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(-) Description

Title :  FUNCTIONAL AND STRUCTURAL CHARACTERIZATION OF PYRUVATE DECARBOXYLASE FROM GLUCONOACETOBACTER DIAZOTROPHICUS
 
Authors :  L. J. Vanzyl, W. -D. Schubert, M. Tuffin, D. A. Cowan
Date :  29 Jan 14  (Deposition) - 01 Oct 14  (Release) - 08 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.69
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. J. Van Zyl, W. Schubert, M. I. Tuffin, D. A. Cowan
Structure And Functional Characterization Of Pyruvate Decarboxylase From Gluconacetobacter Diazotrophicus.
Bmc Struct. Biol. V. 14 21 2014
PubMed-ID: 25369873  |  Reference-DOI: 10.1186/S12900-014-0021-1

(-) Compounds

Molecule 1 - PYRUVATE DECARBOXYLASE
    Atcc: ATCC 49037
    Chains: A, B
    EC Number: 4.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28A
    Expression System Vector Type: PLASMID
    Organism Scientific: GLUCONACETOBACTER DIAZOTROPHICUS PAL 5
    Organism Taxid: 272568
    Other Details: AMERICAN TYPE CULTURE COLLECTION

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2SO42Ligand/IonSULFATE ION
3TPP2Ligand/IonTHIAMINE DIPHOSPHATE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SO44Ligand/IonSULFATE ION
3TPP4Ligand/IonTHIAMINE DIPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:385 , ASP A:386 , GLY A:409 , HIS A:410 , ILE A:411 , GLY A:435 , ASP A:436 , GLY A:437 , SER A:438 , ASN A:463 , GLY A:465 , TYR A:466 , THR A:467 , ILE A:468 , GLU A:469 , MG A:601 , HOH A:2367 , HOH A:2479 , HOH A:2480 , HOH A:2515 , HOH A:2630 , ALA B:25 , GLY B:26 , GLU B:50 , VAL B:75 , HIS B:114BINDING SITE FOR RESIDUE TPP A 600
2AC2SOFTWAREASP A:436 , ASN A:463 , GLY A:465 , TPP A:600 , HOH A:2515BINDING SITE FOR RESIDUE MG A 601
3AC3SOFTWAREALA A:25 , GLY A:26 , GLU A:50 , VAL A:75 , HIS A:114 , HOH A:2147 , GLY B:385 , ASP B:386 , GLY B:409 , HIS B:410 , ILE B:411 , GLY B:435 , ASP B:436 , GLY B:437 , SER B:438 , ASN B:463 , GLY B:465 , TYR B:466 , THR B:467 , ILE B:468 , GLU B:469 , MG B:601 , HOH B:2406 , HOH B:2407 , HOH B:2437 , HOH B:2535BINDING SITE FOR RESIDUE TPP B 600
4AC4SOFTWAREASP B:436 , ASN B:463 , GLY B:465 , TPP B:600 , HOH B:2437BINDING SITE FOR RESIDUE MG B 601
5AC5SOFTWARELEU A:373 , GLN A:429 , ARG A:518 , HOH A:2469 , HOH A:2597 , HOH A:2631BINDING SITE FOR RESIDUE SO4 A1556
6AC6SOFTWAREARG A:377 , GLN A:429 , HIS B:398BINDING SITE FOR RESIDUE SO4 A1557

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4COK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4COK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4COK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4COK)

(-) Exons   (0, 0)

(no "Exon" information available for 4COK)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:549
 aligned with A9H275_GLUDA | A9H275 from UniProtKB/TrEMBL  Length:558

