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(-) Description

Title :  THE CRYSTAL STRUCTURE OF ASPARTATE AMINOTRANSFERASE WHICH BELONGS TO SUBGROUP IV FROM THERMUS THERMOPHILUS
 
Authors :  Y. Katsura, M. Shirouzu, H. Yamaguchi, R. Ishitani, O. Nureki, S. Kuramitsu, H. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  04 Mar 02  (Deposition) - 25 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Wild Type, Pyridoxal-5'-Phosphate Form, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Katsura, M. Shirouzu, H. Yamaguchi, R. Ishitani, O. Nureki, S. Kuramitsu, H. Hayashi, S. Yokoyama
Crystal Structure Of A Putative Aspartate Aminotransferase Belonging To Subgroup Iv.
Proteins V. 55 487 2004
PubMed-ID: 15103612  |  Reference-DOI: 10.1002/PROT.20020
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE ASPARTATE AMINOTRANSFERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 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
1LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:85 , ARG A:89 , LLP A:185 , ARG B:28 , TRP B:229 , THR B:230 , HOH B:2035 , HOH B:2102 , HOH B:2112BINDING SITE FOR RESIDUE PO4 B 3693
2AC2SOFTWAREHIS A:27 , ALA A:228 , THR A:230 , PHE B:86 , ARG B:89 , LLP B:185BINDING SITE FOR RESIDUE PO4 B 3694

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:8 -Pro A:9
2Gly B:8 -Pro B:9

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1IUG)

(-) Exons   (0, 0)

(no "Exon" information available for 1IUG)

(-) 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:348
 aligned with P83786_THETH | P83786 from UniProtKB/TrEMBL  Length:352

    Alignment length:348
                                    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       291       301       311       321       331       341        
         P83786_THETH     2 DWLLTPGPVRLHPKALEALARPQLHHRTEAAREVFLKARGLLREAFRTEGEVLILTGSGTLAMEALVKNLFAPGERVLVPVYGKFSERFYEIALEAGLVVERLDYPYGDTPRPEDVAKEGYAGLLLVHSETSTGALADLPALARAFKEKNPEGLVGADMVTSLLVGEVALEAMGVDAAASGSQXGLMCPPGLGFVALSPRALERLKPRGYYLDLARELKAQKEGESAWTPAINLVLAVAAVLEEVLPRLEEHLALKAWQNALLYGVGEEGGLRPVPKRFSPAVAAFYLPEGVPYARVKEAFAQRGAVIAGGQGPLKGKVFRLSLMGAYDRYEALGVAGMFREVLEEIL 349
               SCOP domains d1iuga_ A: Subgroup IV putative aspartate aminotransferase                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1iugA01    1iugA02 A:13-249 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                         1iugA01 A:2-12,A:250-349 Aspartate Aminotransferase, domain 1                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee........hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhh..eeeeee..................eeeee..........hhhhhhhhhhhhh...eeeee...........hhhhh..eeeee..........eeeeeehhhhhhh........hhhhhhhhhh........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..ee.........eeee.....hhhhhhhhhhh..ee.ee.hhhhh..eeee......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1iug A   2 DWLLTPGPVRLHPKALEALARPQLHHRTEAAREVFLKARGLLREAFRTEGEVLILTGSGTLAMEALVKNLFAPGERVLVPVYGKFSERFYEIALEAGLVVERLDYPYGDTPRPEDVAKEGYAGLLLVHSETSTGALADLPALARAFKEKNPEGLVGADMVTSLLVGEVALEAMGVDAAASGSQkGLMCPPGLGFVALSPRALERLKPRGYYLDLARELKAQKEGESAWTPAINLVLAVAAVLEEVLPRLEEHLALKAWQNALLYGVGEEGGLRPVPKRFSPAVAAFYLPEGVPYARVKEAFAQRGAVIAGGQGPLKGKVFRLSLMGAYDRYEALGVAGMFREVLEEIL 349
                                    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       291       301       311       321       331       341        
                                                                                                                                                                                                                 185-LLP                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:348
 aligned with P83786_THETH | P83786 from UniProtKB/TrEMBL  Length:352

    Alignment length:348
                                    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       291       301       311       321       331       341        
         P83786_THETH     2 DWLLTPGPVRLHPKALEALARPQLHHRTEAAREVFLKARGLLREAFRTEGEVLILTGSGTLAMEALVKNLFAPGERVLVPVYGKFSERFYEIALEAGLVVERLDYPYGDTPRPEDVAKEGYAGLLLVHSETSTGALADLPALARAFKEKNPEGLVGADMVTSLLVGEVALEAMGVDAAASGSQXGLMCPPGLGFVALSPRALERLKPRGYYLDLARELKAQKEGESAWTPAINLVLAVAAVLEEVLPRLEEHLALKAWQNALLYGVGEEGGLRPVPKRFSPAVAAFYLPEGVPYARVKEAFAQRGAVIAGGQGPLKGKVFRLSLMGAYDRYEALGVAGMFREVLEEIL 349
               SCOP domains d1iugb_ B: Subgroup IV putative aspartate aminotransferase                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1iugB01    1iugB02 B:13-249 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                         1iugB01 B:2-12,B:250-349 Aspartate Aminotransferase, domain 1                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee........hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhh..eeeeee..................eeeee..........hhhhhhhhhhhhh...eeeee...........hhhhh..eeeee..........eeeeeehhhhhhh........hhhhhhhhhh........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.............eeee.....hhhhhhhhhhh..ee.ee.hhhhh..eeee......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1iug B   2 DWLLTPGPVRLHPKALEALARPQLHHRTEAAREVFLKARGLLREAFRTEGEVLILTGSGTLAMEALVKNLFAPGERVLVPVYGKFSERFYEIALEAGLVVERLDYPYGDTPRPEDVAKEGYAGLLLVHSETSTGALADLPALARAFKEKNPEGLVGADMVTSLLVGEVALEAMGVDAAASGSQkGLMCPPGLGFVALSPRALERLKPRGYYLDLARELKAQKEGESAWTPAINLVLAVAAVLEEVLPRLEEHLALKAWQNALLYGVGEEGGLRPVPKRFSPAVAAFYLPEGVPYARVKEAFAQRGAVIAGGQGPLKGKVFRLSLMGAYDRYEALGVAGMFREVLEEIL 349
                                    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       291       301       311       321       331       341        
                                                                                                                                                                                                                 185-LLP
   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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IUG)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (P83786_THETH | P83786)
molecular function
    GO:0004069    L-aspartate:2-oxoglutarate aminotransferase activity    Catalysis of the reaction: L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate.
    GO:0080130    L-phenylalanine:2-oxoglutarate aminotransferase activity    Catalysis of the reaction: L-phenylalanine + 2-oxoglutarate = phenylpyruvate + L-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: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.

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