Probable pyruvate-flavodoxin oxidoreductase - ydbK

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P52647 (NIFJ_ECOLI) Reviewed, UniProtKB/Swiss-Prot

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

Clusters with 100%, 90%, 50% identity |

Documents (2) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Probable pyruvate-flavodoxin oxidoreductase
EC=1.2.7.-

Gene names

Name:	ydbK
Ordered Locus Names:	b1378, JW1372

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	1174 AA.
Sequence status	Complete.
Protein existence	Inferred 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.

Ontologies

Keywords
Biological process	Electron transport Transport
Domain	Repeat
Ligand	4Fe-4S Iron Iron-sulfur Metal-binding
Molecular function	Oxidoreductase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	electron transport chain Inferred from electronic annotation. Source: InterPro response to oxidative stress Inferred from mutant phenotype PubMed 22515487. Source: EcoCyc
Molecular_function	4 iron, 4 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW iron ion binding Inferred from electronic annotation. Source: InterPro pyruvate-flavodoxin oxidoreductase activity Inferred from direct assay PubMed 24025246. Source: EcoCyc thiamine pyrophosphate binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 1174

1174

Probable pyruvate-flavodoxin oxidoreductase

PRO_0000215557

Regions

Domain

680 – 709

4Fe-4S ferredoxin-type 1

Domain

736 – 765

4Fe-4S ferredoxin-type 2

Sites

Metal binding

689

Iron-sulfur 1 (4Fe-4S) Potential

Metal binding

692

Iron-sulfur 1 (4Fe-4S) Potential

Metal binding

695

Iron-sulfur 1 (4Fe-4S) Potential

Metal binding

699

Iron-sulfur 2 (4Fe-4S) Potential

Metal binding

745

Iron-sulfur 2 (4Fe-4S) Potential

Metal binding

748

Iron-sulfur 2 (4Fe-4S) Potential

Metal binding

751

Iron-sulfur 2 (4Fe-4S) Potential

Metal binding

755

Iron-sulfur 1 (4Fe-4S) Potential

Experimental info

Sequence conflict

A → R Ref.4

Sequence conflict

T → S Ref.4

Sequences

Sequence

Length

Mass (Da)

Tools

P52647 [UniParc].

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

FASTA

1,174

128,824

        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' referencesShow '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. 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.
PIR	E64888.
RefSeq	NP_415896.1. NC_000913.3. YP_489646.1. NC_007779.1.
3D structure databases
ProteinModelPortal	P52647.
SMR	P52647. Positions 680-707, 740-771.
ModBase	Search...
MobiDB	Search...
Protein-protein interaction databases
DIP	DIP-11636N.
IntAct	P52647. 10 interactions.
MINT	MINT-1299276.
STRING	511145.b1378.
Chemistry
DrugBank	DB00698. Nitrofurantoin.
Proteomic databases
PaxDb	P52647.
PRIDE	P52647.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAC74460; AAC74460; b1378. BAA14982; BAA14982; BAA14982.
GeneID	12932682. 946587.
KEGG	ecj:Y75_p1354. eco:b1378.
PATRIC	32118040. VBIEscCol129921_1440.
Organism-specific databases
EchoBASE	EB2975.
EcoGene	EG13183. ydbK.
Phylogenomic databases
eggNOG	COG0674.
HOGENOM	HOG000266425.
KO	K03737.
OMA	CVLAIFN.
OrthoDB	EOG68H83G.
PhylomeDB	P52647.
Enzyme and pathway databases
BioCyc	EcoCyc:G6701-MONOMER. ECOL316407:JW1372-MONOMER. MetaCyc:G6701-MONOMER.
Gene expression databases
Genevestigator	P52647.
Family and domain databases
Gene3D	3.40.50.920. 1 hit. 3.40.50.970. 2 hits. 3.40.920.10. 1 hit. 4.10.780.10. 1 hit.
InterPro	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]
Pfam	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]
PIRSF	PIRSF000159. NifJ. 1 hit.
SMART	SM00890. EKR. 1 hit. [Graphical view]
SUPFAM	SSF52518. SSF52518. 2 hits. SSF52922. SSF52922. 1 hit. SSF53323. SSF53323. 1 hit.
TIGRFAMs	TIGR02176. pyruv_ox_red. 1 hit.
PROSITE	PS00198. 4FE4S_FER_1. 2 hits. PS51379. 4FE4S_FER_2. 2 hits. [Graphical view]
ProtoNet	Search...
Other
PRO	P52647.

Entry information

Entry name

NIFJ_ECOLI

Accession

Primary (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 status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic 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

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Chemistry

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents