidesulfovibrio fructosivorans ) [TaxId: 878 ],	SCOPe (2.08)
E [auth R]	d4uper_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	Nickel-iron hydrogenase, large subunit	automated matches	(Solidesulfovibrio fructosivorans ) [TaxId: 878 ],	SCOPe (2.08)
F [auth S]	d4upes_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	Nickel-iron hydrogenase, large subunit	automated matches	(Solidesulfovibrio fructosivorans ) [TaxId: 878 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	HydA C-terminal domain-like	8037588	3001861	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nqo6/HydA N-terminal domain-like	8054419	3002291	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nqo6/HydA N-terminal domain-like	8054419	3002291	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HydA C-terminal domain-like	8037588	3001861	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	HydA C-terminal domain-like	8037588	3001861	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nqo6/HydA N-terminal domain-like	8054419	3002291	SCOP2B (2022-06-29)
D [auth Q]	SCOP2B Superfamily	HydB/Nqo4-like	8037575	3001849	SCOP2B (2022-06-29)
E [auth R]	SCOP2B Superfamily	HydB/Nqo4-like	8037575	3001849	SCOP2B (2022-06-29)
F [auth S]	SCOP2B Superfamily	HydB/Nqo4-like	8037575	3001849	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	Oxidored_q6	e4upeA2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Oxidored_q6	ECOD (1.6)
A	NiFe_hyd_SSU_C	e4upeA1	A: few secondary structure elements	X: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)	H: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)	T: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit	F: NiFe_hyd_SSU_C	ECOD (1.6)
B	Oxidored_q6	e4upeB2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Oxidored_q6	ECOD (1.6)
B	NiFe_hyd_SSU_C	e4upeB1	A: few secondary structure elements	X: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)	H: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)	T: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit	F: NiFe_hyd_SSU_C	ECOD (1.6)
C	Oxidored_q6	e4upeC2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Oxidored_q6	ECOD (1.6)
C	NiFe_hyd_SSU_C	e4upeC1	A: few secondary structure elements	X: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)	H: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)	T: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit	F: NiFe_hyd_SSU_C	ECOD (1.6)
D [auth Q]	NiFeSe_Hases_2nd	e4upeQ2	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: NiFeSe_Hases_2nd	ECOD (1.6)
D [auth Q]	NiFeSe_Hases_1st	e4upeQ4	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: NiFeSe_Hases_1st	ECOD (1.6)
D [auth Q]	NiFeSe_Hases_3rd	e4upeQ3	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: NiFeSe_Hases_3rd	ECOD (1.6)
D [auth Q]	NiFeSe_Hases_3rd_1	e4upeQ1	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: NiFeSe_Hases_3rd_1	ECOD (1.6)
E [auth R]	NiFeSe_Hases_2nd	e4upeR4	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: NiFeSe_Hases_2nd	ECOD (1.6)
E [auth R]	NiFeSe_Hases_1st	e4upeR1	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: NiFeSe_Hases_1st	ECOD (1.6)
E [auth R]	NiFeSe_Hases_3rd	e4upeR3	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: NiFeSe_Hases_3rd	ECOD (1.6)
E [auth R]	NiFeSe_Hases_3rd_1	e4upeR2	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: NiFeSe_Hases_3rd_1	ECOD (1.6)
F [auth S]	NiFeSe_Hases_2nd	e4upeS4	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: NiFeSe_Hases_2nd	ECOD (1.6)
F [auth S]	NiFeSe_Hases_1st	e4upeS1	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: NiFeSe_Hases_1st	ECOD (1.6)
F [auth S]	NiFeSe_Hases_3rd	e4upeS3	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: NiFeSe_Hases_3rd	ECOD (1.6)
F [auth S]	NiFeSe_Hases_3rd_1	e4upeS2	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: NiFeSe_Hases_3rd_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.700	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	CATH (4.3.0)
