Structure of PDB 8dqv Chain D

Receptor sequence

>8dqvD (length=322) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

ASVLWFQGGACSGNTMSFLNADEPNVVDLIVDFGLDLLWHPSLGLELGNN
AQKVFWDCAKGERPLDIFVFEGTVIEAPNGTGQMDMFAGRPMKDWVTDLA
GAAQIVVAIGDCACFGGIPAMEPNPSGSTGLQFHKREKGGFLGPDFRSKM
GLPVINVPGCPAHPDWITQILVALATGRAGDITLDDLHRPETFFKTFTQT
GCTRVQFFEYKQSTLSFGEGTRTGCLFYEFGCRGPMTHSPCNRILWNRQS
SKTRAGMPCLGCTEPEFPHFDLAPGTVFKTQKVSGMIPKEVPEGTDHLTY
MGLAAAARIAAPQWSKEDMFVV

3D structure

• PDB: 8dqv Structural basis for bacterial energy extraction from atmospheric hydrogen.
• Chain: D
• Resolution: 1.52 Å

Enzymatic activity

• Enzyme Commision number: 1.12.99.6: hydrogenase (acceptor).

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	VK3	D	K212 Q213 S214 F228 Y229 Y301 M302	K211 Q212 S213 F227 Y228 Y300 M301
BS02	F3S	D	T199 C242 W247 K253 C260 L261 G262 C263 T264	T198 C241 W246 K252 C259 L260 G261 C262 T263
BS03	F3S	D	Q200 C203 R205 V206 F209 C226 L227 F228 C233 P236 T254	Q199 C202 R204 V205 F208 C225 L226 F227 C232 P235 T253
BS04	F3S	D	A11 C12 G14 N15 G111 D112 C113 C161 P162	A10 C11 G13 N14 G110 D111 C112 C160 P161

Gene Ontology

Molecular Function

• GO:0008901 ferredoxin hydrogenase activity
• GO:0009055 electron transfer activity
• GO:0016491 oxidoreductase activity
• GO:0033748 hydrogenase (acceptor) activity
• GO:0046872 metal ion binding
• 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:0044569 [Ni-Fe] hydrogenase complex

External links

• PDB: RCSB:8dqv, PDBe:8dqv, PDBj:8dqv
• PDBsum: 8dqv
• PubMed: 36890228
• UniProt: A0QUM6