Structure of PDB 2c42 Chain B

Receptor sequence

>2c42B (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: 2c42 Flexibility of Thiamine Diphosphate Revealed by Kinetic Crystallographic Studies of the Reaction of Pyruvate-Ferredoxin Oxidoreductase with Pyruvate.
• Chain: B
• Resolution: 1.78 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	SF4	B	W684 C689 I690 Q691 C692 N693 C695 C755 P756 A761 L762	W683 C688 I689 Q690 C691 N692 C694 C754 P755 A760 L761
BS02	SF4	B	P682 C699 A703 I704 C745 M746 G747 C748 G749 C751	P681 C698 A702 I703 C744 M745 G746 C747 G748 C750
BS03	SF4	B	K459 A811 C812 C815 E817 C840 C1071 I1072	K458 A810 C811 C814 E816 C839 C1070 I1071
BS04	TPP	B	P29 I30 E64 Q88 E817 T838 G839 C840 F869 G962 D963 G964 V993 Y994 S995 N996 T997	P28 I29 E63 Q87 E816 T837 G838 C839 F868 G961 D962 G963 V992 Y993 S994 N995 T996
BS05	PYR	B	T31 R114 N996 T997	T30 R113 N995 T996
BS06	MG	B	D963 T991 V993	D962 T990 V992
BS07	CA	B	D983 V984 N985 A1056 E1057 F1059 G1061 S1063	D982 V983 N984 A1055 E1056 F1058 G1060 S1062

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:2c42, PDBe:2c42, PDBj:2c42
• PDBsum: 2c42
• PubMed: 16472741
• UniProt: P94692|PFOR_DESAF Pyruvate:ferredoxin oxidoreductase (Gene Name=por)