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(-) Description

Title :  CRYSTAL STRUCTURE OF L-3-HYDROXYNORVALINE BOUND L-THREONINE DEHYDROGENASE (Y137F) FROM HYPERTHERMOPHILIC ARCHAEON THERMOPLASMA VOLCANIUM
 
Authors :  K. Yoneda, H. Sakuraba, T. Ohshima
Date :  14 Jun 10  (Deposition) - 15 Jun 11  (Release) - 02 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym./Biol. Unit :  A,B
Keywords :  L-Threonine Dehydrogenase, Thermoplasma Volcanium, L-3- Hydroxynorvaline, 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
    Chains: A, B
    EC Number: 1.1.1.103
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: THERMOPLASMA VOLCANIUM
    Organism Taxid: 273116
    Strain: GSS1
    Synonym: L-THREONINE DEHYDROGENASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3VAH2Ligand/Ion(3R)-3-HYDROXY-L-NORVALINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:74 , THR A:112 , ILE A:113 , PHE A:137 , GLY A:177 , THR A:178 , THR A:179 , NAD A:3001BINDING SITE FOR RESIDUE VAH A 318
2AC2SOFTWARESER 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 , PHE A:137 , LYS A:141 , TYR A:164 , PRO A:165 , ILE A:167 , VAH A:318 , HOH A:348 , HOH A:352 , HOH A:359 , HOH A:360 , HOH A:450BINDING SITE FOR RESIDUE NAD A 3001
3AC3SOFTWAREGLU A:173 , TYR A:187 , SER A:248 , HOH A:429BINDING SITE FOR RESIDUE MPD A 5276
4AC4SOFTWARESER B:74 , THR B:112 , ILE B:113 , PHE B:137 , THR B:178 , THR B:179 , NAD B:3002BINDING SITE FOR RESIDUE VAH B 318
5AC5SOFTWARESER 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 , VAL B:87 , PRO B:110 , SER B:111 , THR B:112 , PHE B:137 , LYS B:141 , TYR B:164 , PRO B:165 , ILE B:167 , VAH B:318 , HOH B:347 , HOH B:349 , HOH B:362 , HOH B:375BINDING SITE FOR RESIDUE NAD B 3002
6AC6SOFTWAREGLU A:153 , LYS A:154 , ASP A:224 , HOH A:324 , ARG B:134 , LYS B:268 , ILE B:269 , THR B:272BINDING SITE FOR RESIDUE MPD B 5277

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3AJR)

(-) 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:314
 aligned with Q97BK3_THEVO | Q97BK3 from UniProtKB/TrEMBL  Length:317

    Alignment length:314
                                    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 MILVTGSSGQIGTELVPYLAEKYGKKNVIASDIVQRDTGGIKFITLDVSNRDEIDRAVEKYSIDAIFHLAGILSAKGEKDPALAYKVNMNGTYNILEAAKQHRVEKVVIPSTIGVFGPETPKNKVPSITITRPRTMYGVTKIAAELLGQYYYEKFGLDVRSLRYPGIISYKAEPTAGTTDYAVEIFYYAVKREKYKCYLAPNRALPMMYMPDALKALVDLYEADRDKLVLRNGYNVTAYTFTPSELYSKIKERIPEFEIEYKEDFRDKIAATWPESLDSSEASNEWGFSIEYDLDRTIDDMIDHISEKLGIEGK 314
               SCOP domains d3ajra_ A: automated matches                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhhhhh...eeeee..........eee....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
                 3ajr A   1 MILVTGSSGQIGTELVPYLAEKYGKKNVIASDIVQRDTGGIKFITLDVSNRDEIDRAVEKYSIDAIFHLAGILSAKGEKDPALAYKVNMNGTYNILEAAKQHRVEKVVIPSTIGVFGPETPKNKVPSITITRPRTMFGVTKIAAELLGQYYYEKFGLDVRSLRYPGIISYKAEPTAGTTDYAVEIFYYAVKREKYKCYLAPNRALPMMYMPDALKALVDLYEADRDKLVLRNGYNVTAYTFTPSELYSKIKERIPEFEIEYKEDFRDKIAATWPESLDSSEASNEWGFSIEYDLDRTIDDMIDHISEKLGIEGK 314
                                    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:308
 aligned with Q97BK3_THEVO | Q97BK3 from UniProtKB/TrEMBL  Length:317

    Alignment length:308
                                    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 MILVTGSSGQIGTELVPYLAEKYGKKNVIASDIVQRDTGGIKFITLDVSNRDEIDRAVEKYSIDAIFHLAGILSAKGEKDPALAYKVNMNGTYNILEAAKQHRVEKVVIPSTIGVFGPETPKNKVPSITITRPRTMYGVTKIAAELLGQYYYEKFGLDVRSLRYPGIISYKAEPTAGTTDYAVEIFYYAVKREKYKCYLAPNRALPMMYMPDALKALVDLYEADRDKLVLRNGYNVTAYTFTPSELYSKIKERIPEFEIEYKEDFRDKIAATWPESLDSSEASNEWGFSIEYDLDRTIDDMIDHISEK 308
               SCOP domains d3ajrb_ B: automated matches                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhhhhh...eeeee..........eee....hhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhh..................hhhhhhhhhhhhhhhhhhhhhh.eeeeeee.eee...........hhhhhhhhhhhh...eee.......eeeeehhhhhhhhhhhhhhhhhhh...eeee...eeehhhhhhhhhhhhh....eee..hhhhhhhhh......hhhhhhhhh.....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ajr B   1 MILVTGSSGQIGTELVPYLAEKYGKKNVIASDIVQRDTGGIKFITLDVSNRDEIDRAVEKYSIDAIFHLAGILSAKGEKDPALAYKVNMNGTYNILEAAKQHRVEKVVIPSTIGVFGPETPKNKVPSITITRPRTMFGVTKIAAELLGQYYYEKFGLDVRSLRYPGIISYKAEPTAGTTDYAVEIFYYAVKREKYKCYLAPNRALPMMYMPDALKALVDLYEADRDKLVLRNGYNVTAYTFTPSELYSKIKERIPEFEIEYKEDFRDKIAATWPESLDSSEASNEWGFSIEYDLDRTIDDMIDHISEK 308
                                    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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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  3ajr
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 Related Entries

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

UniProtKB/TrEMBL
        Q97BK3_THEVO | Q97BK3: 3a1n 3a4v 3a9w

(-) Related Entries Specified in the PDB File

3a1n L-THREONINE DEHYDROGENASE FROM HYPERTHERMOPHILIC ARCHAEON THERMOPLASMA VOLCANIUM (WILD)
3a4v L-THREONINE DEHYDROGENASE FROM HYPERTHERMOPHILIC ARCHAEON THERMOPLASMA VOLCANIUM (WILD+PYRUVATE)
3a9w L-THREONINE DEHYDROGENASE FROM HYPERTHERMOPHILIC ARCHAEON THERMOPLASMA VOLCANIUM (Y137F+L-THREONINE)