Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  D-THREO-3-HYDROXYASPARTATE DEHYDRATASE FROM DELFTIA SP. HT23 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 :  2.30
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  (1, 2)

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

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:41 , LYS A:43 , ALA A:84 , 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 , HOH A:603 , HOH A:606BINDING SITE FOR RESIDUE PLP A 401
2AC2SOFTWAREHIS 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 , HOH B:536BINDING SITE FOR RESIDUE PLP B 401

(-) SS Bonds  (0, 0)

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

(-) 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 3WQF)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WQF)

(-) 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:378
                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeeehhhhhhhhhhhhhhhhhh..ee..hhhhh.hhhhhhhhhhh....eee.hhhhhhhhhhh...eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh...eeeeeee.......ee..hhhhhhhhhhhhhhh..eeeeeee.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
                 3wqf A   3 DTLLTLDTPAAVIDLDRMQRNIARMQQRMDAQGVRLRPHVKTSKSVPVAAAQRAAGASGITVSTLKEAEQFFAAGTTDILYAVSMAPHRLPQALQLRRRGCDLKLIVDSVAAAQAIAAFGREQGEAFEVWIEIDTDGHRSGVGADDTPLLLAIGRTLHDGGMRLGGVLTHAGSSYELDTPEALQALAERERAGCVQAAEALRAAGLPCPVVSVGSTPTALAASRLDGVTEVRAGVYVFFDLVMRNIGVCAAEDVALSVLATVIGHQADKGWAIVDAGWMAMSRDRGTARQKQDFGYGQVCDLQGRVMPGFVLTGANQEHGILARADGAAEADIATRFPLGTRLRILPNHACATGAQFPAYQALAADGSVQTWERLHGW 380
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372        


Chain B from PDB  Type:PROTEIN  Length:379
                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeehhhhhhhhhhhhhhhhhh..ee..hhhhh.hhhhhhhhhhh....eee.hhhhhhhhhhh...eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh...eeeeeee.......ee..hhhhhhhhhhhhhhh..eeeeee..........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
                 3wqf B   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
   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 3WQF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    PLP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Thr A:10 - Pro A:11   [ RasMol ]  
    Thr B:10 - Pro B:11   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3wqf
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DTHAD_DELSH | B2DFG5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  4.3.1.27
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  DTHAD_DELSH | B2DFG5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        DTHAD_DELSH | B2DFG5: 3wqc 3wqd 3wqe 3wqg 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
3wqg C353A MUTANT IN THE METAL-FREE FORM