Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1FRV

CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF NI-FE HYDROGENASE

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0008901	molecular_function	ferredoxin hydrogenase activity
A	0009055	molecular_function	electron transfer activity
A	0009061	biological_process	anaerobic respiration
A	0009375	cellular_component	ferredoxin hydrogenase complex
A	0016020	cellular_component	membrane
A	0016491	molecular_function	oxidoreductase activity
A	0042597	cellular_component	periplasmic space
A	0044569	cellular_component	[Ni-Fe] hydrogenase complex
A	0046872	molecular_function	metal ion binding
A	0047806	molecular_function	cytochrome-c3 hydrogenase activity
A	0051536	molecular_function	iron-sulfur cluster binding
A	0051538	molecular_function	3 iron, 4 sulfur cluster binding
A	0051539	molecular_function	4 iron, 4 sulfur cluster binding
B	0008901	molecular_function	ferredoxin hydrogenase activity
B	0016151	molecular_function	nickel cation binding
B	0016491	molecular_function	oxidoreductase activity
B	0042597	cellular_component	periplasmic space
B	0046872	molecular_function	metal ion binding
B	0047806	molecular_function	cytochrome-c3 hydrogenase activity
C	0008901	molecular_function	ferredoxin hydrogenase activity
C	0009055	molecular_function	electron transfer activity
C	0009061	biological_process	anaerobic respiration
C	0009375	cellular_component	ferredoxin hydrogenase complex
C	0016020	cellular_component	membrane
C	0016491	molecular_function	oxidoreductase activity
C	0042597	cellular_component	periplasmic space
C	0044569	cellular_component	[Ni-Fe] hydrogenase complex
C	0046872	molecular_function	metal ion binding
C	0047806	molecular_function	cytochrome-c3 hydrogenase activity
C	0051536	molecular_function	iron-sulfur cluster binding
C	0051538	molecular_function	3 iron, 4 sulfur cluster binding
C	0051539	molecular_function	4 iron, 4 sulfur cluster binding
D	0008901	molecular_function	ferredoxin hydrogenase activity
D	0016151	molecular_function	nickel cation binding
D	0016491	molecular_function	oxidoreductase activity
D	0042597	cellular_component	periplasmic space
D	0046872	molecular_function	metal ion binding
D	0047806	molecular_function	cytochrome-c3 hydrogenase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NI B 538

Chain	Residue
B	CYS65
B	VAL67
B	CYS68
B	CYS530
B	CYS533
B	FEL537

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NI D 538

Chain	Residue
D	CYS65
D	CYS68
D	CYS530
D	CYS533
D	FEL537

site_id	AC3
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SF4 A 265

Chain	Residue
A	VAL184
A	HIS185
A	CYS188
A	ARG190
A	CYS213
A	LEU214
A	CYS219
A	GLY221
A	VAL240

site_id	AC4
Number of Residues	11
Details	BINDING SITE FOR RESIDUE F3S A 266

Chain	Residue
A	THR224
A	ASN226
A	CYS228
A	PHE233
A	TRP238
A	PRO239
A	CYS246
A	ILE247
A	CYS249
B	LYS216
B	GLN221

site_id	AC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SF4 A 267

Chain	Residue
A	CYS17
A	GLY19
A	CYS20
A	GLY110
A	THR111
A	CYS112
A	CYS148
A	PRO149
B	HIS219

site_id	AC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE FEL B 537

Chain	Residue
B	CYS68
B	HIS72
B	ARG463
B	VAL484
B	SER486
B	CYS533
B	NI538

site_id	AC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SF4 C 265

Chain	Residue
C	HIS185
C	CYS188
C	ARG190
C	LEU191
C	CYS213
C	LEU214
C	CYS219

site_id	AC8
Number of Residues	10
Details	BINDING SITE FOR RESIDUE F3S C 266

Chain	Residue
C	VAL184
C	THR224
C	ASN226
C	CYS228
C	PHE233
C	TRP238
C	CYS246
C	ILE247
C	CYS249
D	GLN221

site_id	AC9
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SF4 C 267

Chain	Residue
C	CYS17
C	CYS20
C	THR111
C	CYS112
C	CYS148
C	PRO149
D	ARG63
D	HIS219

site_id	BC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE FEL D 537

Chain	Residue
D	CYS68
D	VAL71
D	HIS72
D	ALA461
D	VAL484
D	SER486
D	CYS533
D	NI538