A	4.10.480.10	Few Secondary Structures	Irregular	Cytochrome-c3 Hydrogenase	Chain A, domain 2	CATH (4.3.0)
B	3.40.50.700	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	CATH (4.3.0)
B	4.10.480.10	Few Secondary Structures	Irregular	Cytochrome-c3 Hydrogenase	Chain A, domain 2	CATH (4.3.0)
C	3.40.50.700	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	CATH (4.3.0)
C	4.10.480.10	Few Secondary Structures	Irregular	Cytochrome-c3 Hydrogenase	Chain A, domain 2	CATH (4.3.0)
D [auth Q]	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (4.3.0)
E [auth R]	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (4.3.0)
F [auth S]	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF14720	NiFe/NiFeSe hydrogenase small subunit C-terminal (NiFe_hyd_SSU_C)	NiFe/NiFeSe hydrogenase small subunit C-terminal	-	Family
A, B, C	PF01058	NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6)	NADH ubiquinone oxidoreductase, 20 Kd subunit	-	Family
D [auth Q], E [auth R], F [auth S]	PF00374	Nickel-dependent hydrogenase (NiFeSe_Hases)	Nickel-dependent hydrogenase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	NIFE-HYDROGENASE SMALL SUBUNIT	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 iron-sulfur cluster binding binding 3 iron, 4 sulfur cluster binding metal cluster binding small molecule binding oxidoreductase activity, acting on hydrogen as donor, cytochrome as acceptor cytochrome-c3 hydrogenase activity 4 iron, 4 sulfur cluster binding electron transfer activity 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 iron-sulfur cluster binding binding 3 iron, 4 sulfur cluster binding metal cluster binding small molecule binding oxidoreductase activity, acting on hydrogen as donor, cytochrome as acceptor cytochrome-c3 hydrogenase activity 4 iron, 4 sulfur cluster binding electron transfer activity cation binding ion binding metal ion binding	cellular respiration energy derivation by oxidation of organic compounds cellular metabolic process metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration	membrane cellular anatomical entity protein-containing complex catalytic complex oxidoreductase complex ferredoxin hydrogenase complex intracellular protein-containing complex [Ni-Fe] hydrogenase complex periplasmic space
D [auth Q], E [auth R], F [auth S]	NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT	oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor oxidoreductase activity, acting on hydrogen as donor, cytochrome as acceptor cytochrome-c3 hydrogenase activity catalytic activity cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor ferredoxin hydrogenase activity	-	periplasmic space cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR006311	Twin-arginine translocation pathway, signal sequence	Conserved Site
A, B, C	IPR001821	[NiFe]-hydrogenase, small subunit	Family
A, B, C	IPR027394	Cytochrome-c3 hydrogenase, C-terminal	Domain
A, B, C	IPR006137	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	Domain
A, B, C	IPR037024	[NiFe]-hydrogenase, small subunit, N-terminal domain superfamily	Homologous Superfamily
A, B, C	IPR019546	Twin-arginine translocation pathway, signal sequence, bacterial/archaeal	Conserved Site
A, B, C	IPR037148	[NiFe]-hydrogenase, small subunit, C-terminal domain superfamily	Homologous Superfamily
D [auth Q], E [auth R], F [auth S]	IPR001501	Nickel-dependent hydrogenase, large subunit	Family
D [auth Q], E [auth R], F [auth S]	IPR029014	[NiFe]-hydrogenase, large subunit	Homologous Superfamily
D [auth Q], E [auth R], F [auth S]	IPR018194	Nickel-dependent hydrogenase, large subunit, nickel binding site	Binding Site
D [auth Q], E [auth R], F [auth S]	IPR050867	[NiFe]/[NiFeSe] hydrogenase large subunit	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
D [auth Q], E [auth R], F [auth S]	CSX	Parent Component: CYS RESID: AA0451 PSI-MOD : 2'-(S-L-cysteinyl)-6'-hydroxy-L-tryptophan sulfoxide MOD:01380

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.