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(-) Description

Title :  D-THREO-3-HYDROXYASPARTATE DEHYDRATASE FROM DELFTIA SP. HT23 COMPLEXED WITH D-ERYTHRO-3-HYDROXYASPARTATE
 
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 :  1.50
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
    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  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
19992Ligand/Ion(3S)-3-HYDROXY-D-ASPARTIC ACID
2MG5Ligand/IonMAGNESIUM ION
3PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:41 , LYS A:43 , ARG A:141 , HIS A:172 , TYR A:177 , SER A:217 , THR A:218 , ARG A:234 , ALA A:235 , GLY A:236 , VAL A:237 , 999 A:403 , HOH A:566 , HOH A:568 , HOH A:603BINDING SITE FOR RESIDUE PLP A 401
2AC2SOFTWAREHIS A:351 , CYS A:353 , 999 A:403 , HOH A:603 , HOH A:611 , HOH B:566BINDING SITE FOR RESIDUE MG A 402
3AC3SOFTWARELYS A:43 , HIS A:140 , ARG A:141 , HIS A:172 , TYR A:177 , HIS A:351 , PLP A:401 , MG A:402 , HOH A:517 , HOH A:581 , HOH A:600 , HOH A:603 , HOH A:611 , ASN B:318 , GLN B:319 , MG B:401 , HOH B:553 , HOH B:566BINDING SITE FOR RESIDUE 999 A 403
4AC4SOFTWAREHIS A:140 , 999 A:403 , HOH A:581 , ASN B:318 , HOH B:736BINDING SITE FOR RESIDUE MG B 401
5AC5SOFTWAREHIS B:41 , LYS B:43 , ARG B:141 , HIS B:172 , TYR B:177 , SER B:217 , THR B:218 , ARG B:234 , ALA B:235 , GLY B:236 , VAL B:237 , 999 B:405 , HOH B:528 , HOH B:544 , HOH B:588BINDING SITE FOR RESIDUE PLP B 402
6AC6SOFTWAREHOH A:563 , HIS B:351 , CYS B:353 , 999 B:405 , HOH B:588 , HOH B:595BINDING SITE FOR RESIDUE MG B 403
7AC7SOFTWAREASN A:318 , HIS B:140 , 999 B:405 , HOH B:677 , HOH B:735BINDING SITE FOR RESIDUE MG B 404
8AC8SOFTWAREASN A:318 , GLN A:319 , HOH A:547 , HOH A:563 , LYS B:43 , HIS B:140 , ARG B:141 , HIS B:172 , TYR B:177 , HIS B:351 , PLP B:402 , MG B:403 , MG B:404 , HOH B:517 , HOH B:582 , HOH B:588 , HOH B:595 , HOH B:677BINDING SITE FOR RESIDUE 999 B 405
9AC9SOFTWAREHOH A:615 , HOH B:651 , HOH B:697BINDING SITE FOR RESIDUE MG B 406

(-) SS Bonds  (0, 0)

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

(-) 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 3WQD)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WQD)

(-) 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.hhhhhhhhhhh....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..hhhhhhh...eeeee.....eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wqd A   2 QDTLLTLDTPAAVIDLDRMQRNIARMQQRMDAQGVRLRPHVKTSKSVPVAAAQRAAGASGITVSTLKEAEQFFAAGTTDILYAVSMAPHRLPQALQLRRRGCDLKLIVDSVAAAQAIAAFGREQGEAFEVWIEIDTDGHRSGVGADDTPLLLAIGRTLHDGGMRLGGVLTHAGSSYELDTPEALQALAERERAGCVQAAEALRAAGLPCPVVSVGSTPTALAASRLDGVTEVRAGVYVFFDLVMRNIGVCAAEDVALSVLATVIGHQADKGWAIVDAGWMAMSRDRGTARQKQDFGYGQVCDLQGRVMPGFVLTGANQEHGILARADGAAEADIATRFPLGTRLRILPNHACATGAQFPAYQALAADGSVQTWERLHGW 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.ee..hhhhh.hhhhhhhhhhhh...eee.hhhhhhhhhhh...eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh...eeeeeee.......ee..hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhh.......ee..hhhhh.hhhhhhhh..hhhhh.eeeeeeeeeeehhhheeee..hhhhhh..hhhhhh.......eee.....eeeeeeeeee....eeeee.......hhhhhh....eeeee..hhhhhhh...eeeee.....eeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wqd B  -8 HHHHHHAMSMQDTLLTLDTPAAVIDLDRMQRNIARMQQRMDAQGVRLRPHVKTSKSVPVAAAQRAAGASGITVSTLKEAEQFFAAGTTDILYAVSMAPHRLPQALQLRRRGCDLKLIVDSVAAAQAIAAFGREQGEAFEVWIEIDTDGHRSGVGADDTPLLLAIGRTLHDGGMRLGGVLTHAGSSYELDTPEALQALAERERAGCVQAAEALRAAGLPCPVVSVGSTPTALAASRLDGVTEVRAGVYVFFDLVMRNIGVCAAEDVALSVLATVIGHQADKGWAIVDAGWMAMSRDRGTARQKQDFGYGQVCDLQGRVMPGFVLTGANQEHGILARADGAAEADIATRFPLGTRLRILPNHACATGAQFPAYQALAADGSVQTWERLHGW 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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  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 3WQD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

(-) Related Entries Specified in the PDB File

3wqc WILD-TYPE ENZYME
3wqe WILD-TYPE ENZYME COMPLEXED WITH D-ALLOTHREONINE
3wqf WILD-TYPE ENZYME IN THE METAL-FREE FORM
3wqg C353A MUTANT IN THE METAL-FREE FORM