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Protein

Probable pyruvate-flavodoxin oxidoreductase

Gene

ydbK

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -Protein inferred from homologyi

Functioni

Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin.Curated

Catalytic activityi

Pyruvate + CoA + oxidized flavodoxin = acetyl-CoA + CO2 + reduced flavodoxin.

Cofactori

[4Fe-4S] clusterBy similarityNote: Binds 3 [4Fe-4S] clusters per subunit.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi689Iron-sulfur 1 (4Fe-4S)By similarity1
Metal bindingi692Iron-sulfur 1 (4Fe-4S)By similarity1
Metal bindingi695Iron-sulfur 1 (4Fe-4S)By similarity1
Metal bindingi699Iron-sulfur 2 (4Fe-4S)By similarity1
Metal bindingi745Iron-sulfur 2 (4Fe-4S)By similarity1
Metal bindingi748Iron-sulfur 2 (4Fe-4S)By similarity1
Metal bindingi751Iron-sulfur 2 (4Fe-4S)By similarity1
Metal bindingi755Iron-sulfur 1 (4Fe-4S)By similarity1
Metal bindingi819Iron-sulfur 3 (4Fe-4S)By similarity1
Metal bindingi822Iron-sulfur 3 (4Fe-4S)By similarity1
Metal bindingi847Iron-sulfur 3 (4Fe-4S)By similarity1
Metal bindingi1071Iron-sulfur 3 (4Fe-4S)By similarity1

GO - Molecular functioni

GO - Biological processi

  • electron transport chain Source: InterPro
  • response to oxidative stress Source: EcoCyc

Keywordsi

Molecular functionOxidoreductase
Biological processElectron transport, Transport
Ligand4Fe-4S, Iron, Iron-sulfur, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:G6701-MONOMER
MetaCyc:G6701-MONOMER

Names & Taxonomyi

Protein namesi
Recommended name:
Probable pyruvate-flavodoxin oxidoreductase (EC:1.2.7.-)
Gene namesi
Name:ydbK
Ordered Locus Names:b1378, JW1372
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13183 ydbK

Pathology & Biotechi

Chemistry databases

DrugBankiDB00698 Nitrofurantoin

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002155571 – 1174Probable pyruvate-flavodoxin oxidoreductaseAdd BLAST1174

Proteomic databases

EPDiP52647
PaxDbiP52647
PRIDEiP52647

Interactioni

Protein-protein interaction databases

BioGridi426167623 interactors.
DIPiDIP-11636N
IntActiP52647 10 interactors.
STRINGi316385.ECDH10B_1502

Structurei

3D structure databases

ProteinModelPortaliP52647
SMRiP52647
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini680 – 7094Fe-4S ferredoxin-type 1PROSITE-ProRule annotationAdd BLAST30
Domaini736 – 7654Fe-4S ferredoxin-type 2PROSITE-ProRule annotationAdd BLAST30

Sequence similaritiesi

Belongs to the NifJ family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiENOG4105D95 Bacteria
COG0674 LUCA
COG1013 LUCA
COG1014 LUCA
HOGENOMiHOG000266425
InParanoidiP52647
KOiK03737
OMAiNTVMQVC
PhylomeDBiP52647

Family and domain databases

Gene3Di3.40.50.9201 hit
3.40.920.101 hit
4.10.780.101 hit
InterProiView protein in InterPro
IPR017896 4Fe4S_Fe-S-bd
IPR017900 4Fe4S_Fe_S_CS
IPR033412 PFOR_II
IPR037112 Pyrv-flavodox_OxR_EKR_sf
IPR019456 Pyrv-flavodox_OxRtase_EKR
IPR019752 Pyrv/ketoisovalerate_OxRed_cat
IPR002880 Pyrv_Fd/Flavodoxin_OxRdtase_N
IPR011895 Pyrv_flavodox_OxRed
IPR002869 Pyrv_flavodox_OxRed_cen
IPR029061 THDP-binding
IPR011766 TPP_enzyme-bd_C
IPR009014 Transketo_C/PFOR_II
PfamiView protein in Pfam
PF10371 EKR, 1 hit
PF17147 PFOR_II, 1 hit
PF01558 POR, 1 hit
PF01855 POR_N, 1 hit
PF02775 TPP_enzyme_C, 1 hit
PIRSFiPIRSF000159 NifJ, 1 hit
SMARTiView protein in SMART
SM00890 EKR, 1 hit
SUPFAMiSSF52518 SSF52518, 2 hits
SSF52922 SSF52922, 1 hit
SSF53323 SSF53323, 1 hit
TIGRFAMsiTIGR02176 pyruv_ox_red, 1 hit
PROSITEiView protein in PROSITE
PS00198 4FE4S_FER_1, 2 hits
PS51379 4FE4S_FER_2, 2 hits

Sequencei

Sequence statusi: Complete.

