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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE DIENELACTONE HYDROLASE MUTANT(E36D, C123S, A134S, S208G, A229V, K234R)- 1.4 A
 
Authors :  H. -K. Kim, J. -W. Liu, P. D. Carr, D. L. Ollis
Date :  27 Apr 05  (Deposition) - 05 Jul 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha And Beta Proteins, 3-D Structure, Serine Esterase, Hydrolase, Aromatic Hydrocarbons, Catabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. K. Kim, J. W. Liu, P. D. Carr, D. L. Ollis
Following Directed Evolution With Crystallography: Structural Changes Observed In Changing The Substrate Specificity Of Dienelactone Hydrolase.
Acta Crystallogr. , Sect. D V. 61 920 2005
PubMed-ID: 15983415  |  Reference-DOI: 10.1107/S0907444905009042

(-) Compounds

Molecule 1 - CARBOXYMETHYLENEBUTENOLIDASE
    Chains: A
    EC Number: 3.1.1.45
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCY76
    Expression System Strain: DH5ALPHA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CLCD
    Mutation: YES
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
    Synonym: DIENELACTONE HYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:38 , PRO A:75 , ARG A:81 , SER A:203 , ARG A:206 , SER A:209 , GOL A:1101 , GOL A:1104 , HOH A:2774 , HOH A:2865 , HOH A:2869BINDING SITE FOR RESIDUE SO4 A 2719
2AC2SOFTWAREASP A:36 , ILE A:37 , PHE A:38 , ARG A:81 , SER A:123 , HIS A:202 , SO4 A:2719BINDING SITE FOR RESIDUE GOL A 1101
3AC3SOFTWAREGLU A:46 , TRP A:50 , TYR A:122 , ALA A:205 , ASN A:221 , HOH A:2755 , HOH A:2758BINDING SITE FOR RESIDUE GOL A 1102
4AC4SOFTWAREHIS A:172 , PHE A:173 , TYR A:212 , ALA A:217 , ASN A:221 , HOH A:2755 , HOH A:2805BINDING SITE FOR RESIDUE GOL A 1103
5AC5SOFTWAREASP A:36 , PHE A:38 , TYR A:122 , TYR A:145 , SER A:203 , ARG A:206 , SO4 A:2719 , HOH A:2720 , HOH A:2760BINDING SITE FOR RESIDUE GOL A 1104
6AC6SOFTWARETRP A:88 , GLN A:89 , ALA A:214 , SER A:215 , HOH A:2759 , HOH A:2782 , HOH A:2815 , HOH A:2889BINDING SITE FOR RESIDUE GOL A 1105

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZI8)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:26 -Pro A:27

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZI8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZI8)

(-) Exons   (0, 0)

(no "Exon" information available for 1ZI8)

(-) 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:233
 aligned with CLCD_PSEPU | P0A114 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:233
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   
           CLCD_PSEPU     1 MLTEGISIQSYDGHTFGALVGSPAKAPAPVIVIAQEIFGVNAFMRETVSWLVDQGYAAVCPDLYARQAPGTALDPQDERQREQAYKLWQAFDMEAGVGDLEAAIRYARHQPYSNGKVGLVGYCLGGALAFLVAAKGYVDRAVGYYGVGLEKQLKKVPEVKHPALFHMGGQDHFVPAPSRQLITEGFGANPLLQVHWYEEAGHSFARTSSSGYVASAAALANERRLDFLAPLQS 233
               SCOP domains d1zi8a_ A: automated matches                                                                                                                                                                                                              SCOP domains
               CATH domains 1zi8A00 A:1-233  [code=3.40.50.1820, no name defined]                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee.....ee.eeee......eeeeeee......hhhhhhhhhhhhhh..eeeee.hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeehhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhh....eeeeee...............hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zi8 A   1 MLTEGISIQSYDGHTFGALVGSPAKAPAPVIVIAQDIFGVNAFMRETVSWLVDQGYAAVCPDLYARQAPGTALDPQDERQREQAYKLWQAFDMEAGVGDLEAAIRYARHQPYSNGKVGLVGYSLGGALAFLVASKGYVDRAVGYYGVGLEKQLNKVPEVKHPALFHMGGQDHFVPAPSRQLITEGFGANPLLQVHWYEEAGHSFARTGSSGYVASAAALANERTLDFLVPLQS 233
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1ZI8)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CLCD_PSEPU | P0A114)
molecular function
    GO:0052689    carboxylic ester hydrolase activity    Catalysis of the hydrolysis of a carboxylic ester bond.
    GO:0008806    carboxymethylenebutenolidase activity    Catalysis of the reaction: 4-carboxymethylenebut-2-en-4-olide + H2O = 4 oxohex-2-enedioate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
    GO:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.

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    Ala A:26 - Pro A:27   [ RasMol ]  
 

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  1zi8
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  CLCD_PSEPU | P0A114
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  3.1.1.45
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 Related Entries

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

UniProtKB/Swiss-Prot
        CLCD_PSEPU | P0A114: 1ggv 1zi6 1zi9 1zic 1zix 1ziy 1zj4 1zj5 4p92

(-) Related Entries Specified in the PDB File

1din THE SAME PROTEIN WITH ONLY C123S MUTATION
1ggv THE SAME PROTEIN WITH ONLY C123S MUTATION AND WITH PMS MOITY ON THE RESIDUE 123
1zi6 THE SAME PROTEIN, C123S MUTANT AT 1.7 A
1zi9 THE SAME PROTEIN, E36D, C123S MUTANT AT 1.5 A
1zic THE SAME PROTEIN, C123S, R206A MUTANT AT 1.7 A
1zix THE SAME PROTEIN, E36D, R105H, C123S, G211D, K234N MUTANT AT 1.8 A
1ziy THE SAME PROTEIN, C123S MUTANT COMPLEXED WITH PMSF AT 1.9 A
1zj4 THE SAME PROTEIN, E36D, C123S MUTANT COMPLEXED WITH PMSF AT 1.7 A
1zj5 THE SAME PROTEIN, E36D, C123S, A134S, S208G, A229V, K234R MUTANT COMPLEXED WITH PMSF AT 1.7 A