Structure of PDB 1yq9 Chain B

Receptor sequence
>1yq9B (length=260) Species: 879 (Megalodesulfovibrio gigas) [Search protein sequence]
KRPSVVYLHNAECTGCSESVLRTVDPYVDELILDVISMDYHETLMAGAGH
AVEEALHEAIKGDFVCVIEGGIPMGDGGYWGKVGGRNMYDICAEVAPKAK
AVIAIGTCATYGGVQAAKPNPTGTVGVNEALGKLGVKAINIAGCPPNPMN
FVGTVVHLLTKGMPELDKQGRPVMFFGETVHDNCPRLKHFEAGEFATSFG
SPEAKKGYCLYELGCKGPDTYNNCPKQLFNQVNWPVQAGHPCIACSEPNF
WDLYSPFYSA
3D structure
PDB1yq9 Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases.
ChainB
Resolution2.35 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) C17 C20 C112 C148 H185 C188 C213 C219 C228 P239 C246 C249
Catalytic site (residue number reindexed from 1) C13 C16 C108 C144 H181 C184 C209 C215 C224 P235 C242 C245
Enzyme Commision number 1.12.2.1: cytochrome-c3 hydrogenase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 SF4 B H185 C188 R190 L191 C213 L214 Y215 C219 P222 H181 C184 R186 L187 C209 L210 Y211 C215 P218
BS02 F3S B C228 F233 W238 P239 C246 I247 C249 C224 F229 W234 P235 C242 I243 C245
BS03 SF4 B E16 C17 G19 C20 G110 C112 C148 P149 E12 C13 G15 C16 G106 C108 C144 P145
Gene Ontology
Molecular Function
GO:0008901 ferredoxin hydrogenase activity
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0047806 cytochrome-c3 hydrogenase activity
GO:0051536 iron-sulfur cluster binding
GO:0051538 3 iron, 4 sulfur cluster binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0009061 anaerobic respiration
Cellular Component
GO:0009375 ferredoxin hydrogenase complex
GO:0016020 membrane
GO:0042597 periplasmic space
GO:0044569 [Ni-Fe] hydrogenase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1yq9, PDBe:1yq9, PDBj:1yq9
PDBsum1yq9
PubMed15803334
UniProtP12943|PHNS_MEGGA Periplasmic [NiFe] hydrogenase small subunit (Gene Name=hydA)

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