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P52647

- NIFJ_ECOLI

UniProt

P52647 - NIFJ_ECOLI

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Protein

Probable pyruvate-flavodoxin oxidoreductase

Gene

ydbK

Organism
Escherichia coli (strain K12)
Status
Reviewed - 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.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi689 – 6891Iron-sulfur 1 (4Fe-4S)Sequence Analysis
Metal bindingi692 – 6921Iron-sulfur 1 (4Fe-4S)Sequence Analysis
Metal bindingi695 – 6951Iron-sulfur 1 (4Fe-4S)Sequence Analysis
Metal bindingi699 – 6991Iron-sulfur 2 (4Fe-4S)Sequence Analysis
Metal bindingi745 – 7451Iron-sulfur 2 (4Fe-4S)Sequence Analysis
Metal bindingi748 – 7481Iron-sulfur 2 (4Fe-4S)Sequence Analysis
Metal bindingi751 – 7511Iron-sulfur 2 (4Fe-4S)Sequence Analysis
Metal bindingi755 – 7551Iron-sulfur 1 (4Fe-4S)Sequence Analysis

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: Chromosome, UP000000625: 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 680-771.
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.
OMAiCVLAIFN.
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.

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:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
Links Updated
U00096 Genomic DNA. Translation: AAC74460.1 .
AP009048 Genomic DNA. Translation: BAA14982.1 .
U36928 Genomic DNA. No translation available.
PIRi E64888.
RefSeqi NP_415896.1. NC_000913.3.
YP_489646.1. NC_007779.1.

3D structure databases

ProteinModelPortali P52647.
SMRi P52647. Positions 680-771.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-11636N.
IntActi P52647. 10 interactions.
MINTi MINT-1299276.
STRINGi 511145.b1378.

Chemistry

DrugBanki DB00698. Nitrofurantoin.

Proteomic databases

PaxDbi P52647.
PRIDEi P52647.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC74460 ; AAC74460 ; b1378 .
BAA14982 ; BAA14982 ; BAA14982 .
GeneIDi 12932682.
946587.
KEGGi ecj:Y75_p1354.
eco:b1378.
PATRICi 32118040. VBIEscCol129921_1440.

Organism-specific databases

EchoBASEi EB2975.
EcoGenei EG13183. ydbK.

Phylogenomic databases

eggNOGi COG0674.
HOGENOMi HOG000266425.
InParanoidi P52647.
KOi K03737.
OMAi CVLAIFN.
OrthoDBi EOG68H83G.
PhylomeDBi P52647.

Enzyme and pathway databases

BioCyci EcoCyc:G6701-MONOMER.
ECOL316407:JW1372-MONOMER.
MetaCyc:G6701-MONOMER.

Miscellaneous databases

PROi P52647.

Gene expression databases

Genevestigatori P52647.

Family and domain databases

Gene3Di 3.40.50.920. 1 hit.
3.40.50.970. 2 hits.
3.40.920.10. 1 hit.
4.10.780.10. 1 hit.
InterProi IPR001450. 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 ]
Pfami PF10371. EKR. 1 hit.
PF00037. Fer4. 2 hits.
PF01558. POR. 1 hit.
PF01855. POR_N. 1 hit.
PF02775. TPP_enzyme_C. 1 hit.
[Graphical view ]
PIRSFi PIRSF000159. NifJ. 1 hit.
SMARTi SM00890. EKR. 1 hit.
[Graphical view ]
SUPFAMi SSF52518. SSF52518. 2 hits.
SSF52922. SSF52922. 1 hit.
SSF53323. SSF53323. 1 hit.
TIGRFAMsi TIGR02176. pyruv_ox_red. 1 hit.
PROSITEi PS00198. 4FE4S_FER_1. 2 hits.
PS51379. 4FE4S_FER_2. 2 hits.
[Graphical view ]
ProtoNeti Search...

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(2006) [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(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-53.
    Strain: K12.
  5. Rudd K.E.
    Unpublished observations (MAR-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: October 29, 2014
This is version 133 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