site_id	CT1
Number of Residues	6
Details	THE ACTIVE SITE CONTAINS TWO METALS: NI AND (PROBABLY) FE. THE LATTER ASSIGNMENT HAS BEEN CONFIRMED BY AN ANOMALOUS DIFFERENCE MAP AND BY A METAL ANALYSIS. THE PUTATIVE FE HAS 3 NON-PROTEIN LIGANDS (L) OF YET UNKNOWN IDENTITY. THESE LIGANDS WERE MODELED AS WATER DURING REFINEMENT. THE USED CRYSTALS MOST LIKELY CONTAIN A MIXTURE OF SEVERAL ACTIVE SITE REDOX STATES (SEE NATURE PUBLICATION). THE ACTUAL OXIDATION STATE OF THE NI AND PUTATIVE FE IN EACH OF THESE STATES IS STILL A MATTER OF INVESTIGATION. THE RESIDUES OF THE ACTIVE SITE ARE LISTED IN THE SITE RECORDS BELOW.

Chain	Residue
B	CYS65
B	CYS68
B	CYS530
B	CYS533
B	FEL537
B	NI538

site_id	CT2
Number of Residues	6
Details	THE ACTIVE SITE CONTAINS TWO METALS: NI AND (PROBABLY) FE. THE LATTER ASSIGNMENT HAS BEEN CONFIRMED BY AN ANOMALOUS DIFFERENCE MAP AND BY A METAL ANALYSIS. THE PUTATIVE FE HAS 3 NON-PROTEIN LIGANDS (L) OF YET UNKNOWN IDENTITY. THESE LIGANDS WERE MODELED AS WATER DURING REFINEMENT. THE USED CRYSTALS MOST LIKELY CONTAIN A MIXTURE OF SEVERAL ACTIVE SITE REDOX STATES (SEE NATURE PUBLICATION). THE ACTUAL OXIDATION STATE OF THE NI AND PUTATIVE FE IN EACH OF THESE STATES IS STILL A MATTER OF INVESTIGATION. THE RESIDUES OF THE ACTIVE SITE ARE LISTED IN THE SITE RECORDS BELOW.

Chain	Residue
D	CYS533
D	FEL537
D	NI538
D	CYS65
D	CYS68
D	CYS530

Functional Information from PROSITE/UniProt

site_id	PS00507
Number of Residues	26
Details	NI_HGENASE_L_1 Nickel-dependent hydrogenases large subunit signature 1. RGLEmilkgrdprdaqhftQRaCGVC

Chain	Residue	Details
B	ARG43-CYS68

site_id	PS00508
Number of Residues	10
Details	NI_HGENASE_L_2 Nickel-dependent hydrogenases large subunit signature 2. YDPCIACgv.H

Chain	Residue	Details
B	TYR527-HIS536

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	26
Details	Binding site: {}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"7854413","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	3
Details	Annotated By Reference To The Literature 1cc1

Chain	Residue	Details
A	THR18
B	CYS530
B	GLU18

site_id	CSA2
Number of Residues	3
Details	Annotated By Reference To The Literature 1cc1

Chain	Residue	Details
C	THR18
D	CYS530
D	GLU18

site_id	CSA3
Number of Residues	1
Details	Annotated By Reference To The Literature 1cc1

Chain	Residue	Details
B	CYS530

site_id	CSA4
Number of Residues	1
Details	Annotated By Reference To The Literature 1cc1

Chain	Residue	Details
D	CYS530

site_id	MCSA1
Number of Residues	8
Details	M-CSA 126

Chain	Residue	Details
B	GLU18	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
B	CYS65	activator, metal ligand
B	CYS68	activator, electrostatic stabiliser, metal ligand
B	HIS72	electrostatic stabiliser, hydrogen bond donor
B	ARG463	electrostatic stabiliser, hydrogen bond donor
B	SER486	electrostatic stabiliser, hydrogen bond donor
B	CYS530	hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor
B	CYS533	activator, electrostatic stabiliser, metal ligand

site_id	MCSA2
Number of Residues	8
Details	M-CSA 126

Chain	Residue	Details
D	GLU18	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
D	CYS65	activator, metal ligand
D	CYS68	activator, electrostatic stabiliser, metal ligand
D	HIS72	electrostatic stabiliser, hydrogen bond donor
D	ARG463	electrostatic stabiliser, hydrogen bond donor
D	SER486	electrostatic stabiliser, hydrogen bond donor
D	CYS530	hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor
D	CYS533	activator, electrostatic stabiliser, metal ligand

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)