    Alignment length:555
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550     
         A9H275_GLUDA     1 MTYTVGRYLADRLAQIGLKHHFAVAGDYNLVLLDQLLLNTDMQQIYCSNELNCGFSAEGYARANGAAAAIVTFSVGALSAFNALGGAYAENLPVILISGAPNANDHGTGHILHHTLGTTDYGYQLEMARHITCAAESIVAAEDAPAKIDHVIRTALREKKPAYLEIACNVAGAPCVRPGGIDALLSPPAPDEASLKAAVDAALAFIEQRGSVTMLVGSRIRAAGAQAQAVALADALGCAVTTMAAAKSFFPEDHPGYRGHYWGEVSSPGAQQAVEGADGVICLAPVFNDYATVGWSAWPKGDNVMLVERHAVTVGGVAYAGIDMRDFLTRLAAHTVRRDATARGGAYVTPQTPAAAPTAPLNNAEMARQIGALLTPRTTLTAETGDSWFNAVRMKLPHGARVELEMQWGHIGWSVPAAFGNALAAPERQHVLMVGDGSFQLTAQEVAQMIRHDLPVIIFLINNHGYTIEVMIHDGPYNNVKNWDYAGLMEVFNAGEGNGLGLRARTGGELAAAIEQARANRNGPTLIECTLDRDDCTQELVTWGKRVAAANARPP 555
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh...eeee..hhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhh...eeeeeee.hhhhh...............hhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhh..eeeeee................------.hhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhh.eeeee.hhh.........eeeeehhhhh..hhhhhhhh..eeeee....................eeeee..eeee..eeee..hhhhhhhhhhhhh..........................hhhhhhhhhhhhh...eeeee..hhhhhhhhh.......eee.........hhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhhhhh....eeeeee...hhhhhh...hhhhh....hhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cok A   1 MTYTVGRYLADRLAQIGLKHHFAVAGDYNLVLLDQLLLNTDMQQIYCSNELNCGFSAEGYARANGAAAAIVTFSVGALSAFNALGGAYAENLPVILISGAPNANDHGTGHILHHTLGTTDYGYQLEMARHITCAAESIVAAEDAPAKIDHVIRTALREKKPAYLEIACNVAGAPCVRPGGIDA------PDEASLKAAVDAALAFIEQRGSVTMLVGSRIRAAGAQAQAVALADALGCAVTTMAAAKSFFPEDHPGYRGHYWGEVSSPGAQQAVEGADGVICLAPVFNDYATVGWSAWPKGDNVMLVERHAVTVGGVAYAGIDMRDFLTRLAAHTVRRDATARGGAYVTPQTPAAAPTAPLNNAEMARQIGALLTPRTTLTAETGDSWFNAVRMKLPHGARVELEMQWGHIGWSVPAAFGNALAAPERQHVLMVGDGSFQLTAQEVAQMIRHDLPVIIFLINNHGYTIEVMIHDGPYNNVKNWDYAGLMEVFNAGEGNGLGLRARTGGELAAAIEQARANRNGPTLIECTLDRDDCTQELVTWGKRVAAANARPP 555
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  |    190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550     
                                                                                                                                                                                                                183    190                                                                                                                                                                                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:549
 aligned with A9H275_GLUDA | A9H275 from UniProtKB/TrEMBL  Length:558

    Alignment length:556
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550      
         A9H275_GLUDA     1 MTYTVGRYLADRLAQIGLKHHFAVAGDYNLVLLDQLLLNTDMQQIYCSNELNCGFSAEGYARANGAAAAIVTFSVGALSAFNALGGAYAENLPVILISGAPNANDHGTGHILHHTLGTTDYGYQLEMARHITCAAESIVAAEDAPAKIDHVIRTALREKKPAYLEIACNVAGAPCVRPGGIDALLSPPAPDEASLKAAVDAALAFIEQRGSVTMLVGSRIRAAGAQAQAVALADALGCAVTTMAAAKSFFPEDHPGYRGHYWGEVSSPGAQQAVEGADGVICLAPVFNDYATVGWSAWPKGDNVMLVERHAVTVGGVAYAGIDMRDFLTRLAAHTVRRDATARGGAYVTPQTPAAAPTAPLNNAEMARQIGALLTPRTTLTAETGDSWFNAVRMKLPHGARVELEMQWGHIGWSVPAAFGNALAAPERQHVLMVGDGSFQLTAQEVAQMIRHDLPVIIFLINNHGYTIEVMIHDGPYNNVKNWDYAGLMEVFNAGEGNGLGLRARTGGELAAAIEQARANRNGPTLIECTLDRDDCTQELVTWGKRVAAANARPPR 556
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh...eeee..hhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhh...eeeeeee.hhhhh...............hhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhh..eeeeee................-------hhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhh.eeeee.hhh.........eeeeehhhhh..hhhhhhhh..eeeee....................eeeee..eeee..eeee..hhhhhhhhhhhhh..........................hhhhhhhhhhhhh...eeeee..hhhhhhhhh.......eee.........hhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhhhhh....eeeeee...hhhhhh...hhhhh....hhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cok B   1 MTYTVGRYLADRLAQIGLKHHFAVAGDYNLVLLDQLLLNTDMQQIYCSNELNCGFSAEGYARANGAAAAIVTFSVGALSAFNALGGAYAENLPVILISGAPNANDHGTGHILHHTLGTTDYGYQLEMARHITCAAESIVAAEDAPAKIDHVIRTALREKKPAYLEIACNVAGAPCVRPGGIDA-------DEASLKAAVDAALAFIEQRGSVTMLVGSRIRAAGAQAQAVALADALGCAVTTMAAAKSFFPEDHPGYRGHYWGEVSSPGAQQAVEGADGVICLAPVFNDYATVGWSAWPKGDNVMLVERHAVTVGGVAYAGIDMRDFLTRLAAHTVRRDATARGGAYVTPQTPAAAPTAPLNNAEMARQIGALLTPRTTLTAETGDSWFNAVRMKLPHGARVELEMQWGHIGWSVPAAFGNALAAPERQHVLMVGDGSFQLTAQEVAQMIRHDLPVIIFLINNHGYTIEVMIHDGPYNNVKNWDYAGLMEVFNAGEGNGLGLRARTGGELAAAIEQARANRNGPTLIECTLDRDDCTQELVTWGKRVAAANARPPR 556
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  |      -|      200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550      
                                                                                                                                                                                                                183     191
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4COK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4COK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4COK)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A9H275_GLUDA | A9H275)
molecular function
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0030976    thiamine pyrophosphate binding    Interacting selectively and non-covalently with thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.

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  4cok
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