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P52647 (NIFJ_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 131. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Probable pyruvate-flavodoxin oxidoreductase

EC=1.2.7.-
Gene names
Name:ydbK
Ordered Locus Names:b1378, JW1372
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length1174 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

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

Catalytic activity

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

Sequence similarities

Belongs to the NifJ family.

Contains 2 4Fe-4S ferredoxin-type domains.

Sequence caution

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 11741174Probable pyruvate-flavodoxin oxidoreductase
PRO_0000215557

Regions

Domain680 – 709304Fe-4S ferredoxin-type 1
Domain736 – 765304Fe-4S ferredoxin-type 2

Sites

Metal binding6891Iron-sulfur 1 (4Fe-4S) Potential
Metal binding6921Iron-sulfur 1 (4Fe-4S) Potential
Metal binding6951Iron-sulfur 1 (4Fe-4S) Potential
Metal binding6991Iron-sulfur 2 (4Fe-4S) Potential
Metal binding7451Iron-sulfur 2 (4Fe-4S) Potential
Metal binding7481Iron-sulfur 2 (4Fe-4S) Potential
Metal binding7511Iron-sulfur 2 (4Fe-4S) Potential
Metal binding7551Iron-sulfur 1 (4Fe-4S) Potential

Experimental info

Sequence conflict401A → R Ref.4
Sequence conflict511T → S Ref.4

Sequences

Sequence LengthMass (Da)Tools
P52647 [UniParc].

Last modified November 1, 1997. Version 2.
Checksum: 2BBD1112285DC0F8

FASTA1,174128,824
        10         20         30         40         50         60 
MITIDGNGAV ASVAFRTSEV IAIYPITPSS TMAEQADAWA GNGLKNVWGD TPRVVEMQSE 

        70         80         90        100        110        120 
AGAIATVHGA LQTGALSTSF TSSQGLLLMI PTLYKLAGEL TPFVLHVAAR TVATHALSIF 

       130        140        150        160        170        180 
GDHSDVMAVR QTGCAMLCAA NVQEAQDFAL ISQIATLKSR VPFIHFFDGF RTSHEINKIV 

       190        200        210        220        230        240 
PLADDTILDL MPQVEIDAHR ARALNPEHPV IRGTSANPDT YFQSREATNP WYNAVYDHVE 

       250        260        270        280        290        300 
QAMNDFSAAT GRQYQPFEYY GHPQAERVII LMGSAIGTCE EVVDELLTRG EKVGVLKVRL 

       310        320        330        340        350        360 
YRPFSAKHLL QALPGSVRSV AVLDRTKEPG AQAEPLYLDV MTALAEAFNN GERETLPRVI 

       370        380        390        400        410        420 
GGRYGLSSKE FGPDCVLAVF AELNAAKPKA RFTVGIYDDV TNLSLPLPEN TLPNSAKLEA 

       430        440        450        460        470        480 
LFYGLGSDGS VSATKNNIKI IGNSTPWYAQ GYFVYDSKKA GGLTVSHLRV SEQPIRSAYL 

       490        500        510        520        530        540 
ISQADFVGCH QLQFIDKYQM AERLKPGGIF LLNTPYSADE VWSRLPQEVQ AVLNQKKARF 

       550        560        570        580        590        600 
YVINAAKIAR ECGLAARINT VMQMAFFHLT QILPGDSALA ELQGAIAKSY SSKGQDLVER 

       610        620        630        640        650        660 
NWQALALARE SVEEVPLQPV NPHSANRPPV VSDAAPDFVK TVTAAMLAGL GDALPVSALP 

       670        680        690        700        710        720 
PDGTWPMGTT RWEKRNIAEE IPIWKEELCT QCNHCVAACP HSAIRAKVVP PEAMENAPAS 

       730        740        750        760        770        780 
LHSLDVKSRD MRGQKYVLQV APEDCTGCNL CVEVCPAKDR QNPEIKAINM MSRLEHVEEE 

