Structure of PDB 2pda Chain A

Receptor sequence

>2pdaA (length=1231) Species: 873 (Desulfocurvibacter africanus)

GKKMMTTDGNTATAHVAYAMSEVAAIYPITPSSTMGEEADDWAAQGRKNI
FGQTLTIREMQSEAGAAGAVHGALAAGALTTTFTASQGLLLMIPNMYKIS
GELLPGVFHVTARAIAAHALSIFGDHQDIYAARQTGFAMLASSSVQEAHD
MALVAHLAAIESNVPFMHFFDGFRTSHEIQKIEVLDYADMASLVNQKALA
EFRAKSMNPEHPHVRGTAQNPDIYFQGREAANPYYLKVPGIVAEYMQKVA
SLTGRSYKLFDYVGAPDAERVIVSMGSSCETIEEVINHLAAKGEKIGLIK
VRLYRPFVSEAFFAALPASAKVITVLDRTKEPGAPGDPLYLDVCSAFVER
GEAMPKILAGRYGLGSKEFSPAMVKSVYDNMSGAKKNHFTVGIEDDVTGT
SLPVDNAFADTTPKGTIQCQFWGLGADGTVGANKQAIKIIGDNTDLFAQG
YFSYDSKKSGGITISHLRFGEKPIQSTYLVNRADYVACHNPAYVGIYDIL
EGIKDGGTFVLNSPWSSLEDMDKHLPSGIKRTIANKKLKFYNIDAVKIAT
DVGLGGRINMIMQTAFFKLAGVLPFEKAVDLLKKSIHKAYGKKGEKIVKM
NTDAVDQAVTSLQEFKYPDSWKDAPAETKAEPMTNEFFKNVVKPILTQQG
DKLPVSAFEADGRFPLGTSQFEKRGVAINVPQWVPENCIQCNQCAFVCPH
SAILPVLAKEEELVGAPANFTALEAKGKELKGYKFRIQINTLDCMGCGNC
ADICPPKEKALVMQPLDTQRDAQVPNLEYAARIPVKSEVLPRDSLKGSQF
QEPLMEFSGACSGCGETPYVRVITQLFGERMFIANATGCSSIWGASAPSM
PYKTNRLGQGPAWGNSLFEDAAEYGFGMNMSMFARRTHLADLAAKALESD
ASGDVKEALQGWLAGKNDPIKSKEYGDKLKKLLAGQKDGLLGQIAAMSDL
YTKKSVWIFGGDGWAYDIGYGGLDHVLASGEDVNVFVMDTEVYSNTGGQS
SKATPTGAVAKFAAAGKRTGKKDLARMVMTYGYVYVATVSMGYSKQQFLK
VLKEAESFPGPSLVIAYATCINQGLRKGMGKSQDVMNTAVKSGYWPLFRY
DPRLAAQGKNPFQLDSKAPDGSVEEFLMAQNRFAVLDRSFPEDAKRLRAQ
VAHELDVRFKELEHMAATNIFESFAPAGGKADGSVDFGEGAEFCTRDDTP
MMARPDSGEACDQNRAGTSEQQGDLSKRTKK

3D structure

• PDB: 2pda Crystal structures of the key anaerobic enzyme pyruvate:ferredoxin oxidoreductase, free and in complex with pyruvate.
• Chain: A
• Resolution: 3.0 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): T31 E64 R114 N996
• Catalytic site (residue number reindexed from 1): T30 E63 R113 N995
• Enzyme Commision number: 1.2.7.1: pyruvate synthase.

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	MG	A	D963 T991 V993	D962 T990 V992
BS02	CA	A	D983 N985 A1056 E1057 F1059 G1061 S1063	D982 N984 A1055 E1056 F1058 G1060 S1062
BS03	SF4	A	W684 C689 I690 C692 C695 I738 C755 P756 A761 L762	W683 C688 I689 C691 C694 I737 C754 P755 A760 L761
BS04	SF4	A	P682 C699 A703 I704 C745 M746 G747 C748 G749 C751	P681 C698 A702 I703 C744 M745 G746 C747 G748 C750
BS05	SF4	A	K459 C812 C815 E817 C840 S995 C1071 I1072	K458 C811 C814 E816 C839 S994 C1070 I1071
BS06	TPP	A	P29 I30 E64 C840 F869 E870 G962 D963 G964 V993 S995 N996	P28 I29 E63 C839 F868 E869 G961 D962 G963 V992 S994 N995
BS07	PYR	A	T31 R114 N996 T997	T30 R113 N995 T996

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0005506 iron ion binding
• GO:0016491 oxidoreductase activity
• GO:0016903 oxidoreductase activity, acting on the aldehyde or oxo group of donors
• GO:0019164 pyruvate synthase activity
• GO:0030976 thiamine pyrophosphate binding
• GO:0046872 metal ion binding
• GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process

• GO:0006086 acetyl-CoA biosynthetic process from pyruvate
• GO:0006979 response to oxidative stress
• GO:0022900 electron transport chain

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:2pda, PDBe:2pda, PDBj:2pda
• PDBsum: 2pda
• PubMed: 10048931
• UniProt: P94692|PFOR_DESAF Pyruvate:ferredoxin oxidoreductase (Gene Name=por)