P52647-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MITIDGNGAV ASVAFRTSEV IAIYPITPSS TMAEQADAWA GNGLKNVWGD
60 70 80 90 100
TPRVVEMQSE AGAIATVHGA LQTGALSTSF TSSQGLLLMI PTLYKLAGEL
110 120 130 140 150
TPFVLHVAAR TVATHALSIF GDHSDVMAVR QTGCAMLCAA NVQEAQDFAL
160 170 180 190 200
ISQIATLKSR VPFIHFFDGF RTSHEINKIV PLADDTILDL MPQVEIDAHR
210 220 230 240 250
ARALNPEHPV IRGTSANPDT YFQSREATNP WYNAVYDHVE QAMNDFSAAT
260 270 280 290 300
GRQYQPFEYY GHPQAERVII LMGSAIGTCE EVVDELLTRG EKVGVLKVRL
310 320 330 340 350
YRPFSAKHLL QALPGSVRSV AVLDRTKEPG AQAEPLYLDV MTALAEAFNN
360 370 380 390 400
GERETLPRVI GGRYGLSSKE FGPDCVLAVF AELNAAKPKA RFTVGIYDDV
410 420 430 440 450
TNLSLPLPEN TLPNSAKLEA LFYGLGSDGS VSATKNNIKI IGNSTPWYAQ
460 470 480 490 500
GYFVYDSKKA GGLTVSHLRV SEQPIRSAYL ISQADFVGCH QLQFIDKYQM
510 520 530 540 550
AERLKPGGIF LLNTPYSADE VWSRLPQEVQ AVLNQKKARF YVINAAKIAR
560 570 580 590 600
ECGLAARINT VMQMAFFHLT QILPGDSALA ELQGAIAKSY SSKGQDLVER
610 620 630 640 650
NWQALALARE SVEEVPLQPV NPHSANRPPV VSDAAPDFVK TVTAAMLAGL
660 670 680 690 700
GDALPVSALP PDGTWPMGTT RWEKRNIAEE IPIWKEELCT QCNHCVAACP
710 720 730 740 750
HSAIRAKVVP PEAMENAPAS LHSLDVKSRD MRGQKYVLQV APEDCTGCNL
760 770 780 790 800
CVEVCPAKDR QNPEIKAINM MSRLEHVEEE KINYDFFLNL PEIDRSKLER
810 820 830 840 850
IDIRTSQLIT PLFEYSGACS GCGETPYIKL LTQLYGDRML IANATGCSSI
860 870 880 890 900
YGGNLPSTPY TTDANGRGPA WANSLFEDNA EFGLGFRLTV DQHRVRVLRL
910 920 930 940 950
LDQFADKIPA ELLTALKSDA TPEVRREQVA ALRQQLNDVA EAHELLRDAD
960 970 980 990 1000
ALVEKSIWLI GGDGWAYDIG FGGLDHVLSL TENVNILVLD TQCYSNTGGQ
1010 1020 1030 1040 1050
ASKATPLGAV TKFGEHGKRK ARKDLGVSMM MYGHVYVAQI SLGAQLNQTV
1060 1070 1080 1090 1100
KAIQEAEAYP GPSLIIAYSP CEEHGYDLAL SHDQMRQLTA TGFWPLYRFD
1110 1120 1130 1140 1150
PRRADEGKLP LALDSRPPSE APEETLLHEQ RFRRLNSQQP EVAEQLWKDA
1160 1170
AADLQKRYDF LAQMAGKAEK SNTD
Length:1,174
Mass (Da):128,824
Last modified:November 1, 1997 - v2
Checksum:i2BBD1112285DC0F8
GO

Sequence cautioni

The sequence U36928 differs from that shown. Reason: Frameshift at position 35.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti40A → R (PubMed:9025293).Curated1
Sequence conflicti51T → S (PubMed:9025293).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA Translation: AAC74460.1
AP009048 Genomic DNA Translation: BAA14982.1
U36928 Genomic DNA No translation available.
PIRiE64888
RefSeqiNP_415896.1, NC_000913.3
WP_000628244.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC74460; AAC74460; b1378
BAA14982; BAA14982; BAA14982
GeneIDi946587
KEGGiecj:JW1372
eco:b1378
PATRICifig|511145.12.peg.1440

Similar proteinsi

Entry informationi

Entry nameiNIFJ_ECOLI
AccessioniPrimary (citable) accession number: P52647
Secondary accession number(s): P77238
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: November 1, 1997
Last modified: March 28, 2018
This is version 159 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome