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(-) Description

Title :  CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY PYRIDOXYL-D-ALANINE
 
Authors :  D. Peisach, D. M. Chipman, D. Ringe
Date :  20 Jan 98  (Deposition) - 29 Apr 98  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminotransferase, Pyridoxal Phosphate, Transaminase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Peisach, D. M. Chipman, P. W. Van Ophem, J. M. Manning, D. Ringe
Crystallographic Study Of Steps Along The Reaction Pathway Of D-Amino Acid Aminotransferase.
Biochemistry V. 37 4958 1998
PubMed-ID: 9538014  |  Reference-DOI: 10.1021/BI972884D
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - D-AMINO ACID AMINOTRANSFERASE
    Chains: A, B
    EC Number: 2.6.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BACILLUS SP.
    Organism Taxid: 72579
    Strain: YM-1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1PDD2Ligand/IonN-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:31 , ARG A:50 , LYS A:145 , GLU A:177 , GLY A:178 , SER A:180 , SER A:181 , ASN A:182 , GLY A:203 , ILE A:204 , THR A:205 , SER A:240 , THR A:241 , HOH A:675 , HOH A:692 , HOH A:718 , ARG B:98 , HIS B:100BINDING SITE FOR RESIDUE PDD A 285
2AC2SOFTWAREARG A:98 , HIS A:100 , TYR B:31 , HIS B:47 , ARG B:50 , LYS B:145 , GLU B:177 , SER B:180 , SER B:181 , ASN B:182 , LEU B:201 , GLY B:203 , ILE B:204 , THR B:205 , SER B:240 , THR B:241 , HOH B:686 , HOH B:697 , HOH B:804BINDING SITE FOR RESIDUE PDD B 285
3ASAUNKNOWNPDD A:285 , LYS A:145 , TYR A:31 , HIS B:100 , ARG B:98 , GLU A:177ACTIVE SITE A, INACTIVATED BY PHOSPHOPYRIDOXYL D -ALANINE.
4ASBUNKNOWNPDD B:285 , LYS B:145 , TYR B:31 , HIS A:100 , ARG A:98 , GLU B:177ACTIVE SITE B, INACTIVATED BY PHOSPHOPYRIDOXYL D -ALANINE.

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3DAA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_4PS00770 Aminotransferases class-IV signature.DAAA_BACYM178-207
 		  2A:177-206
B:177-206

(-) Exons   (0, 0)

(no "Exon" information available for 3DAA)

(-) 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:277
 aligned with DAAA_BACYM | P19938 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:277
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       
           DAAA_BACYM     2 GYTLWNDQIVKDEEVKIDKEDRGYQFGDGVYEVVKVYNGEMFTVNEHIDRLYASAEKIRITIPYTKDKFHQLLHELVEKNELNTGHIYFQVTRGTSPRAHQFPENTVKPVIIGYTKENPRPLENLEKGVKATFVEDIRWLRCDIKSLNLLGAVLAKQEAHEKGCYEAILHRNNTVTEGSSSNVFGIKDGILYTHPANNMILKGITRDVVIACANEINMPVKEIPFTTHEALKMDELFVTSTTSEITPVIEIDGKLIRDGKVGEWTRKLQKQFETKIP 278
               SCOP domains d3daaa_ A: D-aminoacid aminotransferase                                                                                                                                                                                                                                               SCOP domains
               CATH domains 3daaA01 A:1-118  [code=3.30.470.10, no name defined]                                                                  3daaA02 A:119-277 D-amino Acid Aminotransferase, subunit A, domain 2                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeehhh.......hhhh...eeeeeeee.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh....eeeeeeee.................eeeeeeee....hhhhhh.eeeeeee..............hhhhhhhhhhhh....eeeee...........eeeeee..eeee..........hhhhhhhhhhhh...eee.....hhhhhh..eeeeee...eeeeeeee...........hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_4           ----------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3daa A   1 GYTLWNDQIVKDEEVKIDKEDRGYQFGDGVYEVVKVYNGEMFTVNEHIDRLYASAEKIRITIPYTKDKFHQLLHELVEKNELNTGHIYFQVTRGTSPRAHQFPENTVKPVIIGYTKENPRPLENLEKGVKATFVEDIRWLRCDIKSLNLLGAVLAKQEAHEKGCYEAILHRNNTVTEGSSSNVFGIKDGILYTHPANNMILKGITRDVVIACANEINMPVKEIPFTTHEALKMDELFVTSTTSEITPVIEIDGKLIRDGKVGEWTRKLQKQFETKIP 277
                                    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       


Chain B from PDB  Type:PROTEIN  Length:277
 aligned with DAAA_BACYM | P19938 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:277
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       
           DAAA_BACYM     2 GYTLWNDQIVKDEEVKIDKEDRGYQFGDGVYEVVKVYNGEMFTVNEHIDRLYASAEKIRITIPYTKDKFHQLLHELVEKNELNTGHIYFQVTRGTSPRAHQFPENTVKPVIIGYTKENPRPLENLEKGVKATFVEDIRWLRCDIKSLNLLGAVLAKQEAHEKGCYEAILHRNNTVTEGSSSNVFGIKDGILYTHPANNMILKGITRDVVIACANEINMPVKEIPFTTHEALKMDELFVTSTTSEITPVIEIDGKLIRDGKVGEWTRKLQKQFETKIP 278
               SCOP domains d3daab_ B: D-aminoacid aminotransferase                                                                                                                                                                                                                                               SCOP domains
               CATH domains 3daaB01 B:1-118  [code=3.30.470.10, no name defined]                                                                  3daaB02 B:119-277 D-amino Acid Aminotransferase, subunit A, domain 2                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeehhh.......hhhh...eeeeeeee.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh.....eeeeeeee.................eeeeeeee....hhhhhh.eeeeeee..............hhhhhhhhhhhhh...eeeee...........eeeeee..eeee..........hhhhhhhhhhhh...........hhhhh...eeeeee...eeeeeeee...........hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_4           ----------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3daa B   1 GYTLWNDQIVKDEEVKIDKEDRGYQFGDGVYEVVKVYNGEMFTVNEHIDRLYASAEKIRITIPYTKDKFHQLLHELVEKNELNTGHIYFQVTRGTSPRAHQFPENTVKPVIIGYTKENPRPLENLEKGVKATFVEDIRWLRCDIKSLNLLGAVLAKQEAHEKGCYEAILHRNNTVTEGSSSNVFGIKDGILYTHPANNMILKGITRDVVIACANEINMPVKEIPFTTHEALKMDELFVTSTTSEITPVIEIDGKLIRDGKVGEWTRKLQKQFETKIP 277
                                    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
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DAAA_BACYM | P19938)
molecular function
    GO:0047810    D-alanine:2-oxoglutarate aminotransferase activity    Catalysis of the reaction: D-alanine + 2-oxoglutarate = pyruvate + D-glutamate.
    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.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0046437    D-amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of D-amino acids, the D-enantiomers of amino acids.
    GO:0019478    D-amino acid catabolic process    The chemical reactions and pathways resulting in the breakdown of D-amino acids, the D-enantiomers of amino acids.
    GO:0046416    D-amino acid metabolic process    The chemical reactions and pathways involving D-amino acids, the D-enantiomers of amino acids.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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        DAAA_BACYM | P19938: 1a0g 1daa 1g2w 2daa 2dab 3lqs 4daa 5daa

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