Structure of PDB 6tg9 Chain E

Receptor sequence

>6tg9E (length=949) Species: 1415161 (Rhodobacter capsulatus Y262)

PPLDWTQDMGTPKREGAPVHLTIDGVEVTVPAGTSVLRAAAEAGISIPKL
CATDNVEPVGSCRLCMVEIEGMRGTPTSCTTPVAPGMRVHTQTPQLQKLR
RGVMELYISDHPLDCLTCAANGDCELQDMAGAVGLREVRYQAKDTHFARR
DATGPNPRYIPKDNSNPYFSYDPAKCIVCMRCVRACEEVQGTFALTVMGR
GFDARISPAAPDFLSSDCVSCGACVQACPTATLVEKSVERIGTPERKVVT
TCAYCGVGCSFEAHMLGDQLVRMVPWKGGAANRGHSCVKGRFAYGYATHQ
DRILKPMIRDKITDPWREVNWTEALDFTATRLRALRDSHGADALGVITSS
RCTNEETYLVQKLARAVFGTNNTDTCARVCHSPTGYGLKQTFGTSAGTQD
FDSVEETDLALVIGANPTDGHPVFASRLRKRLRAGAKLIVVDPRRIDLLN
TPHRGEAWHLQLKPGTNVAVMTAMAHVIVTEQIFDKRFIGDRCDWDEWAD
YAEFVANPEYAPEAVESLTGVPAGLLRQAARAYAAAPNAAIYYGLGVTEH
SQGSTTVIAIANLAMMTGNIGRPGVGVNPLRGQNNVQGSCDMGSFPHEFP
GYRHVSDDATRGLFERTWGVTLSSEPGLRIPNMLDAAVEGRFKALYVQGE
DILQSDPDTRHVSAGLAAMDLVIVHDLFLNETANYAHVFLPGSTFLEKDG
TFTNAERRINRVRRVMAPKAGFADWEVTQMLANALGAGWHYTHPSEIMAE
IAATTPGFAAVTYEMLDARGSVQWPCNEKAPEGSPIMHVEGFVRGKGRFI
RTAYLPTDEKTGPRFPLLLTTGRILSQYNVGAQTRRTENTVWHGEDRLEI
HPTDAETRGIRDGDWVRLASRAGETTLRATVTDRVSPGVVYTTFHHPDTQ
ANVVTTDTSDWATNCPEYKVTAVQVAASNGPSDWQQDYAAQAAAARRIE

3D structure

• PDB: 6tg9 Cryo-EM structures reveal intricate Fe-S cluster arrangement and charging in Rhodobacter capsulatus formate dehydrogenase.
• Chain: E
• Resolution: 3.24 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): K295 C386 H387 L551 G588 Q589
• Catalytic site (residue number reindexed from 1): K289 C380 H381 L545 G582 Q583
• Enzyme Commision number: 1.17.1.9: formate dehydrogenase.

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	MGD	E	R357 C358 C386 Q589 G655 E656 S661 N686 S699 K704 D730 T827 R829 N835 V836 Q839 N908 Y924	R351 C352 C380 Q583 G649 E650 S655 N680 S693 K698 D724 T821 R823 N829 V830 Q833 N902 Y918
BS02	MGD	E	C261 K295 G420 A421 D425 G426 H427 P449 R450 P470 N473 L551 G552 H556 G588 Q589 T826 R829 I830 L831 K925	C255 K289 G414 A415 D419 G420 H421 P443 R444 P464 N467 L545 G546 H550 G582 Q583 T820 R823 I824 L825 K919
BS03	FES	E	C57 V65 G66 C68 C71 C85	C51 V59 G60 C62 C65 C79
BS04	SF4	E	H117 C121 C124 A126 C130 T236 A237	H111 C115 C118 A120 C124 T230 A231
BS05	SF4	E	C182 I183 V184 C185 M186 C188 I212 C234	C176 I177 V178 C179 M180 C182 I206 C228
BS06	SF4	E	C192 C224 S226 C227 G228 C230	C186 C218 S220 C221 G222 C224
BS07	SF4	E	C258 Y260 C261 V263 C265 F267 C293 K295 V429	C252 Y254 C255 V257 C259 F261 C287 K289 V423

Gene Ontology

Molecular Function

• GO:0008863 formate dehydrogenase (NAD+) activity
• GO:0016491 oxidoreductase activity
• GO:0043546 molybdopterin cofactor binding
• GO:0046872 metal ion binding
• GO:0051536 iron-sulfur cluster binding
• GO:0051537 2 iron, 2 sulfur cluster binding
• GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process

• GO:0015942 formate metabolic process
• GO:0045333 cellular respiration

Cellular Component

• GO:1990204 oxidoreductase complex

External links

• PDB: RCSB:6tg9, PDBe:6tg9, PDBj:6tg9
• PDBsum: 6tg9
• PubMed: 32313256
• UniProt: D5AQH0