       790        800        810        820        830        840 
KINYDFFLNL PEIDRSKLER IDIRTSQLIT PLFEYSGACS GCGETPYIKL LTQLYGDRML 

       850        860        870        880        890        900 
IANATGCSSI YGGNLPSTPY TTDANGRGPA WANSLFEDNA EFGLGFRLTV DQHRVRVLRL 

       910        920        930        940        950        960 
LDQFADKIPA ELLTALKSDA TPEVRREQVA ALRQQLNDVA EAHELLRDAD ALVEKSIWLI 

       970        980        990       1000       1010       1020 
GGDGWAYDIG FGGLDHVLSL TENVNILVLD TQCYSNTGGQ ASKATPLGAV TKFGEHGKRK 

      1030       1040       1050       1060       1070       1080 
ARKDLGVSMM MYGHVYVAQI SLGAQLNQTV KAIQEAEAYP GPSLIIAYSP CEEHGYDLAL 

      1090       1100       1110       1120       1130       1140 
SHDQMRQLTA TGFWPLYRFD PRRADEGKLP LALDSRPPSE APEETLLHEQ RFRRLNSQQP 

      1150       1160       1170 
EVAEQLWKDA AADLQKRYDF LAQMAGKAEK SNTD 

« Hide

References

« Hide 'large scale' references
[1]"A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map."
Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T., Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K. expand/collapse author list , Nakade S., Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y., Wada C., Yamamoto Y., Horiuchi T.
DNA Res. 3:363-377(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[2]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U00096 Genomic DNA. Translation: AAC74460.1.
AP009048 Genomic DNA. Translation: BAA14982.1.
U36928 Genomic DNA. No translation available.
PIRE64888.
RefSeqNP_415896.1. NC_000913.3.
YP_489646.1. NC_007779.1.

3D structure databases

ProteinModelPortalP52647.
SMRP52647. Positions 680-707, 740-771.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-11636N.
IntActP52647. 10 interactions.
MINTMINT-1299276.
STRING511145.b1378.

Chemistry

DrugBankDB00698. Nitrofurantoin.

Proteomic databases

PaxDbP52647.
PRIDEP52647.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC74460; AAC74460; b1378.
BAA14982; BAA14982; BAA14982.
GeneID12932682.
946587.
KEGGecj:Y75_p1354.
eco:b1378.
PATRIC32118040. VBIEscCol129921_1440.

Organism-specific databases

EchoBASEEB2975.
EcoGeneEG13183. ydbK.

Phylogenomic databases

eggNOGCOG0674.
HOGENOMHOG000266425.
KOK03737.
OMACVLAIFN.
OrthoDBEOG68H83G.
PhylomeDBP52647.

Enzyme and pathway databases

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

Gene expression databases

GenevestigatorP52647.

Family and domain databases

Gene3D3.40.50.920. 1 hit.
3.40.50.970. 2 hits.
3.40.920.10. 1 hit.
4.10.780.10. 1 hit.
InterProIPR001450. 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]
PfamPF10371. EKR. 1 hit.
PF00037. Fer4. 2 hits.
PF01558. POR. 1 hit.
PF01855. POR_N. 1 hit.
PF02775. TPP_enzyme_C. 1 hit.
[Graphical view]
PIRSFPIRSF000159. NifJ. 1 hit.
SMARTSM00890. EKR. 1 hit.
[Graphical view]
SUPFAMSSF52518. SSF52518. 2 hits.
SSF52922. SSF52922. 1 hit.
SSF53323. SSF53323. 1 hit.
TIGRFAMsTIGR02176. pyruv_ox_red. 1 hit.
PROSITEPS00198. 4FE4S_FER_1. 2 hits.
PS51379. 4FE4S_FER_2. 2 hits.
[Graphical view]
ProtoNetSearch...

Other

PROP52647.

Entry information

Entry nameNIFJ_ECOLI
AccessionPrimary (citable) accession number: P52647
Secondary accession number(s): P77238
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: November 1, 1997
Last modified: July 9, 2014
This is version 131 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene