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(-) Description

Title :  CRYSTAL STRUCTURE OF L-THREONINE DEHYDROGENASE FROM HYPERTHERMOPHILIC ARCHAEON THERMOPLASMA VOLCANIUM
 
Authors :  K. Yoneda, H. Sakuraba, T. Ohshima
Date :  18 Apr 09  (Deposition) - 31 Mar 10  (Release) - 02 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym./Biol. Unit :  A,B
Keywords :  L-Threonine Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Yoneda, H. Sakuraba, T. Araki, T. Ohshima
Crystal Structure Of Binary And Ternary Complexes Of Archaeal Udp-Galactose 4-Epimerase-Like L-Threonine Dehydrogenase From Thermoplasma Volcanium.
J. Biol. Chem. V. 287 12966 2012
PubMed-ID: 22374996  |  Reference-DOI: 10.1074/JBC.M111.336958

(-) Compounds

Molecule 1 - NDP-SUGAR EPIMERASE
    ChainsA, B
    EC Number1.1.1.103
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificTHERMOPLASMA VOLCANIUM
    Organism Taxid50339
    SynonymL-THREONINE DEHYDROGENASE

 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
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:8 , GLY A:9 , GLN A:10 , ILE A:11 , ASP A:32 , ILE A:33 , LEU A:46 , ASP A:47 , VAL A:48 , LEU A:69 , ALA A:70 , GLY A:71 , LEU A:73 , VAL A:87 , PRO A:110 , SER A:111 , TYR A:137 , LYS A:141 , TYR A:164 , HOH A:328 , HOH A:378 , HOH A:390BINDING SITE FOR RESIDUE NAD A 3001
2AC2SOFTWARESER B:8 , GLY B:9 , GLN B:10 , ILE B:11 , ASP B:32 , ILE B:33 , LEU B:46 , ASP B:47 , VAL B:48 , LEU B:69 , ALA B:70 , GLY B:71 , LEU B:73 , PRO B:110 , SER B:111 , TYR B:137 , LYS B:141 , TYR B:164 , HOH B:362 , HOH B:367 , HOH B:402 , HOH B:445BINDING SITE FOR RESIDUE NAD B 3002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3A1N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3A1N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3A1N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3A1N)

(-) Exons   (0, 0)

(no "Exon" information available for 3A1N)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:315
 aligned with Q97BK3_THEVO | Q97BK3 from UniProtKB/TrEMBL  Length:317

    Alignment length:315
                                    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     
         Q97BK3_THEVO     1 MILVTGSSGQIGTELVPYLAEKYGKKNVIASDIVQRDTGGIKFITLDVSNRDEIDRAVEKYSIDAIFHLAGILSAKGEKDPALAYKVNMNGTYNILEAAKQHRVEKVVIPSTIGVFGPETPKNKVPSITITRPRTMYGVTKIAAELLGQYYYEKFGLDVRSLRYPGIISYKAEPTAGTTDYAVEIFYYAVKREKYKCYLAPNRALPMMYMPDALKALVDLYEADRDKLVLRNGYNVTAYTFTPSELYSKIKERIPEFEIEYKEDFRDKIAATWPESLDSSEASNEWGFSIEYDLDRTIDDMIDHISEKLGIEGKH 315
               SCOP domains d3a1na_ A: automated matches                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhhhhhhhhh...eeeee.........eeee....hhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhh..................hhhhhhhhhhhhhhhhhhhhhh.eeeeeee.eee...........hhhhhhhhhhhh...eee.......eeeeehhhhhhhhhhhhhhhhhhh.....ee...eeehhhhhhhhhhh......eee..hhhhhhhh.......hhhhhhhhh.....hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a1n A   1 MILVTGSSGQIGTELVPYLAEKYGKKNVIASDIVQRDTGGIKFITLDVSNRDEIDRAVEKYSIDAIFHLAGILSAKGEKDPALAYKVNMNGTYNILEAAKQHRVEKVVIPSTIGVFGPETPKNKVPSITITRPRTMYGVTKIAAELLGQYYYEKFGLDVRSLRYPGIISYKAEPTAGTTDYAVEIFYYAVKREKYKCYLAPNRALPMMYMPDALKALVDLYEADRDKLVLRNGYNVTAYTFTPSELYSKIKERIPEFEIEYKEDFRDKIAATWPESLDSSEASNEWGFSIEYDLDRTIDDMIDHISEKLGIEGKH 315
                                    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     

Chain B from PDB  Type:PROTEIN  Length:309
 aligned with Q97BK3_THEVO | Q97BK3 from UniProtKB/TrEMBL  Length:317

    Alignment length:309
                                    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         
         Q97BK3_THEVO     1 MILVTGSSGQIGTELVPYLAEKYGKKNVIASDIVQRDTGGIKFITLDVSNRDEIDRAVEKYSIDAIFHLAGILSAKGEKDPALAYKVNMNGTYNILEAAKQHRVEKVVIPSTIGVFGPETPKNKVPSITITRPRTMYGVTKIAAELLGQYYYEKFGLDVRSLRYPGIISYKAEPTAGTTDYAVEIFYYAVKREKYKCYLAPNRALPMMYMPDALKALVDLYEADRDKLVLRNGYNVTAYTFTPSELYSKIKERIPEFEIEYKEDFRDKIAATWPESLDSSEASNEWGFSIEYDLDRTIDDMIDHISEKL 309
               SCOP domains d3a1nb_ B: automated matches                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhhhhhhhhh...eeeee..........eee....hhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhh..................hhhhhhhhhhhhhhhhhhhhhh.eeeeeee.eee...........hhhhhhhhhhhh..eeee.......eeeeehhhhhhhhhhhhhh........eeee...eeehhhhhhhhhhh.....eeee..hhhhhhhhh......hhhhhhhhh.....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a1n B   1 MILVTGSSGQIGTELVPYLAEKYGKKNVIASDIVQRDTGGIKFITLDVSNRDEIDRAVEKYSIDAIFHLAGILSAKGEKDPALAYKVNMNGTYNILEAAKQHRVEKVVIPSTIGVFGPETPKNKVPSITITRPRTMYGVTKIAAELLGQYYYEKFGLDVRSLRYPGIISYKAEPTAGTTDYAVEIFYYAVKREKYKCYLAPNRALPMMYMPDALKALVDLYEADRDKLVLRNGYNVTAYTFTPSELYSKIKERIPEFEIEYKEDFRDKIAATWPESLDSSEASNEWGFSIEYDLDRTIDDMIDHISEKL 309
                                    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         

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3A1N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3A1N)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q97BK3_THEVO | Q97BK3)
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:0050662    coenzyme binding    Interacting selectively and non-covalently with a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q97BK3_THEVO | Q97BK33a4v 3a9w 3ajr

(-) Related Entries Specified in the PDB File

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