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(-) Description

Title :  CRYSTAL STRUCTURE OF GLUTAMATE DECARBOXYLASE DOMAIN OF DIAMINOBUTYRATE-PYRUVATE TRANSAMINASE AND L-2,4-DIAMINOBUTYRATE DECARBOXYLASE FROM VIBRIO PARAHAEMOLYTICUS
 
Authors :  J. Osipiuk, A. Sather, M. Gu, A. Joachimiak, Midwest Center For Stru Genomics (Mcsg)
Date :  14 Jul 07  (Deposition) - 31 Jul 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Apc91511. 1, Glutamate Decarboxylase, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Aminotransferase, Pyridoxal Phosphate, Pyruvate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osipiuk, A. Sather, M. Gu, A. Joachimiak
X-Ray Crystal Structure Of Glutamate Decarboxylase Domain O Diaminobutyrate-Pyruvate Transaminase And L-2, 4-Diaminobutyrate Decarboxylase From Vibrio Parahaemolyticus.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIAMINOBUTYRATE-PYRUVATE TRANSAMINASE AND L-2,4- DIAMINOBUTYRATE DECARBOXYLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN, RESIDUES 465-958
    Gene: VP1942
    Organism Scientific: VIBRIO PARAHAEMOLYTICUS
    Organism Taxid: 223926
    Strain: RIMD 2210633

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 40)

Asymmetric/Biological Unit (2, 40)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MSE38Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:605 , TRP A:609 , HOH A:1044 , HOH A:1155 , ASN B:530BINDING SITE FOR RESIDUE EDO A 961
2AC2SOFTWAREASN A:530 , LYS B:605 , TRP B:609 , HOH B:1069BINDING SITE FOR RESIDUE EDO B 962

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile A:792 -Ser A:793
2Ile B:792 -Ser B:793

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2QMA)

(-) 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:463
 aligned with Q87NC6_VIBPA | Q87NC6 from UniProtKB/TrEMBL  Length:958

    Alignment length:483
                                   484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954   
         Q87NC6_VIBPA   475 APQEEWKKHFIHTGELGSAEFASVMSHTTSAMKSVFEQVNAPYSGMDPKALEDAINAVDLDNKNAPLKSVIDDVAELVAKNAIFTQHPDCIAHLHTPPLMPAVAAEAMIAALNQSMDSWDQASSATYVEQKVVNWLCDKYDLSEKADGIFTSGGTQSNQMGLMLARDWIADKLSGHSIQKLGLPDYADKLRIVCSKKSHFTVQKSASWMGLGEKAVMTVDANADGTMDITKLDEVIAQAKAEGLIPFAIVGTAGTTDHGAIDDLDFIADMAVKHDMWMHVDGAYGGALILSSHKSRLKGVERAHSISVDFHKLFYQTISCGALLVNDKSNFKFLLHHADYLNREHDELPNLVDKSIATTKRFDALKVFMTMQNVGPKALGDMYDHLLAQTLEVADMIRTNDQFELLAEPSLSTVLFRATHETADLDELNKALRLEALTRGIAVLGETIVDGKTALKFTILNPCLTTSDFESLLSKINMLAVEL 957
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------2qmaA02      -2qmaA03 A:575-844 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                         -2qmaA02 A:561-573,A:846-957 Aspartate Aminotransferase, domain 1                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh........hhhhhhhhhhhhh....................hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhh.eeeeee....hhhhhhhhhh..hhh.eeee........hhhhhhhhhhhhhhh..eeeeeeee..........hhhhhhhhhhhhh.eeeeee.hhhhhhhh.hhhhhhhhhhh.eeeee...........eeeee.hhhhhhhhh.--------------------......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.......eeeeee.....hhhhhhhhhhhhhhhh.....eeeee..eeeeeee......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qma A 475 APQEEWKKHFIHTGELGSAEFASVmSHTTSAmKSVFEQVNAPYSGmDPKALEDAINAVDLDNKNAPLKSVIDDVAELVAKNAIFTQHPDCIAHLHTPPLmPAVAAEAmIAALNQSmDSWDQASSATYVEQKVVNWLCDKYDLSEKADGIFTSGGTQSNQmGLmLARDWIADKLSGHSIQKLGLPDYADKLRIVCSKKSHFTVQKSASWmGLGEKAVmTVDANADGTmDITKLDEVIAQAKAEGLIPFAIVGTAGTTDHGAIDDLDFIADmAVKHDmWmHVDGAYGGALILSSHKSRLKGVERAHSISVDFHKLFYQTISCGALLVNDKSNFKFLLH--------------------ATTKRFDALKVFmTmQNVGPKALGDmYDHLLAQTLEVADmIRTNDQFELLAEPSLSTVLFRATHETADLDELNKALRLEALTRGIAVLGETIVDGKTALKFTILNPCLTTSDFESLLSKINmLAVEL 957
                                   484       494    |  504 |     514     | 524       534       544       554       564       574       584     | 594       604       614       624       634  |    644       654       664       674       684      |694      |704       714       724       734       744     | 754       764       774       784       794       804     |   -         -      |834       844|      854 |     864     | 874       884       894       904       914       924       934       944       954   
                                                  499-MSE  |           520-MSE                                               574-MSE 582-MSE 590-MSE                                     634-MSE                                          683-MSE 691-MSE   701-MSE                                    744-MSE | |                                                       810                  831         843-MSE      856-MSE       870-MSE                                                                           952-MSE 
                                                         506-MSE                                                                                                                            637-MSE                                                                                                          750-MSE                                                                                        845-MSE                                                                                                            
                                                                                                                                                                                                                                                                                                               752-MSE                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:459
 aligned with Q87NC6_VIBPA | Q87NC6 from UniProtKB/TrEMBL  Length:958

