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Protein

Pyruvate decarboxylase

Gene

pdc

Organism
Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

A 2-oxo acid = an aldehyde + CO2.

Cofactori

Protein has several cofactor binding sites:

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei27 – 271SubstrateBy similarity
Binding sitei50 – 501Thiamine pyrophosphate
Binding sitei114 – 1141SubstrateBy similarity
Metal bindingi440 – 4401Magnesium
Metal bindingi467 – 4671Magnesium
Metal bindingi469 – 4691Magnesium; via carbonyl oxygen
Binding sitei473 – 4731SubstrateBy similarity

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Ligandi

Magnesium, Metal-binding, Thiamine pyrophosphate

Enzyme and pathway databases

BRENDAi4.1.1.1. 6765.
SABIO-RKP06672.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyruvate decarboxylase (EC:4.1.1.1)
Short name:
PDC
Gene namesi
Name:pdc
Ordered Locus Names:ZMO1360
OrganismiZymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)
Taxonomic identifieri264203 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaSphingomonadalesSphingomonadaceaeZymomonas
Proteomesi
  • UP000001173 Componenti: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi50 – 501E → Q: Almost complete loss of activity. 2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 568568Pyruvate decarboxylasePRO_0000090773Add
BLAST

Interactioni

Subunit structurei

Homotetramer.

Structurei

Secondary structure

1
568
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi5 – 1511Combined sources
Beta strandi19 – 235Combined sources
Turni27 – 293Combined sources
Helixi30 – 378Combined sources
Beta strandi42 – 465Combined sources
Helixi50 – 6415Combined sources
Beta strandi67 – 715Combined sources
Turni73 – 764Combined sources
Helixi77 – 8913Combined sources
Beta strandi94 – 1007Combined sources
Helixi103 – 1053Combined sources
Turni106 – 1094Combined sources
Beta strandi117 – 1193Combined sources
Helixi123 – 1286Combined sources
Helixi129 – 1313Combined sources
Beta strandi135 – 1384Combined sources
Helixi141 – 1433Combined sources
Helixi144 – 15815Combined sources
Beta strandi162 – 1676Combined sources
Helixi168 – 1703Combined sources
Beta strandi173 – 1753Combined sources
Helixi182 – 1854Combined sources
Helixi192 – 20615Combined sources
Beta strandi212 – 2165Combined sources
Turni218 – 2247Combined sources
Helixi226 – 23611Combined sources
Beta strandi239 – 2435Combined sources
Helixi244 – 2463Combined sources
Beta strandi257 – 2615Combined sources
Helixi263 – 2653Combined sources
Helixi270 – 2767Combined sources
Beta strandi278 – 2847Combined sources
Turni289 – 2968Combined sources
Turni301 – 3033Combined sources
Beta strandi304 – 3074Combined sources
Beta strandi309 – 3146Combined sources
Beta strandi317 – 3215Combined sources
Helixi324 – 33411Combined sources
Helixi340 – 3478Combined sources
Helixi367 – 3759Combined sources
Beta strandi382 – 3865Combined sources
Helixi390 – 3967Combined sources
Beta strandi405 – 4073Combined sources
Turni410 – 4123Combined sources
Turni415 – 4173Combined sources
Helixi418 – 42811Combined sources
Beta strandi432 – 4398Combined sources
Helixi440 – 4467Combined sources
Helixi447 – 4493Combined sources
Helixi450 – 4556Combined sources
Beta strandi461 – 4666Combined sources
Helixi471 – 4744Combined sources
Helixi480 – 4823Combined sources
Helixi489 – 4979Combined sources
Turni498 – 5003Combined sources
Beta strandi501 – 5033Combined sources
Beta strandi508 – 5147Combined sources
Helixi515 – 52713Combined sources
Beta strandi533 – 5386Combined sources
Helixi546 – 56015Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1ZPDX-ray1.86A/B/E/F1-566[»]
2WVAX-ray2.20A/B/E/F/V/X/Y/Z1-568[»]
2WVGX-ray1.75A/B/E/F1-568[»]
2WVHX-ray2.30A/B/E/F/V/X/Y/Z1-568[»]
3OE1X-ray1.98A/B/C/D1-568[»]
4ZP1X-ray2.21A/B/C/D1-568[»]
ProteinModelPortaliP06672.
SMRiP06672. Positions 2-566.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP06672.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni390 – 47283Thiamine pyrophosphate bindingAdd
BLAST

Sequence similaritiesi

Belongs to the TPP enzyme family.Curated

Phylogenomic databases

HOGENOMiHOG000061335.
KOiK04103.
OMAiDTHIGSV.
OrthoDBiEOG62ZHQW.

