PDC_ZYMMO
ID PDC_ZYMMO Reviewed; 568 AA.
AC P06672; Q56994; Q5NMS6;
DT 01-JAN-1988, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1988, sequence version 1.
DT 03-AUG-2022, entry version 160.
DE RecName: Full=Pyruvate decarboxylase;
DE Short=PDC;
DE EC=4.1.1.1;
GN Name=pdc; OrderedLocusNames=ZMO1360;
OS Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales;
OC Zymomonadaceae; Zymomonas.
OX NCBI_TaxID=264203;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 29191 / DSM 3580 / JCM 10190 / CECT 560 / NBRC 13756 / NCIMB
RC 11199 / NRRL B-4490 / ZM6;
RX PubMed=3546263; DOI=10.1128/jb.169.3.1024-1028.1987;
RA Neale A.D., Scopes R.K., Wettenhall R.E.H., Hoogenraad N.J.;
RT "Pyruvate decarboxylase of Zymomonas mobilis: isolation, properties, and
RT genetic expression in Escherichia coli.";
RL J. Bacteriol. 169:1024-1028(1987).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PARTIAL PROTEIN SEQUENCE.
RC STRAIN=ATCC 29191 / DSM 3580 / JCM 10190 / CECT 560 / NBRC 13756 / NCIMB
RC 11199 / NRRL B-4490 / ZM6;
RX PubMed=3029726; DOI=10.1093/nar/15.4.1753;
RA Neale A.D., Scopes R.K., Wettenhall R.E.H., Hoogenraad N.J.;
RT "Nucleotide sequence of the pyruvate decarboxylase gene from Zymomonas
RT mobilis.";
RL Nucleic Acids Res. 15:1753-1761(1987).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 31821 / ZM4 / CP4;
RX PubMed=3029037; DOI=10.1128/jb.169.3.949-954.1987;
RA Conway T., Osman Y.A., Konnan J.I., Hoffmann E.M., Ingram L.O.;
RT "Promoter and nucleotide sequences of the Zymomonas mobilis pyruvate
RT decarboxylase.";
RL J. Bacteriol. 169:949-954(1987).
RN [4]
RP SEQUENCE REVISION TO 11-12; 65-66; 251-262 AND 558-568.
RA Ingram L.O.;
RL Submitted (JUN-2002) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 29191 / DSM 3580 / JCM 10190 / CECT 560 / NBRC 13756 / NCIMB
RC 11199 / NRRL B-4490 / ZM6;
RX PubMed=2838467; DOI=10.1128/jb.170.7.3310-3313.1988;
RA Reynen M., Sahm H.;
RT "Comparison of the structural genes for pyruvate decarboxylase in different
RT Zymomonas mobilis strains.";
RL J. Bacteriol. 170:3310-3313(1988).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Candy J.M., Diefenbach R.J., Mattick J.S., Duggleby R.G.;
RL Submitted (APR-1991) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 31821 / ZM4 / CP4;
RA Um H.W., Kang H.S.;
RL Submitted (JAN-1999) to the EMBL/GenBank/DDBJ databases.
RN [8]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 31821 / ZM4 / CP4;
RX PubMed=15592456; DOI=10.1038/nbt1045;
RA Seo J.-S., Chong H., Park H.S., Yoon K.-O., Jung C., Kim J.J., Hong J.H.,
RA Kim H., Kim J.-H., Kil J.-I., Park C.J., Oh H.-M., Lee J.-S., Jin S.-J.,
RA Um H.-W., Lee H.-J., Oh S.-J., Kim J.Y., Kang H.L., Lee S.Y., Lee K.J.,
RA Kang H.S.;
RT "The genome sequence of the ethanologenic bacterium Zymomonas mobilis
RT ZM4.";
RL Nat. Biotechnol. 23:63-68(2005).
RN [9]
RP MUTAGENESIS.
RX PubMed=8645153; DOI=10.1042/bj3150745;
RA Candy J.M., Koga J., Nixon P.F., Duggleby R.G.;
RT "The role of residues glutamate-50 and phenylalanine-496 in Zymomonas
RT mobilis pyruvate decarboxylase.";
RL Biochem. J. 315:745-751(1996).
RN [10]
RP MUTAGENESIS.
RX PubMed=9655927; DOI=10.1016/s0167-4838(98)00077-6;
RA Candy J.M., Duggleby R.G.;
RT "Structure and properties of pyruvate decarboxylase and site-directed
RT mutagenesis of the Zymomonas mobilis enzyme.";
RL Biochim. Biophys. Acta 1385:323-338(1998).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
RX PubMed=9685367; DOI=10.1074/jbc.273.32.20196;
RA Dobritzsch D., Koenig S., Schneider G., Lu G.;
RT "High-resolution crystal structure of pyruvate decarboxylase from Zymomonas
RT mobilis. Implications for substrate activation in pyruvate
RT decarboxylases.";
RL J. Biol. Chem. 273:20196-20204(1998).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2-oxocarboxylate + H(+) = an aldehyde + CO2;
CC Xref=Rhea:RHEA:11628, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:17478, ChEBI:CHEBI:35179; EC=4.1.1.1;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Note=Binds 1 Mg(2+) per subunit.;
CC -!- COFACTOR:
CC Name=thiamine diphosphate; Xref=ChEBI:CHEBI:58937;
CC Note=Binds 1 thiamine pyrophosphate per subunit.;
CC -!- SUBUNIT: Homotetramer.
CC -!- MISCELLANEOUS: Rapid and exclusive production of ethanol as the end
CC product of sugar fermentation by the bacterium Zymononas mobilis is due
CC to the presence of pyruvate decarboxylase.
CC -!- SIMILARITY: Belongs to the TPP enzyme family. {ECO:0000305}.
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DR EMBL; M15368; AAA27697.1; -; Genomic_DNA.
DR EMBL; M15393; AAA27696.2; -; Genomic_DNA.
DR EMBL; M20667; AAA27685.1; -; Genomic_DNA.
DR EMBL; X59558; CAA42157.1; -; Genomic_DNA.
DR EMBL; AF124349; AAD19711.1; -; Genomic_DNA.
DR EMBL; AE008692; AAV89984.1; -; Genomic_DNA.
DR PIR; A26672; DCZYPZ.
DR PIR; A26947; DCZYPC.
DR RefSeq; WP_011241152.1; NZ_CP035711.1.
DR PDB; 1ZPD; X-ray; 1.86 A; A/B/E/F=1-566.
DR PDB; 2WVA; X-ray; 2.20 A; A/B/E/F/V/X/Y/Z=1-568.
DR PDB; 2WVG; X-ray; 1.75 A; A/B/E/F=1-568.
DR PDB; 2WVH; X-ray; 2.30 A; A/B/E/F/V/X/Y/Z=1-568.
DR PDB; 3OE1; X-ray; 1.98 A; A/B/C/D=1-568.
DR PDB; 4ZP1; X-ray; 2.21 A; A/B/C/D=1-568.
DR PDB; 5TMA; X-ray; 1.67 A; A/B=1-568.
DR PDBsum; 1ZPD; -.
DR PDBsum; 2WVA; -.
DR PDBsum; 2WVG; -.
DR PDBsum; 2WVH; -.
DR PDBsum; 3OE1; -.
DR PDBsum; 4ZP1; -.
DR PDBsum; 5TMA; -.
DR AlphaFoldDB; P06672; -.
DR SASBDB; P06672; -.
DR SMR; P06672; -.
DR STRING; 264203.ZMO1360; -.
DR DrugBank; DB04272; Citric acid.
DR EnsemblBacteria; AAV89984; AAV89984; ZMO1360.
DR GeneID; 58027105; -.
DR KEGG; zmo:ZMO1360; -.
DR eggNOG; COG3961; Bacteria.
DR HOGENOM; CLU_013748_0_2_5; -.
DR OMA; EQRYNDI; -.
DR OrthoDB; 391134at2; -.
DR BioCyc; MetaCyc:MON-16791; -.
DR BRENDA; 4.1.1.1; 6765.
DR SABIO-RK; P06672; -.
DR EvolutionaryTrace; P06672; -.
DR PRO; PR:P06672; -.
DR Proteomes; UP000001173; Chromosome.
DR GO; GO:0000287; F:magnesium ion binding; IEA:InterPro.
DR GO; GO:0004737; F:pyruvate decarboxylase activity; IEA:UniProtKB-EC.
DR GO; GO:0030976; F:thiamine pyrophosphate binding; IEA:InterPro.
DR GO; GO:0044281; P:small molecule metabolic process; IEA:UniProt.
DR InterPro; IPR029035; DHS-like_NAD/FAD-binding_dom.
DR InterPro; IPR029061; THDP-binding.
DR InterPro; IPR012000; Thiamin_PyroP_enz_cen_dom.
DR InterPro; IPR012001; Thiamin_PyroP_enz_TPP-bd_dom.
DR InterPro; IPR000399; TPP-bd_CS.
DR InterPro; IPR012110; TPP_enzyme.
DR InterPro; IPR011766; TPP_enzyme-bd_C.
DR PANTHER; PTHR43452; PTHR43452; 1.
DR Pfam; PF02775; TPP_enzyme_C; 1.
DR Pfam; PF00205; TPP_enzyme_M; 1.
DR Pfam; PF02776; TPP_enzyme_N; 1.
DR PIRSF; PIRSF036565; Pyruvt_ip_decrb; 1.
DR SUPFAM; SSF52467; SSF52467; 1.
DR SUPFAM; SSF52518; SSF52518; 2.
DR PROSITE; PS00187; TPP_ENZYMES; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Decarboxylase; Direct protein sequencing; Lyase; Magnesium;
KW Metal-binding; Reference proteome; Thiamine pyrophosphate.
FT CHAIN 1..568
FT /note="Pyruvate decarboxylase"
FT /id="PRO_0000090773"
FT REGION 390..472
FT /note="Thiamine pyrophosphate binding"
FT BINDING 27
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 50
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT BINDING 114
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 440
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 467
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 469
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 473
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT MUTAGEN 50
FT /note="E->Q: Almost complete loss of activity."
FT /evidence="ECO:0000269|PubMed:8645153,
FT ECO:0000269|PubMed:9655927"
FT CONFLICT 78
FT /note="L -> H (in Ref. 5; AAA27685)"
FT /evidence="ECO:0000305"
FT CONFLICT 157..158
FT /note="RE -> AK (in Ref. 5; AAA27685)"
FT /evidence="ECO:0000305"
FT CONFLICT 200
FT /note="E -> D (in Ref. 5; AAA27685)"
FT /evidence="ECO:0000305"
FT CONFLICT 233
FT /note="A -> T (in Ref. 5; AAA27685)"
FT /evidence="ECO:0000305"
FT CONFLICT 315..316
FT /note="NG -> RR (in Ref. 5; AAA27685)"
FT /evidence="ECO:0000305"
FT CONFLICT 317
FT /note="I -> V (in Ref. 3; AAA27696)"
FT /evidence="ECO:0000305"
FT CONFLICT 341
FT /note="A -> S (in Ref. 5; AAA27685)"
FT /evidence="ECO:0000305"
FT CONFLICT 507
FT /note="G -> A (in Ref. 5; AAA27685)"
FT /evidence="ECO:0000305"
FT HELIX 5..15
FT /evidence="ECO:0007829|PDB:5TMA"
FT STRAND 19..23
FT /evidence="ECO:0007829|PDB:5TMA"
FT HELIX 27..29
FT /evidence="ECO:0007829|PDB:5TMA"
FT HELIX 30..37
FT /evidence="ECO:0007829|PDB:5TMA"
FT STRAND 43..46
FT /evidence="ECO:0007829|PDB:5TMA"
FT HELIX 50..64
FT /evidence="ECO:0007829|PDB:5TMA"
FT STRAND 67..71
FT /evidence="ECO:0007829|PDB:5TMA"
FT TURN 73..76
FT /evidence="ECO:0007829|PDB:5TMA"
FT HELIX 77..89
FT /evidence="ECO:0007829|PDB:5TMA"
FT STRAND 94..100
FT /evidence="ECO:0007829|PDB:5TMA"
FT HELIX 103..105
FT /evidence="ECO:0007829|PDB:5TMA"
FT TURN 106..109
FT /evidence="ECO:0007829|PDB:5TMA"
FT STRAND 117..119
FT /evidence="ECO:0007829|PDB:5TMA"
FT HELIX 123..129
FT /evidence="ECO:0007829|PDB:5TMA"
FT STRAND 133..138
FT /evidence="ECO:0007829|PDB:5TMA"
FT HELIX 141..143
FT /evidence="ECO:0007829|PDB:5TMA"
FT HELIX 144..158
FT /evidence="ECO:0007829|PDB:5TMA"
FT STRAND 162..167
FT /evidence="ECO:0007829|PDB:5TMA"
FT HELIX 168..170
FT /evidence="ECO:0007829|PDB:2WVG"
FT STRAND 173..175
FT /evidence="ECO:0007829|PDB:5TMA"
FT HELIX 181..184
FT /evidence="ECO:0007829|PDB:5TMA"
FT HELIX 192..205
FT /evidence="ECO:0007829|PDB:5TMA"
FT TURN 206..208
FT /evidence="ECO:0007829|PDB:5TMA"
FT STRAND 212..216
FT /evidence="ECO:0007829|PDB:5TMA"
FT TURN 218..224
FT /evidence="ECO:0007829|PDB:5TMA"
FT HELIX 226..236
FT /evidence="ECO:0007829|PDB:5TMA"
FT STRAND 239..243
FT /evidence="ECO:0007829|PDB:5TMA"
FT HELIX 244..246
FT /evidence="ECO:0007829|PDB:5TMA"
FT STRAND 257..261
FT /evidence="ECO:0007829|PDB:5TMA"
FT HELIX 263..265
FT /evidence="ECO:0007829|PDB:5TMA"
FT HELIX 270..275
FT /evidence="ECO:0007829|PDB:5TMA"
FT STRAND 278..284
FT /evidence="ECO:0007829|PDB:5TMA"
FT TURN 289..296
FT /evidence="ECO:0007829|PDB:5TMA"
FT TURN 301..303
FT /evidence="ECO:0007829|PDB:5TMA"
FT STRAND 304..307
FT /evidence="ECO:0007829|PDB:5TMA"
FT STRAND 309..314
FT /evidence="ECO:0007829|PDB:5TMA"
FT STRAND 317..321
FT /evidence="ECO:0007829|PDB:5TMA"
FT HELIX 324..334
FT /evidence="ECO:0007829|PDB:5TMA"
FT HELIX 340..347
FT /evidence="ECO:0007829|PDB:5TMA"
FT HELIX 367..377
FT /evidence="ECO:0007829|PDB:5TMA"
FT STRAND 382..386
FT /evidence="ECO:0007829|PDB:5TMA"
FT HELIX 390..397
FT /evidence="ECO:0007829|PDB:5TMA"
FT STRAND 405..407
FT /evidence="ECO:0007829|PDB:5TMA"
FT TURN 410..412
FT /evidence="ECO:0007829|PDB:5TMA"
FT TURN 415..417
FT /evidence="ECO:0007829|PDB:5TMA"
FT HELIX 418..428
FT /evidence="ECO:0007829|PDB:5TMA"
FT STRAND 432..439
FT /evidence="ECO:0007829|PDB:5TMA"
FT HELIX 440..446
FT /evidence="ECO:0007829|PDB:5TMA"
FT HELIX 449..455
FT /evidence="ECO:0007829|PDB:5TMA"
FT STRAND 461..466
FT /evidence="ECO:0007829|PDB:5TMA"
FT HELIX 471..474
FT /evidence="ECO:0007829|PDB:5TMA"
FT HELIX 480..482
FT /evidence="ECO:0007829|PDB:5TMA"
FT HELIX 489..497
FT /evidence="ECO:0007829|PDB:5TMA"
FT TURN 498..500
FT /evidence="ECO:0007829|PDB:4ZP1"
FT HELIX 502..504
FT /evidence="ECO:0007829|PDB:5TMA"
FT STRAND 508..512
FT /evidence="ECO:0007829|PDB:5TMA"
FT HELIX 515..527
FT /evidence="ECO:0007829|PDB:5TMA"
FT STRAND 533..538
FT /evidence="ECO:0007829|PDB:5TMA"
FT HELIX 546..560
FT /evidence="ECO:0007829|PDB:5TMA"
SQ SEQUENCE 568 AA; 60926 MW; 9FAC04C77189E75C CRC64;
MSYTVGTYLA ERLVQIGLKH HFAVAGDYNL VLLDNLLLNK NMEQVYCCNE LNCGFSAEGY
ARAKGAAAAV VTYSVGALSA FDAIGGAYAE NLPVILISGA PNNNDHAAGH VLHHALGKTD
YHYQLEMAKN ITAAAEAIYT PEEAPAKIDH VIKTALREKK PVYLEIACNI ASMPCAAPGP
ASALFNDEAS DEASLNAAVE ETLKFIANRD KVAVLVGSKL RAAGAEEAAV KFADALGGAV
ATMAAAKSFF PEENPHYIGT SWGEVSYPGV EKTMKEADAV IALAPVFNDY STTGWTDIPD
PKKLVLAEPR SVVVNGIRFP SVHLKDYLTR LAQKVSKKTG ALDFFKSLNA GELKKAAPAD
PSAPLVNAEI ARQVEALLTP NTTVIAETGD SWFNAQRMKL PNGARVEYEM QWGHIGWSVP
AAFGYAVGAP ERRNILMVGD GSFQLTAQEV AQMVRLKLPV IIFLINNYGY TIEVMIHDGP
YNNIKNWDYA GLMEVFNGNG GYDSGAGKGL KAKTGGELAE AIKVALANTD GPTLIECFIG
REDCTEELVK WGKRVAAANS RKPVNKLL