    Alignment length:483
                                   484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954   
         Q87NC6_VIBPA   475 APQEEWKKHFIHTGELGSAEFASVMSHTTSAMKSVFEQVNAPYSGMDPKALEDAINAVDLDNKNAPLKSVIDDVAELVAKNAIFTQHPDCIAHLHTPPLMPAVAAEAMIAALNQSMDSWDQASSATYVEQKVVNWLCDKYDLSEKADGIFTSGGTQSNQMGLMLARDWIADKLSGHSIQKLGLPDYADKLRIVCSKKSHFTVQKSASWMGLGEKAVMTVDANADGTMDITKLDEVIAQAKAEGLIPFAIVGTAGTTDHGAIDDLDFIADMAVKHDMWMHVDGAYGGALILSSHKSRLKGVERAHSISVDFHKLFYQTISCGALLVNDKSNFKFLLHHADYLNREHDELPNLVDKSIATTKRFDALKVFMTMQNVGPKALGDMYDHLLAQTLEVADMIRTNDQFELLAEPSLSTVLFRATHETADLDELNKALRLEALTRGIAVLGETIVDGKTALKFTILNPCLTTSDFESLLSKINMLAVEL 957
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------2qmaB02      -2qmaB03 B:575-844 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                         -2qmaB02 B:561-573,B:846-957 Aspartate Aminotransferase, domain 1                                                 CATH domains
           Pfam domains (1) -----------------------------------------------Pyridoxal_deC-2qmaB01 B:522-893                                                                                                                                                                                                                                                                                                                                                     ---------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------Pyridoxal_deC-2qmaB02 B:522-893                                                                                                                                                                                                                                                                                                                                                     ---------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh...hhh.eeeeee....hhhhhhhhhh..hhh.eeee........hhhhhhhhhhhhhhh..eeeeeeee..........hhhhhhhhhhhhh.eeeee..hhhhhhhh.hhhhhhhhhhh.eeeee...........eeeee.hhhhhhhhh------------------------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.......eeeeee.....hhhhhhhhhhhhhhhh.....eeeee..eeeeeee......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qma B 475 APQEEWKKHFIHTGELGSAEFASVmSHTTSAmKSVFEQVNAPYSGmDPKALEDAINAVDLDNKNAPLKSVIDDVAELVAKNAIFTQHPDCIAHLHTPPLmPAVAAEAmIAALNQSmDSWDQASSATYVEQKVVNWLCDKYDLSEKADGIFTSGGTQSNQmGLmLARDWIADKLSGHSIQKLGLPDYADKLRIVCSKKSHFTVQKSASWmGLGEKAVmTVDANADGTmDITKLDEVIAQAKAEGLIPFAIVGTAGTTDHGAIDDLDFIADmAVKHDmWmHVDGAYGGALILSSHKSRLKGVERAHSISVDFHKLFYQTISCGALLVNDKSNFKFLL------------------------KRFDALKVFmTmQNVGPKALGDmYDHLLAQTLEVADmIRTNDQFELLAEPSLSTVLFRATHETADLDELNKALRLEALTRGIAVLGETIVDGKTALKFTILNPCLTTSDFESLLSKINmLAVEL 957
                                   484       494    |  504 |     514     | 524       534       544       554       564       574       584     | 594       604       614       624       634  |    644       654       664       674       684      |694      |704       714       724       734       744     | 754       764       774       784       794       804    |    -         -       834       844|      854 |     864     | 874       884       894       904       914       924       934       944       954   
                                                  499-MSE  |           520-MSE                                               574-MSE 582-MSE 590-MSE                                     634-MSE                                          683-MSE 691-MSE   701-MSE                                    744-MSE | |                                                      809                      834      843-MSE      856-MSE       870-MSE                                                                           952-MSE 
                                                         506-MSE                                                                                                                            637-MSE                                                                                                          750-MSE                                                                                        845-MSE                                                                                                            
                                                                                                                                                                                                                                                                                                               752-MSE
   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 2QMA)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PLP_aminotran (240)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q87NC6_VIBPA | Q87NC6)
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: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.
    GO:0008483    transaminase activity    Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0019752    carboxylic acid metabolic process    The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).

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