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(-) Description

Title :  THE COMPLEX STRUCTURE OF THE BRANCHED-CHAIN KETO ACID DECARBOXYLASE (KDCA) FROM LACTOCOCCUS LACTIS WITH 2R-1-HYDROXYETHYL-DEAZATHDP
 
Authors :  C. L. Berthold, D. Gocke, M. D. Wood, F. Leeper, M. Pohl, G. Schneider
Date :  12 Sep 07  (Deposition) - 27 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Kdca, Flavoprotein, Thdp-Dependent Enzymes, Thiamine Pyrophosphate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. L. Berthold, D. Gocke, M. D. Wood, F. Leeper, M. Pohl, G. Schneider
Crystal Structure Of The Branched-Chain Keto Acid Decarboxylase (Kdca) From Lactococcus Lactis Provides Insights Into The Structural Basis For The Chemo- And Enantioselective Carboligation Reaction
Acta Crystallogr. , Sect. D V. 63 1217 2007
PubMed-ID: 18084069  |  Reference-DOI: 10.1107/S0907444907050433

(-) Compounds

Molecule 1 - BRANCHED-CHAIN ALPHA-KETOACID DECARBOXYLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Organism Scientific: LACTOCOCCUS LACTIS
    Organism Taxid: 1358
    Other Details: CHAIN A AND B CONTAIN THE COMPLETE ENZYME SEQUENCE AND SHORT N-TERMINAL TAGS WITH LINKERS, WHICH ARE BOUND IN ADJACENT DIMERS IN THE CRYSTAL.
    Synonym: BRANCHED-CHAIN KETO ACID DECARBOXYLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2R1T2Ligand/Ion2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:429 , ASN A:456 , GLY A:458 , R1T A:1549 , HOH A:2367BINDING SITE FOR RESIDUE MG A1548
2AC2SOFTWAREGLY A:378 , THR A:379 , GLY A:402 , SER A:403 , ILE A:404 , GLY A:428 , ASP A:429 , GLY A:430 , SER A:431 , ASN A:456 , GLY A:458 , TYR A:459 , THR A:460 , VAL A:461 , GLU A:462 , MG A:1548 , HOH A:2327 , HOH A:2367 , HOH A:2477 , HOH A:2478 , PRO B:24 , GLY B:25 , GLU B:49 , VAL B:74 , HIS B:113BINDING SITE FOR RESIDUE R1T A1549
3AC3SOFTWAREASP B:429 , ASN B:456 , GLY B:458 , R1T B:1549 , HOH B:2374BINDING SITE FOR RESIDUE MG B1548
4AC4SOFTWAREPRO A:24 , GLY A:25 , GLU A:49 , VAL A:74 , HIS A:113 , GLY B:378 , THR B:379 , GLY B:402 , SER B:403 , ILE B:404 , GLY B:428 , ASP B:429 , GLY B:430 , SER B:431 , ASN B:456 , GLY B:458 , TYR B:459 , THR B:460 , VAL B:461 , GLU B:462 , MG B:1548 , HOH B:2374 , HOH B:2471 , HOH B:2472BINDING SITE FOR RESIDUE R1T B1549

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VBG)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VBG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VBG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VBG)

(-) Exons   (0, 0)

(no "Exon" information available for 2VBG)

(-) Sequences/Alignments

Asymmetric/Biological 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:546
 aligned with Q6QBS4_9LACT | Q6QBS4 from UniProtKB/TrEMBL  Length:547

