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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)DescriptionActionsGraphical viewLength
Binding sitei27SubstrateBy similarity1
Binding sitei50Thiamine pyrophosphate1
Binding sitei114SubstrateBy similarity1
Metal bindingi440Magnesium1
Metal bindingi467Magnesium1
Metal bindingi469Magnesium; via carbonyl oxygen1
Binding sitei473SubstrateBy similarity1

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)DescriptionActionsGraphical viewLength
Mutagenesisi50E → Q: Almost complete loss of activity. 2 Publications1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000907731 – 568Pyruvate decarboxylaseAdd BLAST568

Interactioni

Subunit structurei

Homotetramer.

Structurei

Secondary structure

1568
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi5 – 15Combined sources11
Beta strandi19 – 23Combined sources5
Turni27 – 29Combined sources3
Helixi30 – 37Combined sources8
Beta strandi42 – 46Combined sources5
Helixi50 – 64Combined sources15
Beta strandi67 – 71Combined sources5
Turni73 – 76Combined sources4
Helixi77 – 89Combined sources13
Beta strandi94 – 100Combined sources7
Helixi103 – 105Combined sources3
Turni106 – 109Combined sources4
Beta strandi117 – 119Combined sources3
Helixi123 – 128Combined sources6
Helixi129 – 131Combined sources3
Beta strandi135 – 138Combined sources4
Helixi141 – 143Combined sources3
Helixi144 – 158Combined sources15
Beta strandi162 – 167Combined sources6
Helixi168 – 170Combined sources3
Beta strandi173 – 175Combined sources3
Helixi182 – 185Combined sources4
Helixi192 – 206Combined sources15
Beta strandi212 – 216Combined sources5
Turni218 – 224Combined sources7
Helixi226 – 236Combined sources11
Beta strandi239 – 243Combined sources5
Helixi244 – 246Combined sources3
Beta strandi257 – 261Combined sources5
Helixi263 – 265Combined sources3
Helixi270 – 276Combined sources7
Beta strandi278 – 284Combined sources7
Turni289 – 296Combined sources8
Turni301 – 303Combined sources3
Beta strandi304 – 307Combined sources4
Beta strandi309 – 314Combined sources6
Beta strandi317 – 321Combined sources5
Helixi324 – 334Combined sources11
Helixi340 – 347Combined sources8
Helixi367 – 375Combined sources9
Beta strandi382 – 386Combined sources5
Helixi390 – 396Combined sources7
Beta strandi405 – 407Combined sources3
Turni410 – 412Combined sources3
Turni415 – 417Combined sources3
Helixi418 – 428Combined sources11
Beta strandi432 – 439Combined sources8
Helixi440 – 446Combined sources7
Helixi447 – 449Combined sources3
Helixi450 – 455Combined sources6
Beta strandi461 – 466Combined sources6
Helixi471 – 474Combined sources4
Helixi480 – 482Combined sources3
Helixi489 – 497Combined sources9
Turni498 – 500Combined sources3
Beta strandi501 – 503Combined sources3
Beta strandi508 – 514Combined sources7
Helixi515 – 527Combined sources13
Beta strandi533 – 538Combined sources6
Helixi546 – 560Combined sources15

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP06672.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni390 – 472Thiamine pyrophosphate bindingAdd BLAST83

Sequence similaritiesi

Belongs to the TPP enzyme family.Curated

Phylogenomic databases

HOGENOMiHOG000061335.
KOiK01568.
OMAiYIEIPTN.

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)DescriptionActionsGraphical viewLength
Sequence conflicti78L → H in AAA27685 (PubMed:2838467).Curated1
Sequence conflicti157 – 158RE → AK in AAA27685 (PubMed:2838467).Curated2
Sequence conflicti200E → D in AAA27685 (PubMed:2838467).Curated1
Sequence conflicti233A → T in AAA27685 (PubMed:2838467).Curated1
Sequence conflicti315 – 316NG → RR in AAA27685 (PubMed:2838467).Curated2
Sequence conflicti317I → V in AAA27696 (PubMed:3029037).Curated1
Sequence conflicti341A → S in AAA27685 (PubMed:2838467).Curated1
Sequence conflicti507G → A in AAA27685 (PubMed:2838467).Curated1

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
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Phylogenomic databases

HOGENOMiHOG000061335.
KOiK01568.
OMAiYIEIPTN.

Enzyme and pathway databases

BRENDAi4.1.1.1. 6765.
SABIO-RKP06672.

Miscellaneous databases

EvolutionaryTraceiP06672.
PROiP06672.

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...

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: November 30, 2016
This is version 134 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.