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(-) Description

Title :  L201A MUTANT OF D-AMINO ACID AMINOTRANSFERASE COMPLEXED WITH PYRIDOXAMINE-5'-PHOSPHATE
 
Authors :  S. Sugio, A. Kashima, K. Kishimoto, D. Peisach, G. A. Petsko, D. Ringe, T. Yoshimura, N. Esaki
Date :  30 Nov 97  (Deposition) - 03 Jun 98  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Aminotransferase, Pyridoxal-5'-Phosphate, D-Amino Acid, D-Alanine, Alpha-Ketoglutamic Acid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Sugio, A. Kashima, K. Kishimoto, D. Peisach, G. A. Petsko, D. Ringe, T. Yoshimura, N. Esaki
Crystal Structures Of L201A Mutant Of D-Amino Acid Aminotransferase At 2. 0 A Resolution: Implication Of The Structural Role Of Leu201 In Transamination.
Protein Eng. V. 11 613 1998
PubMed-ID: 9749913  |  Reference-DOI: 10.1093/PROTEIN/11.8.613
(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 Plasmid: PAZZI
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: BACILLUS SP.
    Organism Taxid: 72579
    Other Details: PYRIDOXAMINE-5'-PHOSPHATES ARE NON-COVALENTLY BOUND TO THE ENZYME MOLECULES
    Strain: YM-1
    Synonym: D-ALANINE AMINOTRANSFERASE, D-ASPARTATE AMINOTRANSFERASE

 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
1PMP2Ligand/Ion4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:31 , ARG A:50 , LYS A:145 , GLU A:177 , SER A:180 , SER A:181 , ASN A:182 , ALA A:201 , GLY A:203 , ILE A:204 , THR A:205 , SER A:240 , THR A:241 , HOH A:322 , HOH A:344 , HOH A:418BINDING SITE FOR RESIDUE PMP A 285
2AC2SOFTWARETYR B:31 , ARG B:50 , LYS B:145 , GLU B:177 , SER B:180 , SER B:181 , ASN B:182 , GLY B:203 , ILE B:204 , THR B:205 , SER B:240 , THR B:241 , HOH B:302 , HOH B:340BINDING SITE FOR RESIDUE PMP B 285
3ASAUNKNOWNPMP A:285 , LYS A:145 , TYR A:31 , GLU A:177 , ARG B:98AN ACTIVE SITE FOR SUBUNIT A.
4ASBUNKNOWNPMP B:285 , LYS B:145 , TYR B:31 , GLU B:177 , ARG A:98AN ACTIVE SITE FOR SUBUNIT B.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1A0G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1A0G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1A0G)

(-) 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 1A0G)

(-) 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:280
 aligned with DAAA_BACYM | P19938 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:280
                                    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       281
           DAAA_BACYM     2 GYTLWNDQIVKDEEVKIDKEDRGYQFGDGVYEVVKVYNGEMFTVNEHIDRLYASAEKIRITIPYTKDKFHQLLHELVEKNELNTGHIYFQVTRGTSPRAHQFPENTVKPVIIGYTKENPRPLENLEKGVKATFVEDIRWLRCDIKSLNLLGAVLAKQEAHEKGCYEAILHRNNTVTEGSSSNVFGIKDGILYTHPANNMILKGITRDVVIACANEINMPVKEIPFTTHEALKMDELFVTSTTSEITPVIEIDGKLIRDGKVGEWTRKLQKQFETKIPKPL 281
               SCOP domains d1a0ga_ A: D-aminoacid aminotransferase                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1a0gA01 A:1-118  [code=3.30.470.10, no name defined]                                                                  1a0gA02 A:119-277 D-amino Acid Aminotransferase, subunit A, domain 2                                                                                           --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeehhh.......hhhhh..eeeeeeee.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh....eeeeeeee.................eeeeeeee....hhhhhh.eeeeeee..............hhhhhhhhhhhhh...eeeee...........eeeeee..eeee..........hhhhhhhhhhhh...eee.....hhhhhh..eeeeee...eeeeeeee...........hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_4           -------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a0g A   1 GYTLWNDQIVKDEEVKIDKEDRGYQFGDGVYEVVKVYNGEMFTVNEHIDRLYASAEKIRITIPYTKDKFHQLLHELVEKNELNTGHIYFQVTRGTSPRAHQFPENTVKPVIIGYTKENPRPLENLEKGVKATFVEDIRWLRCDIKSLNLLGAVLAKQEAHEKGCYEAILHRNNTVTEGSSSNVFGIKDGILYTHPANNMIAKGITRDVVIACANEINMPVKEIPFTTHEALKMDELFVTSTTSEITPVIEIDGKLIRDGKVGEWTRKLQKQFETKIPKPL 280
                                    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


Chain B from PDB  Type:PROTEIN  Length:282
 aligned with DAAA_BACYM | P19938 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:282
                                    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       281  
           DAAA_BACYM     2 GYTLWNDQIVKDEEVKIDKEDRGYQFGDGVYEVVKVYNGEMFTVNEHIDRLYASAEKIRITIPYTKDKFHQLLHELVEKNELNTGHIYFQVTRGTSPRAHQFPENTVKPVIIGYTKENPRPLENLEKGVKATFVEDIRWLRCDIKSLNLLGAVLAKQEAHEKGCYEAILHRNNTVTEGSSSNVFGIKDGILYTHPANNMILKGITRDVVIACANEINMPVKEIPFTTHEALKMDELFVTSTTSEITPVIEIDGKLIRDGKVGEWTRKLQKQFETKIPKPLHI 283
               SCOP domains d1a0gb_ B: D-aminoacid aminotransferase                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1a0gB01 B:1-118  [code=3.30.470.10, no name defined]                                                                  1a0gB02 B:119-277 D-amino Acid Aminotransferase, subunit A, domain 2                                                                                           ----- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eeeehhh.......hhhhh..eeeeeeee.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh....eeeeeeee.................eeeeeeee....hhhhhh.eeeeeee..............hhhhhhhhhhhhh...eeeee...........eeeeee..eeee..........hhhhhhhhhhhh...eee.....hhhhhh..eeeeee...eeeeeeee...........hhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_4           ---------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1a0g B   1 GYTLWNDQIVKDEEVKIDKEDRGYQFGDGVYEVVKVYNGEMFTVNEHIDRLYASAEKIRITIPYTKDKFHQLLHELVEKNELNTGHIYFQVTRGTSPRAHQFPENTVKPVIIGYTKENPRPLENLEKGVKATFVEDIRWLRCDIKSLNLLGAVLAKQEAHEKGCYEAILHRNNTVTEGSSSNVFGIKDGILYTHPANNMIAKGITRDVVIACANEINMPVKEIPFTTHEALKMDELFVTSTTSEITPVIEIDGKLIRDGKVGEWTRKLQKQFETKIPKPLHI 282
                                    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
   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 1A0G)

(-) 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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 Related Entries

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

(-) Related Entries Specified in the PDB File

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