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(-) Description

Title :  D-THREO-3-HYDROXYASPARTATE DEHYDRATASE C353A MUTANT IN THE METAL-FREE FORM
 
Authors :  Y. Yasutake, Y. Matsumoto, M. Wada
Date :  25 Jan 14  (Deposition) - 28 Jan 15  (Release) - 26 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dehydratase, Plp, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Matsumoto, Y. Yasutake, Y. Takeda, T. Tamura, A. Yokota, M. Wada
Structural Insights Into The Substrate Stereospecificity Of D-Threo-3-Hydroxyaspartate Dehydratase From Delftia Sp. Ht23: A Useful Enzyme For The Synthesis Of Optically Pure L-Threo- And D-Erythro-3-Hydroxyaspartate
Appl. Microbiol. Biotechnol. V. 99 7137 2015
PubMed-ID: 25715785  |  Reference-DOI: 10.1007/S00253-015-6479-3

(-) Compounds

Molecule 1 - D-THREO-3-HYDROXYASPARTATE DEHYDRATASE
    Chains: A, B
    EC Number: 4.3.1.27
    Engineered: YES
    Expression System: RHODOCOCCUS ERYTHROPOLIS
    Expression System Plasmid: PTIP-QC2
    Expression System Strain: L88
    Expression System Taxid: 1833
    Expression System Vector Type: PLASMID
    Gene: DTHADH
    Mutation: YES
    Organism Scientific: DELFTIA
    Organism Taxid: 518882
    Strain: HT23
    Synonym: D-THA DH, D-THA DEHYDRATASE, THREO-3-HYDROXY-D-ASPARTATE AMMONIA-LYASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:41 , LYS A:43 , ARG A:141 , HIS A:172 , TYR A:177 , GLY A:216 , SER A:217 , THR A:218 , ARG A:234 , ALA A:235 , GLY A:236 , VAL A:237 , GOL A:402 , HOH A:522 , HOH A:646 , HOH A:698 , HOH A:728 , HOH A:729BINDING SITE FOR RESIDUE PLP A 401
2AC2SOFTWARELYS A:43 , HIS A:140 , ARG A:141 , HIS A:172 , GLY A:174 , TYR A:177 , PLP A:401 , HOH A:728 , ASN B:318BINDING SITE FOR RESIDUE GOL A 402
3AC3SOFTWAREHIS B:41 , LYS B:43 , ARG B:141 , HIS B:172 , TYR B:177 , GLY B:216 , SER B:217 , THR B:218 , ARG B:234 , ALA B:235 , GLY B:236 , VAL B:237 , GOL B:402 , HOH B:517 , HOH B:618 , HOH B:673 , HOH B:701 , HOH B:702BINDING SITE FOR RESIDUE PLP B 401
4AC4SOFTWARELYS B:43 , HIS B:140 , ARG B:141 , HIS B:172 , GLY B:174 , PLP B:401 , HOH B:701BINDING SITE FOR RESIDUE GOL B 402
5AC5SOFTWAREASP A:303 , ARG A:338 , HOH A:671 , HOH A:709 , ALA B:154 , ARG B:157 , THR B:158 , ASP B:161 , HOH B:552 , HOH B:647BINDING SITE FOR RESIDUE GOL B 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:10 -Pro A:11
2Thr B:10 -Pro B:11

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WQG)

(-) 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:379
                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeehhhhhhhhhhhhhhhhhhh.ee..hhhhh.hhhhhhhhhhhh...eee.hhhhhhhhhhh...eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh...eeeeeee.......ee..hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhh.......ee..hhhhh.hhhhhhhh..hhhhh.eeeeeeeeeee....eeee..hhhhhh..hhhhhh.......eee.....eeeeeeeeee....eeeee.......hhhhhh....eeeee..hhhhhhhh..eeeee.....eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wqg A   2 QDTLLTLDTPAAVIDLDRMQRNIARMQQRMDAQGVRLRPHVKTSKSVPVAAAQRAAGASGITVSTLKEAEQFFAAGTTDILYAVSMAPHRLPQALQLRRRGCDLKLIVDSVAAAQAIAAFGREQGEAFEVWIEIDTDGHRSGVGADDTPLLLAIGRTLHDGGMRLGGVLTHAGSSYELDTPEALQALAERERAGCVQAAEALRAAGLPCPVVSVGSTPTALAASRLDGVTEVRAGVYVFFDLVMRNIGVCAAEDVALSVLATVIGHQADKGWAIVDAGWMAMSRDRGTARQKQDFGYGQVCDLQGRVMPGFVLTGANQEHGILARADGAAEADIATRFPLGTRLRILPNHAAATGAQFPAYQALAADGSVQTWERLHGW 380
                                    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       351       361       371         


Chain B from PDB  Type:PROTEIN  Length:389
                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.........eeeeehhhhhhhhhhhhhhhhhhh.eeee.hhhh.hhhhhhhhhhh....eee.hhhhhhhhhhh...eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh...eeeeeee.......ee..hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhh.......eeeehhhhh.hhhhhhhh..hhhhh.eeeeeeeeeeehhhheeee..hhhhhh..hhhhhh.......eeee....eeeeeeeeee....eeeee.......hhhhhh....eeeee..hhhhhhh...eeeee.....eeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wqg B  -8 HHHHHHAMSMQDTLLTLDTPAAVIDLDRMQRNIARMQQRMDAQGVRLRPHVKTSKSVPVAAAQRAAGASGITVSTLKEAEQFFAAGTTDILYAVSMAPHRLPQALQLRRRGCDLKLIVDSVAAAQAIAAFGREQGEAFEVWIEIDTDGHRSGVGADDTPLLLAIGRTLHDGGMRLGGVLTHAGSSYELDTPEALQALAERERAGCVQAAEALRAAGLPCPVVSVGSTPTALAASRLDGVTEVRAGVYVFFDLVMRNIGVCAAEDVALSVLATVIGHQADKGWAIVDAGWMAMSRDRGTARQKQDFGYGQVCDLQGRVMPGFVLTGANQEHGILARADGAAEADIATRFPLGTRLRILPNHAAATGAQFPAYQALAADGSVQTWERLHGW 380
                                     1        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       351       361       371
   Legend:   → Mismatch (orange background)
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  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 3WQG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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  DTHAD_DELSH | B2DFG5
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 Related Entries

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

UniProtKB/Swiss-Prot
        DTHAD_DELSH | B2DFG5: 3wqc 3wqd 3wqe 3wqf 4pb3 4pb4 4pb5

(-) Related Entries Specified in the PDB File

3wqc WILD-TYPE ENZYME
3wqd WILD-TYPE ENZYME COMPLEXED WITH D-ERYTHRO-3-HYDROXYASPARTATE
3wqe WILD-TYPE ENZYME COMPLEXED WITH D-ALLOTHREONINE
3wqf WILD-TYPE ENZYME IN THE METAL-FREE FORM