Family and domain databases

Gene3Di3.40.50.1220. 1 hit.
3.40.50.970. 2 hits.
InterProiIPR029035. DHS-like_NAD/FAD-binding_dom.
IPR029061. THDP-binding.
IPR012000. Thiamin_PyroP_enz_cen_dom.
IPR012001. Thiamin_PyroP_enz_TPP-bd_dom.
IPR000399. TPP-bd_CS.
IPR012110. TPP_enzyme.
IPR011766. TPP_enzyme-bd_C.
[Graphical view]
PfamiPF02775. TPP_enzyme_C. 1 hit.
PF00205. TPP_enzyme_M. 1 hit.
PF02776. TPP_enzyme_N. 1 hit.
[Graphical view]
PIRSFiPIRSF036565. Pyruvt_ip_decrb. 1 hit.
SUPFAMiSSF52467. SSF52467. 1 hit.
SSF52518. SSF52518. 2 hits.
PROSITEiPS00187. TPP_ENZYMES. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P06672-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSYTVGTYLA ERLVQIGLKH HFAVAGDYNL VLLDNLLLNK NMEQVYCCNE
60 70 80 90 100
LNCGFSAEGY ARAKGAAAAV VTYSVGALSA FDAIGGAYAE NLPVILISGA
110 120 130 140 150
PNNNDHAAGH VLHHALGKTD YHYQLEMAKN ITAAAEAIYT PEEAPAKIDH
160 170 180 190 200
VIKTALREKK PVYLEIACNI ASMPCAAPGP ASALFNDEAS DEASLNAAVE
210 220 230 240 250
ETLKFIANRD KVAVLVGSKL RAAGAEEAAV KFADALGGAV ATMAAAKSFF
260 270 280 290 300
PEENPHYIGT SWGEVSYPGV EKTMKEADAV IALAPVFNDY STTGWTDIPD
310 320 330 340 350
PKKLVLAEPR SVVVNGIRFP SVHLKDYLTR LAQKVSKKTG ALDFFKSLNA
360 370 380 390 400
GELKKAAPAD PSAPLVNAEI ARQVEALLTP NTTVIAETGD SWFNAQRMKL
410 420 430 440 450
PNGARVEYEM QWGHIGWSVP AAFGYAVGAP ERRNILMVGD GSFQLTAQEV
460 470 480 490 500
AQMVRLKLPV IIFLINNYGY TIEVMIHDGP YNNIKNWDYA GLMEVFNGNG
510 520 530 540 550
GYDSGAGKGL KAKTGGELAE AIKVALANTD GPTLIECFIG REDCTEELVK
560
WGKRVAAANS RKPVNKLL
Length:568
Mass (Da):60,926
Last modified:January 1, 1988 - v1
Checksum:i9FAC04C77189E75C
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti78 – 781L → H in AAA27685 (PubMed:2838467).Curated
Sequence conflicti157 – 1582RE → AK in AAA27685 (PubMed:2838467).Curated
Sequence conflicti200 – 2001E → D in AAA27685 (PubMed:2838467).Curated
Sequence conflicti233 – 2331A → T in AAA27685 (PubMed:2838467).Curated
Sequence conflicti315 – 3162NG → RR in AAA27685 (PubMed:2838467).Curated
Sequence conflicti317 – 3171I → V in AAA27696 (PubMed:3029037).Curated
Sequence conflicti341 – 3411A → S in AAA27685 (PubMed:2838467).Curated
Sequence conflicti507 – 5071G → A in AAA27685 (PubMed:2838467).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M15368 Genomic DNA. Translation: AAA27697.1.
M15393 Genomic DNA. Translation: AAA27696.2.
M20667 Genomic DNA. Translation: AAA27685.1.
X59558 Genomic DNA. Translation: CAA42157.1.
AF124349 Genomic DNA. Translation: AAD19711.1.
AE008692 Genomic DNA. Translation: AAV89984.1.
PIRiA26672. DCZYPZ.
A26947. DCZYPC.
RefSeqiWP_011241152.1. NC_006526.2.

Genome annotation databases

EnsemblBacteriaiAAV89984; AAV89984; ZMO1360.
KEGGizmo:ZMO1360.
PATRICi32568000. VBIZymMob102260_1287.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M15368 Genomic DNA. Translation: AAA27697.1.
M15393 Genomic DNA. Translation: AAA27696.2.
M20667 Genomic DNA. Translation: AAA27685.1.
X59558 Genomic DNA. Translation: CAA42157.1.
AF124349 Genomic DNA. Translation: AAD19711.1.
AE008692 Genomic DNA. Translation: AAV89984.1.
PIRiA26672. DCZYPZ.
A26947. DCZYPC.
RefSeqiWP_011241152.1. NC_006526.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1ZPDX-ray1.86A/B/E/F1-566[»]
2WVAX-ray2.20A/B/E/F/V/X/Y/Z1-568[»]
2WVGX-ray1.75A/B/E/F1-568[»]
2WVHX-ray2.30A/B/E/F/V/X/Y/Z1-568[»]
3OE1X-ray1.98A/B/C/D1-568[»]
4ZP1X-ray2.21A/B/C/D1-568[»]
ProteinModelPortaliP06672.
SMRiP06672. Positions 2-566.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAV89984; AAV89984; ZMO1360.
KEGGizmo:ZMO1360.
PATRICi32568000. VBIZymMob102260_1287.

