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(-) Description

Title :  CRYSTAL STRUCTURE OF DIAMINOPIMELATE DECARBOXYLASE FROM BRUCELLA MELITENSIS BOUND TO PLP
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  29 Dec 11  (Deposition) - 18 Jan 12  (Release) - 18 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Pyridoxal-Phosphate, Diaminopimelate Decarboxylase, Diaminopimelic Acid Decarboxylase, Meso- Diaminopimelate Decarboxylase, Dap-Decarboxylase, Meso-2, 6- Diaminoheptanedioate Carboxy-Lyase, Lyase, Lysine Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. E. Edwards, A. S. Gardberg, J. J. Letesson, Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
Crystal Structure Of Diaminopimelate Decarboxylase From Brucella Melitensis Bound To Plp
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIAMINOPIMELATE DECARBOXYLASE 1
    Chains: A, B
    EC Number: 4.1.1.20
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAVA0421
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BMEI0084, LYSA1
    Organism Scientific: BRUCELLA MELITENSIS BV. 1
    Organism Taxid: 224914
    Strain: 16M
    Synonym: DAP DECARBOXYLASE 1, DAPDC 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:176 , ARG A:180 , GLU A:224 , HOH A:430 , HOH A:533BINDING SITE FOR RESIDUE SO4 A 423
2AC2SOFTWAREPHE A:303 , ASP A:341 , THR A:349 , LEU A:355 , HOH A:553BINDING SITE FOR RESIDUE EDO A 424
3AC3SOFTWARETHR A:383 , TYR A:384 , SER A:386 , HOH A:634 , SER B:64 , ARG B:89 , VAL B:379 , HOH B:510BINDING SITE FOR RESIDUE EDO A 425
4AC4SOFTWARESER A:64 , ARG A:89 , VAL A:379 , THR B:383 , SER B:386 , HOH B:587BINDING SITE FOR RESIDUE EDO B 423

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VAB)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:28 -Pro A:29
2Thr B:28 -Pro B:29

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VAB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VAB)

(-) Exons   (0, 0)

(no "Exon" information available for 3VAB)

(-) 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:420
 aligned with Q8YJJ9_BRUME | Q8YJJ9 from UniProtKB/TrEMBL  Length:421

    Alignment length:426
                                 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      
         Q8YJJ9_BRUME     - -----MNHFEYRNGVLHAENVSLPEIAKAVGTPFYVYSRATIERHFRVFHDAFADMDTLVTYALKANSNQAVLTALAKLGAGADTVSQGEIRRALAAGIPANRIVFSGVGKTPREMDFALEAGIYCFNVESEPELEILSARAVAAGKVAPVSLRINPDVDAKTHAKISTGKSENKFGIPRDKARAAYARAASLPGLNVVGIDMHIGSQIIDLEPFDNAFALMAELVKELQADGHNIRHVDVGGGLGIPYRTPNTPPPPPVAYAQIVAKHIKPLGLKTVFEPGRLIVGNAGLLVTEVIFVKEGDAKNFVIVDAAMNDLIRPTLYDAFHDIRPVIMPNDNAPRIRADFVGPVCETGDYLGLDREVAKPAPGDLIAICTTGAYGAVLSSTYNSRLLIPEVLGDGERYHVVRPRRTYEELLALDSVPDWL 421
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh..eeee..eeee..eehhhhhhhhh..eeeeehhhhhhhhhhhhhhh....eeeeee.hhh.hhhhhhhhhhh..eeee.hhhhhhhhhhh..hhh.eeee....hhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhh..eeeeeeee...........---.......ee..hhhhhhhhhhhh..eeeeeee.........hhhhhhhhhhhhhhhhhhhhh.....eee...........---...hhhhhhhhhhhhhhhhh.eeee..hhhhhh..eeeeeeeeeeee....eeeee.......hhhhhhh....eee.........eeeeeee........eeeeeeeee......eeeee.....hhhhh.hhhhh....eeeee..eeeeee...hhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vab A  -3 GPGSMVNHFEYRNGVLHAENVSLPEIAKAVGTPFYVYSRATIERHFRVFHDAFADMDTLVTYALkANSNQAVLTALAKLGAGADTVSQGEIRRALAAGIPANRIVFSGVGKTPREMDFALEAGIYCFNVESEPELEILSARAVAAGKVAPVSLRINPDVDAKTHAKI---KSENKFGIPRDKARAAYARAASLPGLNVVGIDMHIGSQIIDLEPFDNAFALMAELVKELQADGHNIRHVDVGGGLGIPYRT---PPPPPVAYAQIVAKHIKPLGLKTVFEPGRLIVGNAGLLVTEVIFVKEGDAKNFVIVDAAMNDLIRPTLYDAFHDIRPVIMPNDNAPRIRADFVGPVCETGDYLGLDREVAKPAPGDLIAICTTGAYGAVLSSTYNSRLLIPEVLGDGERYHVVRPRRTYEELLALDSVPDWL 422
                                     6        16        26        36        46        56    |   66        76        86        96       106       116       126       136       146       156      |  -|      176       186       196       206       216       226       236       246|   |  256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416      
                                                                                           61-LLP                                                                                               163 167                                                                             247 251                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:420
 aligned with Q8YJJ9_BRUME | Q8YJJ9 from UniProtKB/TrEMBL  Length:421

    Alignment length:426
                                 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      
         Q8YJJ9_BRUME     - -----MNHFEYRNGVLHAENVSLPEIAKAVGTPFYVYSRATIERHFRVFHDAFADMDTLVTYALKANSNQAVLTALAKLGAGADTVSQGEIRRALAAGIPANRIVFSGVGKTPREMDFALEAGIYCFNVESEPELEILSARAVAAGKVAPVSLRINPDVDAKTHAKISTGKSENKFGIPRDKARAAYARAASLPGLNVVGIDMHIGSQIIDLEPFDNAFALMAELVKELQADGHNIRHVDVGGGLGIPYRTPNTPPPPPVAYAQIVAKHIKPLGLKTVFEPGRLIVGNAGLLVTEVIFVKEGDAKNFVIVDAAMNDLIRPTLYDAFHDIRPVIMPNDNAPRIRADFVGPVCETGDYLGLDREVAKPAPGDLIAICTTGAYGAVLSSTYNSRLLIPEVLGDGERYHVVRPRRTYEELLALDSVPDWL 421
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh..eeee..eeee..eehhhhhhhhh..eeeeehhhhhhhhhhhhhhh....eeeeee.hhh.hhhhhhhhhh...eeee.hhhhhhhhhhh..hhh.eeee....hhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhh..eeeeeeee...........---.......ee..hhhhhhhhhhhh..eeeeeee.........hhhhhhhhhhhhhhhhhhhhh.....eee...........---...hhhhhhhhhhhhhhhhh.eeee..hhhhhh..eeeeeeeeeeee....eeeee.......hhhhhhh....eee.........eeeeeee........eeeeeeeee......eeeee.....hhhhh.hhhhh....eeeee..eeeeee...hhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vab B  -3 GPGSMVNHFEYRNGVLHAENVSLPEIAKAVGTPFYVYSRATIERHFRVFHDAFADMDTLVTYALkANSNQAVLTALAKLGAGADTVSQGEIRRALAAGIPANRIVFSGVGKTPREMDFALEAGIYCFNVESEPELEILSARAVAAGKVAPVSLRINPDVDAKTHAKI---KSENKFGIPRDKARAAYARAASLPGLNVVGIDMHIGSQIIDLEPFDNAFALMAELVKELQADGHNIRHVDVGGGLGIPYRT---PPPPPVAYAQIVAKHIKPLGLKTVFEPGRLIVGNAGLLVTEVIFVKEGDAKNFVIVDAAMNDLIRPTLYDAFHDIRPVIMPNDNAPRIRADFVGPVCETGDYLGLDREVAKPAPGDLIAICTTGAYGAVLSSTYNSRLLIPEVLGDGERYHVVRPRRTYEELLALDSVPDWL 422
                                     6        16        26        36        46        56    |   66        76        86        96       106       116       126       136       146       156      |  -|      176       186       196       206       216       226       236       246|   |  256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416      
                                                                                           61-LLP                                                                                               163 167                                                                             247 251
   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 3VAB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VAB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VAB)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8YJJ9_BRUME | Q8YJJ9)
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:0008836    diaminopimelate decarboxylase activity    Catalysis of the reaction: meso-2,6-diaminopimelate + H(+) = L-lysine + CO(2).
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
biological process
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0009085    lysine biosynthetic process    The chemical reactions and pathways resulting in the formation of lysine, 2,6-diaminohexanoic acid.
    GO:0009089    lysine biosynthetic process via diaminopimelate    The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.

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