    Alignment length:552
                                 1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545  
         Q6QBS4_9LACT     - -----MYTVGDYLLDRLHELGIEEIFGVPGDYNLQFLDQIISREDMKWIGNANELNASYMADGYARTKKAAAFLTTFGVGELSAINGLAGSYAENLPVVEIVGSPTSKVQNDGKFVHHTLADGDFKHFMKMHEPVTAARTLLTAENATYEIDRVLSQLLKERKPVYINLPVDVAAAKAEKPALSLEKESSTTNTTEQVILSKIEESLKNAQKPVVIAGHEVISFGLEKTVTQFVSETKLPITTLNFGKSAVDESLPSFLGIYNGKLSEISLKNFVESADFILMLGVKLTDSSTGAFTHHLDENKMISLNIDEGIIFNKVVEDFDFRAVVSSLSELKGIEYEGQYIDKQYEEFIPSSAPLSQDRLWQAVESLTQSNETIVAEQGTSFFGASTIFLKSNSRFIGQPLWGSIGYTFPAALGSQIADKESRHLLFIGDGSLQLTVQELGLSIREKLNPICFIINNDGYTVEREIHGPTQSYNDIPMWNYSKLPETFGATEDRVVSKIVRTENEFVSVMKEAQADVNRMYWIELVLEKEDAPKLLKKMGKLFAEQNK 547
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2vbgA01 A:-14-181  [code=3.40.50.970, no name defined]                                                                                                                                    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------2vbgA03 A:351-540  [code=3.40.50.970, no name defined]                                                                                                                                        ------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhh............hhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhh..eeeeeehhhhh...........------hhhhhhhhhhhhhhhhhh..eeeeehhhhhhh.hhhhhhhhhhhhh..eee..............eeee.hhhhhhhhhhhhhhhh.eeeee....hhhhh.......hhh.eeee....eee..eee...hhhhhhhhhhhh........................hhhhhhhhhhhhh...eeeee..hhhhhhhh........eee.........hhhhhhhhhhhhh...eeeeeeehhhhhhhh.hhhhhhhh....eeeeee...hhhhhhhh...hhhhh....hhhhhhhhh......eeeeee.hhhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vbg A -14 HSSGLMYTVGDYLLDRLHELGIEEIFGVPGDYNLQFLDQIISREDMKWIGNANELNASYMADGYARTKKAAAFLTTFGVGELSAINGLAGSYAENLPVVEIVGSPTSKVQNDGKFVHHTLADGDFKHFMKMHEPVTAARTLLTAENATYEIDRVLSQLLKERKPVYINLPVDVAAAKAEKPALSLE------NTTEQVILSKIEESLKNAQKPVVIAGHEVISFGLEKTVTQFVSETKLPITTLNFGKSAVDESLPSFLGIYNGKLSEISLKNFVESADFILMLGVKLTDSSTGAFTHHLDENKMISLNIDEGIIFNKVVEDFDFRAVVSSLSELKGIEYEGQYIDKQYEEFIPSSAPLSQDRLWQAVESLTQSNETIVAEQGTSFFGASTIFLKSNSRFIGQPLWGSIGYTFPAALGSQIADKESRHLLFIGDGSLQLTVQELGLSIREKLNPICFIINNDGYTVEREIHGPTQSYNDIPMWNYSKLPETFGATEDRVVSKIVRTENEFVSVMKEAQADVNRMYWIELVLEKEDAPKLLKKMGKLFAEQNK 547
                                ||   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175     |   -  |    195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545  
                              -10|                                                                                                                                                                                 181    188                                                                                                                                                                                                                                                                                                                                                                       
                                 1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:544
 aligned with Q6QBS4_9LACT | Q6QBS4 from UniProtKB/TrEMBL  Length:547

    Alignment length:552
                                 1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545  
         Q6QBS4_9LACT     - -----MYTVGDYLLDRLHELGIEEIFGVPGDYNLQFLDQIISREDMKWIGNANELNASYMADGYARTKKAAAFLTTFGVGELSAINGLAGSYAENLPVVEIVGSPTSKVQNDGKFVHHTLADGDFKHFMKMHEPVTAARTLLTAENATYEIDRVLSQLLKERKPVYINLPVDVAAAKAEKPALSLEKESSTTNTTEQVILSKIEESLKNAQKPVVIAGHEVISFGLEKTVTQFVSETKLPITTLNFGKSAVDESLPSFLGIYNGKLSEISLKNFVESADFILMLGVKLTDSSTGAFTHHLDENKMISLNIDEGIIFNKVVEDFDFRAVVSSLSELKGIEYEGQYIDKQYEEFIPSSAPLSQDRLWQAVESLTQSNETIVAEQGTSFFGASTIFLKSNSRFIGQPLWGSIGYTFPAALGSQIADKESRHLLFIGDGSLQLTVQELGLSIREKLNPICFIINNDGYTVEREIHGPTQSYNDIPMWNYSKLPETFGATEDRVVSKIVRTENEFVSVMKEAQADVNRMYWIELVLEKEDAPKLLKKMGKLFAEQNK 547
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2vbgB01 B:-14-181  [code=3.40.50.970, no name defined]                                                                                                                                    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------2vbgB03 B:351-540  [code=3.40.50.970, no name defined]                                                                                                                                        ------- CATH domains
           Pfam domains (1) ------TPP_enzyme_N-2vbgB05 B:2-177                                                                                                                                                    -----------------TPP_enzyme_M-2vbgB01 B:195-330                                                                                                          -----------------------------------------------TPP_enzyme_C-2vbgB03 B:378-524                                                                                                                     ----------------------- Pfam domains (1)
           Pfam domains (2) ------TPP_enzyme_N-2vbgB06 B:2-177                                                                                                                                                    -----------------TPP_enzyme_M-2vbgB02 B:195-330                                                                                                          -----------------------------------------------TPP_enzyme_C-2vbgB04 B:378-524                                                                                                                     ----------------------- Pfam domains (2)
         Sec.struct. author .......hhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhh.............hhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhh..eeeeeehhhhh...........------hhhhhhhhhhhhhhhhhh..eeeeehhhhhhh.hhhhhhhhhhhhh..eee..............eeee.hhhhhhhhhhhhhhhh.eeeee....hhhhh.......hhh.eeee....eee..eee...hhhhhhhhhhhh............--..........hhhhhhhhhhhhh...eeeee..hhhhhhhh........eee.........hhhhhhhhhhhhh...eeeeeeehhhhhhhh.hhhhhhhh....eeeeee...hhhhhhhh...hhhhh....hhhhhhhhh......eeeeee.hhhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vbg B -14 HSSGLMYTVGDYLLDRLHELGIEEIFGVPGDYNLQFLDQIISREDMKWIGNANELNASYMADGYARTKKAAAFLTTFGVGELSAINGLAGSYAENLPVVEIVGSPTSKVQNDGKFVHHTLADGDFKHFMKMHEPVTAARTLLTAENATYEIDRVLSQLLKERKPVYINLPVDVAAAKAEKPALSLE------NTTEQVILSKIEESLKNAQKPVVIAGHEVISFGLEKTVTQFVSETKLPITTLNFGKSAVDESLPSFLGIYNGKLSEISLKNFVESADFILMLGVKLTDSSTGAFTHHLDENKMISLNIDEGIIFNKVVEDFDFRAVVSSLSELKGIEYEGQYIDK--EEFIPSSAPLSQDRLWQAVESLTQSNETIVAEQGTSFFGASTIFLKSNSRFIGQPLWGSIGYTFPAALGSQIADKESRHLLFIGDGSLQLTVQELGLSIREKLNPICFIINNDGYTVEREIHGPTQSYNDIPMWNYSKLPETFGATEDRVVSKIVRTENEFVSVMKEAQADVNRMYWIELVLEKEDAPKLLKKMGKLFAEQNK 547
                                ||   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175     |   -  |    195       205       215       225       235       245       255       265       275       285       295       305       315       325       335      |345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545  
                              -10|                                                                                                                                                                                 181    188                                                                                                                                                       342  |                                                                                                                                                                                                          
                                 1                                                                                                                                                                                                                                                                                                                                                     345
   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 2VBG)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Clan: FAD_DHS (82)
(-)
Clan: THDP-binding (106)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q6QBS4_9LACT | Q6QBS4)
molecular function
    GO:0047433    branched-chain-2-oxoacid decarboxylase activity    Catalysis of the reaction: (S)-3-methyl-2-oxopentanoate + H(+) = 2-methylbutanal + CO(2).
    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.
biological process
    GO:0009082    branched-chain amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.

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  2vbg
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q6QBS4_9LACT | Q6QBS4: 2vbf

(-) Related Entries Specified in the PDB File

2vbf THE HOLOSTRUCTURE OF THE BRANCHED-CHAIN KETO ACID DECARBOXYLASE (KDCA) FROM LACTOCOCCUS LACTIS