1CC1 | pdb_00001cc1

CRYSTAL STRUCTURE OF A REDUCED, ACTIVE FORM OF THE NI-FE-SE HYDROGENASE FROM DESULFOMICROBIUM BACULATUM

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth S]	d1cc1s_	Multi-domain proteins (alpha and beta)	HydA/Nqo6-like	HydA/Nqo6-like	Nickel-iron hydrogenase, small subunit	Nickel-iron hydrogenase, small subunit	(Desulfomicrobium baculatum ) [TaxId: 899 ],	SCOPe (2.08)
B [auth L]	d1cc1l_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	Nickel-iron hydrogenase, large subunit	Nickel-iron hydrogenase, large subunit	(Desulfomicrobium baculatum ) [TaxId: 899 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth S]	SCOP2 Family	HydA C-terminal domain-like	8025211	4000435	SCOP2 (2022-06-29)
A [auth S]	SCOP2 Family	Nq06/HydA N-terminal domain-like	8054420	4007641	SCOP2 (2022-06-29)
A [auth S]	SCOP2 Superfamily	HydA C-terminal domain-like	8037590	3001861	SCOP2 (2022-06-29)
A [auth S]	SCOP2 Superfamily	Nqo6/HydA N-terminal domain-like	8054421	3002291	SCOP2 (2022-06-29)
B [auth L]	SCOP2 Family	Nickel-iron hydrogenase, large subunit	8025199	4002888	SCOP2 (2022-06-29)
B [auth L]	SCOP2 Superfamily	HydB/Nqo4-like	8037578	3001849	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)
A [auth S]	Cytochrom_CIII	e1cc1S1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Cytochrom_CIII	ECOD (develop294)
A [auth S]	RecU	e1cc1S2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: RecU	ECOD (develop294)
B [auth L]	NiFeSe_Hases	e1cc1L1	A: beta meanders	X: all-beta domain in nickel-iron hydrogenase large subunit	H: all-beta domain in nickel-iron hydrogenase large subunit	T: all-beta domain in nickel-iron hydrogenase large subunit	F: NiFeSe_Hases	ECOD (develop294)
B [auth L]	NiFeSe_Hases	e1cc1L2	A: a+b two layers	X: alpha-helical domain in nickel-iron hydrogenase, large subunit	H: alpha-helical domain in nickel-iron hydrogenase, large subunit	T: alpha-helical domain in nickel-iron hydrogenase, large subunit	F: NiFeSe_Hases	ECOD (develop294)
B [auth L]	NiFeSe_Hases	e1cc1L3	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit	T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit	F: NiFeSe_Hases	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth S]	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 hydrogenase (acceptor) activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding electron transfer activity cation binding ion 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 hydrogenase (acceptor) activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding electron transfer activity cation binding ion binding metal ion binding	cellular respiration energy derivation by oxidation of organic compounds metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration	cellular anatomical structure membrane protein-containing complex catalytic complex oxidoreductase complex ferredoxin hydrogenase complex intracellular protein-containing complex [Ni-Fe] hydrogenase complex periplasmic space
B [auth L]	HYDROGENASE (LARGE SUBUNIT)	hydrogenase (acceptor) activity oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor 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	-	cellular anatomical structure periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth S]	IPR006311	Twin-arginine translocation pathway, signal sequence	Conserved Site
A [auth S]	IPR001821	[NiFe]-hydrogenase, small subunit	Family
A [auth S]	IPR027394	Cytochrome-c3 hydrogenase, C-terminal	Domain
A [auth S]	IPR006137	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	Domain
A [auth S]	IPR053622	NiFe/NiFeSe hydrogenase small subunit	Family
A [auth S]	IPR037024	[NiFe]-hydrogenase, small subunit, N-terminal domain superfamily	Homologous Superfamily
A [auth S]	IPR019546	Twin-arginine translocation pathway, signal sequence, bacterial/archaeal	Conserved Site
A [auth S]	IPR037148	[NiFe]-hydrogenase, small subunit, C-terminal domain superfamily	Homologous Superfamily
B [auth L]	IPR001501	Nickel-dependent hydrogenase, large subunit	Family
B [auth L]	IPR029014	[NiFe]-hydrogenase, large subunit	Homologous Superfamily
B [auth L]	IPR018194	Nickel-dependent hydrogenase, large subunit, nickel binding site	Binding Site
B [auth L]	IPR050867	[NiFe]/[NiFeSe] hydrogenase large subunit	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A [auth S], B [auth L]	[NiFeSe] hydrogenase M-CSA #443	[NiFeSe] hydrogenases are metalloenzymes that catalyze the reaction H₂ ↔ 2H⁺ + 2e-. They are generally heterodimeric, contain three iron–sulfur clusters in their small subunit and a nickel–iron-containing active site in their large subunit that includes a selenocysteine (SeCys) ligand.	Defined by 19 residues: CYS:A-18 [auth S-18]CYS:A-21 [auth S-21]CYS:A-126 [auth S-126]CYS:A-164 [auth S-164]HIS:A-208 [auth S-208]CYS:A-211 [auth S-211]CYS:A-231 [auth S-231]CYS:A-237 [auth S-237]CYS:A-246 [auth S-246]CYS:A-258 [auth S-258]CYS:A-264 [auth S-264]CYS:A-267 [auth S-267]GLU:B-23 [auth L-23]CYS:B-70 [auth L-70]CYS:B-73 [auth L-73]HIS:B-77 [auth L-77]ARG:B-425 [auth L-425]SEC:B-492 [auth L-492]CYS:B-495 [auth L-495] \| Explore in 3D: M-CSA Motif Definition Up to 10 residues are supported for Structure Motif searching, this motif has 19 residues. EC: 1.18.99.1 (PDB Primary Data) EC: 1.12.99.6 (UniProt)

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.

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