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Protein

Probable pyruvate-flavodoxin oxidoreductase

Gene

ydbK

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi689 – 6891Iron-sulfur 1 (4Fe-4S)By similarity
Metal bindingi692 – 6921Iron-sulfur 1 (4Fe-4S)By similarity
Metal bindingi695 – 6951Iron-sulfur 1 (4Fe-4S)By similarity
Metal bindingi699 – 6991Iron-sulfur 2 (4Fe-4S)By similarity
Metal bindingi745 – 7451Iron-sulfur 2 (4Fe-4S)By similarity
Metal bindingi748 – 7481Iron-sulfur 2 (4Fe-4S)By similarity
Metal bindingi751 – 7511Iron-sulfur 2 (4Fe-4S)By similarity
Metal bindingi755 – 7551Iron-sulfur 1 (4Fe-4S)By similarity
Metal bindingi819 – 8191Iron-sulfur 3 (4Fe-4S)By similarity
Metal bindingi822 – 8221Iron-sulfur 3 (4Fe-4S)By similarity
Metal bindingi847 – 8471Iron-sulfur 3 (4Fe-4S)By similarity
Metal bindingi1071 – 10711Iron-sulfur 3 (4Fe-4S)By similarity

GO - Molecular functioni

  1. 4 iron, 4 sulfur cluster binding Source: UniProtKB-KW
  2. iron ion binding Source: InterPro
  3. pyruvate-flavodoxin oxidoreductase activity Source: EcoCyc
  4. thiamine pyrophosphate binding Source: InterPro

GO - Biological processi

  1. electron transport chain Source: InterPro
  2. response to oxidative stress Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Electron transport, Transport

Keywords - Ligandi

4Fe-4S, Iron, Iron-sulfur, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:G6701-MONOMER.
ECOL316407:JW1372-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13183. ydbK.

Pathology & Biotechi

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 11741174Probable pyruvate-flavodoxin oxidoreductasePRO_0000215557Add
BLAST

Proteomic databases

PaxDbiP52647.
PRIDEiP52647.

Expressioni

Gene expression databases

GenevestigatoriP52647.

Interactioni

Protein-protein interaction databases

DIPiDIP-11636N.
IntActiP52647. 10 interactions.
MINTiMINT-1299276.
STRINGi511145.b1378.

Structurei

3D structure databases

ProteinModelPortaliP52647.
SMRiP52647. Positions 682-759, 1037-1073.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini680 – 709304Fe-4S ferredoxin-type 1PROSITE-ProRule annotationAdd
BLAST
Domaini736 – 765304Fe-4S ferredoxin-type 2PROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the NifJ family.Curated
Contains 2 4Fe-4S ferredoxin-type domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG0674.
HOGENOMiHOG000266425.
InParanoidiP52647.
KOiK03737.
OMAiYHLFDYV.
OrthoDBiEOG68H83G.
PhylomeDBiP52647.

Family and domain databases

Gene3Di3.40.50.920. 1 hit.
3.40.50.970. 2 hits.
3.40.920.10. 1 hit.
4.10.780.10. 1 hit.
InterProiIPR001450. 4Fe4S-bd_dom.
IPR017896. 4Fe4S_Fe-S-bd.
IPR017900. 4Fe4S_Fe_S_CS.
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/Pyr-ferredox_oxred.
[Graphical view]
PfamiPF10371. EKR. 1 hit.
PF00037. Fer4. 2 hits.
PF01558. POR. 1 hit.
PF01855. POR_N. 1 hit.
PF02775. TPP_enzyme_C. 1 hit.
[Graphical view]
PIRSFiPIRSF000159. NifJ. 1 hit.
SMARTiSM00890. EKR. 1 hit.
[Graphical view]
SUPFAMiSSF52518. SSF52518. 2 hits.
SSF52922. SSF52922. 1 hit.
SSF53323. SSF53323. 1 hit.
TIGRFAMsiTIGR02176. pyruv_ox_red. 1 hit.
PROSITEiPS00198. 4FE4S_FER_1. 2 hits.
PS51379. 4FE4S_FER_2. 2 hits.
[Graphical view]

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti40 – 401A → R (PubMed:9025293).Curated
Sequence conflicti51 – 511T → S (PubMed:9025293).Curated

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.
YP_489646.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC74460; AAC74460; b1378.
BAA14982; BAA14982; BAA14982.
GeneIDi12932682.
946587.
KEGGiecj:Y75_p1354.
eco:b1378.
PATRICi32118040. VBIEscCol129921_1440.

Cross-referencesi

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.
YP_489646.1. NC_007779.1.

3D structure databases

ProteinModelPortaliP52647.
SMRiP52647. Positions 682-759, 1037-1073.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-11636N.
IntActiP52647. 10 interactions.
MINTiMINT-1299276.
STRINGi511145.b1378.

Chemistry

DrugBankiDB00698. Nitrofurantoin.

Proteomic databases

PaxDbiP52647.
PRIDEiP52647.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74460; AAC74460; b1378.
BAA14982; BAA14982; BAA14982.
GeneIDi12932682.
946587.
KEGGiecj:Y75_p1354.
eco:b1378.
PATRICi32118040. VBIEscCol129921_1440.

Organism-specific databases

EchoBASEiEB2975.
EcoGeneiEG13183. ydbK.

Phylogenomic databases

eggNOGiCOG0674.
HOGENOMiHOG000266425.
InParanoidiP52647.
KOiK03737.
OMAiYHLFDYV.
OrthoDBiEOG68H83G.
PhylomeDBiP52647.

Enzyme and pathway databases

BioCyciEcoCyc:G6701-MONOMER.
ECOL316407:JW1372-MONOMER.
MetaCyc:G6701-MONOMER.

Miscellaneous databases

PROiP52647.

Gene expression databases

GenevestigatoriP52647.

Family and domain databases

Gene3Di3.40.50.920. 1 hit.
3.40.50.970. 2 hits.
3.40.920.10. 1 hit.
4.10.780.10. 1 hit.
InterProiIPR001450. 4Fe4S-bd_dom.
IPR017896. 4Fe4S_Fe-S-bd.
IPR017900. 4Fe4S_Fe_S_CS.
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/Pyr-ferredox_oxred.
[Graphical view]
PfamiPF10371. EKR. 1 hit.
PF00037. Fer4. 2 hits.
PF01558. POR. 1 hit.
PF01855. POR_N. 1 hit.
PF02775. TPP_enzyme_C. 1 hit.
[Graphical view]
PIRSFiPIRSF000159. NifJ. 1 hit.
SMARTiSM00890. EKR. 1 hit.
[Graphical view]
SUPFAMiSSF52518. SSF52518. 2 hits.
SSF52922. SSF52922. 1 hit.
SSF53323. SSF53323. 1 hit.
TIGRFAMsiTIGR02176. pyruv_ox_red. 1 hit.
PROSITEiPS00198. 4FE4S_FER_1. 2 hits.
PS51379. 4FE4S_FER_2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "The ldhA gene encoding the fermentative lactate dehydrogenase of Escherichia coli."
    Bunch P.K., Mat-Jan F., Lee N., Clark D.P.
    Microbiology 143:187-195(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-53.
    Strain: K12.
  5. Rudd K.E.
    Unpublished observations (FEB-1996)
    Cited for: IDENTIFICATION.

Entry informationi

Entry nameiNIFJ_ECOLI
AccessioniPrimary (citable) accession number: P52647
Secondary accession number(s): P77238
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: November 1, 1997
Last modified: March 4, 2015
This is version 137 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.