Phylogenomic databases

HOGENOMiHOG000061335.
KOiK04103.
OMAiDTHIGSV.
OrthoDBiEOG62ZHQW.

Enzyme and pathway databases

BRENDAi4.1.1.1. 6765.
SABIO-RKP06672.

Miscellaneous databases

EvolutionaryTraceiP06672.

Family and domain databases

Gene3Di3.40.50.1220. 1 hit.
3.40.50.970. 2 hits.
InterProiIPR029035. DHS-like_NAD/FAD-binding_dom.
IPR029061. THDP-binding.
IPR012000. Thiamin_PyroP_enz_cen_dom.
IPR012001. Thiamin_PyroP_enz_TPP-bd_dom.
IPR000399. TPP-bd_CS.
IPR012110. TPP_enzyme.
IPR011766. TPP_enzyme-bd_C.
[Graphical view]
PfamiPF02775. TPP_enzyme_C. 1 hit.
PF00205. TPP_enzyme_M. 1 hit.
PF02776. TPP_enzyme_N. 1 hit.
[Graphical view]
PIRSFiPIRSF036565. Pyruvt_ip_decrb. 1 hit.
SUPFAMiSSF52467. SSF52467. 1 hit.
SSF52518. SSF52518. 2 hits.
PROSITEiPS00187. TPP_ENZYMES. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Pyruvate decarboxylase of Zymomonas mobilis: isolation, properties, and genetic expression in Escherichia coli."
    Neale A.D., Scopes R.K., Wettenhall R.E.H., Hoogenraad N.J.
    J. Bacteriol. 169:1024-1028(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 29191 / DSM 3580 / NBRC 13756 / NCIMB 11199 / NRRL B-4490 / ZM6.
  2. "Nucleotide sequence of the pyruvate decarboxylase gene from Zymomonas mobilis."
    Neale A.D., Scopes R.K., Wettenhall R.E.H., Hoogenraad N.J.
    Nucleic Acids Res. 15:1753-1761(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
    Strain: ATCC 29191 / DSM 3580 / NBRC 13756 / NCIMB 11199 / NRRL B-4490 / ZM6.
  3. "Promoter and nucleotide sequences of the Zymomonas mobilis pyruvate decarboxylase."
    Conway T., Osman Y.A., Konnan J.I., Hoffmann E.M., Ingram L.O.
    J. Bacteriol. 169:949-954(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 31821 / ZM4 / CP4.
  4. Ingram L.O.
    Submitted (JUN-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: SEQUENCE REVISION TO 11-12; 65-66; 251-262 AND 558-568.
  5. "Comparison of the structural genes for pyruvate decarboxylase in different Zymomonas mobilis strains."
    Reynen M., Sahm H.
    J. Bacteriol. 170:3310-3313(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 29191 / DSM 3580 / NBRC 13756 / NCIMB 11199 / NRRL B-4490 / ZM6.
  6. Candy J.M., Diefenbach R.J., Mattick J.S., Duggleby R.G.
    Submitted (APR-1991) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  7. Um H.W., Kang H.S.
    Submitted (JAN-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 31821 / ZM4 / CP4.
  8. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 31821 / ZM4 / CP4.
  9. "The role of residues glutamate-50 and phenylalanine-496 in Zymomonas mobilis pyruvate decarboxylase."
    Candy J.M., Koga J., Nixon P.F., Duggleby R.G.
    Biochem. J. 315:745-751(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS.
  10. "Structure and properties of pyruvate decarboxylase and site-directed mutagenesis of the Zymomonas mobilis enzyme."
    Candy J.M., Duggleby R.G.
    Biochim. Biophys. Acta 1385:323-338(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS.
  11. "High-resolution crystal structure of pyruvate decarboxylase from Zymomonas mobilis. Implications for substrate activation in pyruvate decarboxylases."
    Dobritzsch D., Koenig S., Schneider G., Lu G.
    J. Biol. Chem. 273:20196-20204(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).

Entry informationi

Entry nameiPDC_ZYMMO
AccessioniPrimary (citable) accession number: P06672
Secondary accession number(s): Q56994, Q5NMS6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1988
Last sequence update: January 1, 1988
Last modified: February 17, 2016
This is version 129 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Rapid and exclusive production of ethanol as the end product of sugar fermentation by the bacterium Zymononas mobilis is due to the presence of pyruvate decarboxylase.

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

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 one 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.