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(-) Description

Title :  CRYSTAL STRUCTURE OF ALANINE-PYRUVATE AMINOTRANSFERASE WITH 2-METHYLSERINE
 
Authors :  I. Miyahara, M. Matsumura, M. Goto, R. Omi, K. Hirotsu, Riken Structur Genomics/Proteomics Initiative (Rsgi)
Date :  02 Apr 07  (Deposition) - 15 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminotransferase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Miyahara, M. Matsumura, M. Goto, R. Omi, K. Hirotsu
Hypothetical Alanine Aminotransferase (Ttha0173) From Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - AMINOTRANSFERASE, CLASS V
    Chains: A, B
    EC Number: 2.6.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET11A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1MMM1Ligand/Ion(S,E)-3-HYDROXY-2-((3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL)METHYLENEAMINO)-2-METHYLPROPANOIC ACID
2PMP1Ligand/Ion4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:6 , GLY A:7 , SER A:60 , GLY A:61 , SER A:62 , PHE A:85 , THR A:135 , ASP A:160 , GLN A:185 , LYS A:186 , ARG A:326 , HOH A:4072 , HOH A:4110 , HIS B:26 , TYR B:229 , HIS B:231 , THR B:232BINDING SITE FOR RESIDUE MMM A 500
2AC2SOFTWARETYR A:229 , HIS A:231 , THR A:232 , SER B:60 , GLY B:61 , SER B:62 , MET B:65 , PHE B:85 , GLY B:133 , THR B:135 , ASP B:160 , GLN B:185 , LYS B:186BINDING SITE FOR RESIDUE PMP B 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:7 -Pro A:8
2Gly A:75 -Pro A:76
3Gly B:7 -Pro B:8
4Gly B:75 -Pro B:76

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YRI)

(-) 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:352
 aligned with Q5SLX0_THET8 | Q5SLX0 from UniProtKB/TrEMBL  Length:353

    Alignment length:352
                                    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       290       300       310       320       330       340       350  
         Q5SLX0_THET8     1 MLLLTPGPTPIPERVQKALLRPMRGHLDPEVLRVNRAIQERLAALFDPGEGALVAALAGSGSLGMEAGLANLDRGPVLVLVNGAFSQRVAEMAALHGLDPEVLDFPPGEPVDPEAVARALKRRRYRMVALVHGETSTGVLNPAEAIGALAKEAGALFFLDAVTTLGMLPFSMRAMGVDYAFTGSQKCLSAPPGLAPIAASLEARKAFTGKRGWYLDLARVAEHWERGGYHHTTPVLLHYALLEALDLVLEEGVAARERRAREVYAWVLEELKARGFRPYPKASPLPTVLVVRPPEGVDADRLVRALYAEGVAVAGGIGPTRGQVLRLGLMGEGARREAYQAFLKALDRALAL 352
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----------2yriA02 A:12-252 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                             ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee........hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhh...eeeee..........hhhhhhhhhhhh..eeeee..........hhhhhh..eee.............eeeeehhhhhhhh........hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.........eeeee.....hhhhhhhhhhhh.ee.ee.hhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yri A   1 MLLLTPGPTPIPERVQKALLRPMRGHLDPEVLRVNRAIQERLAALFDPGEGALVAALAGSGSLGMEAGLANLDRGPVLVLVNGAFSQRVAEMAALHGLDPEVLDFPPGEPVDPEAVARALKRRRYRMVALVHGETSTGVLNPAEAIGALAKEAGALFFLDAVTTLGMLPFSMRAMGVDYAFTGSQKCLSAPPGLAPIAASLEARKAFTGKRGWYLDLARVAEHWERGGYHHTTPVLLHYALLEALDLVLEEGVAARERRAREVYAWVLEELKARGFRPYPKASPLPTVLVVRPPEGVDADRLVRALYAEGVAVAGGIGPTRGQVLRLGLMGEGARREAYQAFLKALDRALAL 352
                                    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       290       300       310       320       330       340       350  


Chain B from PDB  Type:PROTEIN  Length:352
 aligned with Q5SLX0_THET8 | Q5SLX0 from UniProtKB/TrEMBL  Length:353

    Alignment length:352
                                    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       290       300       310       320       330       340       350  
         Q5SLX0_THET8     1 MLLLTPGPTPIPERVQKALLRPMRGHLDPEVLRVNRAIQERLAALFDPGEGALVAALAGSGSLGMEAGLANLDRGPVLVLVNGAFSQRVAEMAALHGLDPEVLDFPPGEPVDPEAVARALKRRRYRMVALVHGETSTGVLNPAEAIGALAKEAGALFFLDAVTTLGMLPFSMRAMGVDYAFTGSQKCLSAPPGLAPIAASLEARKAFTGKRGWYLDLARVAEHWERGGYHHTTPVLLHYALLEALDLVLEEGVAARERRAREVYAWVLEELKARGFRPYPKASPLPTVLVVRPPEGVDADRLVRALYAEGVAVAGGIGPTRGQVLRLGLMGEGARREAYQAFLKALDRALAL 352
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----------2yriB02 B:12-252 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                             ---------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Aminotran_5-2yriB01 B:1-330                                                                                                                                                                                                                                                                                                               ---------------------- Pfam domains (1)
           Pfam domains (2) Aminotran_5-2yriB02 B:1-330                                                                                                                                                                                                                                                                                                               ---------------------- Pfam domains (2)
         Sec.struct. author .ee........hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhh...eeeee.......hhhhhhhhh......eeeee.ee....ee.hhhhhhhhhhhhh.eeeee..................eee............eeeeeehhhhhhhh........hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.........eeeee.....hhhhhhhhhhhh.ee.ee.hhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yri B   1 MLLLTPGPTPIPERVQKALLRPMRGHLDPEVLRVNRAIQERLAALFDPGEGALVAALAGSGSLGMEAGLANLDRGPVLVLVNGAFSQRVAEMAALHGLDPEVLDFPPGEPVDPEAVARALKRRRYRMVALVHGETSTGVLNPAEAIGALAKEAGALFFLDAVTTLGMLPFSMRAMGVDYAFTGSQKCLSAPPGLAPIAASLEARKAFTGKRGWYLDLARVAEHWERGGYHHTTPVLLHYALLEALDLVLEEGVAARERRAREVYAWVLEELKARGFRPYPKASPLPTVLVVRPPEGVDADRLVRALYAEGVAVAGGIGPTRGQVLRLGLMGEGARREAYQAFLKALDRALAL 352
                                    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       290       300       310       320       330       340       350
   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 2YRI)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5SLX0_THET8 | Q5SLX0)
molecular function
    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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 Related Entries

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UniProtKB/TrEMBL
        Q5SLX0_THET8 | Q5SLX0: 2yrr

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