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(-) Description

Title :  STRUCTURE OF A Y149F MUTANT OF EPOXIDE HYDROLASE FROM SOLANUM TUBEROSUM
 
Authors :  A. Naworyta, S. L. Mowbray, M. Widersten, A. Thomaeus
Date :  25 Apr 08  (Deposition) - 08 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Epoxide Hydrolase, Alpha/Beta Hydrolase Fold, Y149F, Proton Wire (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Thomaeus, A. Naworyta, S. L. Mowbray, M. Widersten
Removal Of Distal Protein-Water Hydrogen Bonds In A Plant Epoxide Hydrolase Increases Catalytic Turnover But Decreases Thermostability
Protein Sci. V. 17 1275 2008
PubMed-ID: 18515642  |  Reference-DOI: 10.1110/PS.034173.107
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EPOXIDE HYDROLASE
    Chains: A, B
    EC Number: 3.3.2.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGTACSTEH1-5H-Y149F
    Expression System Strain: XL1-BLUE
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: POTATO
    Organism Scientific: SOLANUM TUBEROSUM
    Strain: LEHMI RUSSET

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1PG4-1Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:105 , TRP A:106 , HIS A:131 , PHE A:132 , SER A:133BINDING SITE FOR RESIDUE PG4 A 656

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:33 -Pro A:34
2Phe B:33 -Pro B:34

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3CXU)

(-) Sequences/Alignments

Asymmetric 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:320
 aligned with Q41415_SOLTU | Q41415 from UniProtKB/TrEMBL  Length:321

    Alignment length:320
                                    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
         Q41415_SOLTU     2 EKIEHKMVAVNGLNMHLAELGEGPTILFIHGFPELWYSWRHQMVYLAERGYRAVAPDLRGYGDTTGAPLNDPSKFSILHLVGDVVALLEAIAPNEEKVFVVAHDWGALIAWHLCLFRPDKVKALVNLSVHFSKRNPKMNVVEGLKAIYGEDHYISRFQVPGEIEAEFAPIGAKSVLKKILTYRDPAPFYFPKGKGLEAIPDAPVALSSWLSEEELDYYANKFEQTGFTGAVNYYRALPINWELTAPWTGAQVKVPTKFIVGEFDLVYHIPGAKEYIHNGGFKKDVPLLEEVVVLEGAAHFVSQERPHEISKHIYDFIQKF 321
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee..eeeeeeee....eeeee.....hhhhhhhhhhhhhh...eeeee..............hhhhhhhhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhh...eeeeeee...........hhhhhhhhhhh..hhhhhh...hhhhhhhh..hhhhhhhhhhh.....................hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee..hhhhhh.hhhhhhhhhhhhhhh......eee.....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cxu A   2 KKIEHKMVAVNGLNMHLAELGEGPTILFIHGFPELWYSWRHQMVYLAERGYRAVAPDLRGYGDTTGAPLNDPSKFSILHLVGDVVALLEAIAPNEEKVFVVAHDWGALIAWHLCLFRPDKVKALVNLSVHFSKRNPKMNVVEGLKAIFGEDHYISRFQVPGEIEAEFAPIGAKSVLKKILTYRDPAPFYFPKGKGLEAIPDAPVALSSWLSEEELDYYANKFEQTGFTGAVNYYRALPINWELTAPWTGAQVKVPTKFIVGEFDLVYHIPGAKEYIHNGGFKKDVPLLEEVVVLEGAAHFVSQERPHEISKHIYDFIQKF 321
                                    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


Chain B from PDB  Type:PROTEIN  Length:319
 aligned with Q41415_SOLTU | Q41415 from UniProtKB/TrEMBL  Length:321

    Alignment length:319
                                    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         
         Q41415_SOLTU     3 KIEHKMVAVNGLNMHLAELGEGPTILFIHGFPELWYSWRHQMVYLAERGYRAVAPDLRGYGDTTGAPLNDPSKFSILHLVGDVVALLEAIAPNEEKVFVVAHDWGALIAWHLCLFRPDKVKALVNLSVHFSKRNPKMNVVEGLKAIYGEDHYISRFQVPGEIEAEFAPIGAKSVLKKILTYRDPAPFYFPKGKGLEAIPDAPVALSSWLSEEELDYYANKFEQTGFTGAVNYYRALPINWELTAPWTGAQVKVPTKFIVGEFDLVYHIPGAKEYIHNGGFKKDVPLLEEVVVLEGAAHFVSQERPHEISKHIYDFIQKF 321
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..eeeeeeee....eeeee.....hhhhhhhhhhhhhh...eeeee..............hhhhhhhhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhh...eeeeeee...........hhhhhhhhhhh..hhhhhh...hhhhhhhh..hhhhhhhhhhh.....................hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee.........hhhhhhhhhhhhhhh......eee.....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cxu B   3 KIEHKMVAVNGLNMHLAELGEGPTILFIHGFPELWYSWRHQMVYLAERGYRAVAPDLRGYGDTTGAPLNDPSKFSILHLVGDVVALLEAIAPNEEKVFVVAHDWGALIAWHLCLFRPDKVKALVNLSVHFSKRNPKMNVVEGLKAIFGEDHYISRFQVPGEIEAEFAPIGAKSVLKKILTYRDPAPFYFPKGKGLEAIPDAPVALSSWLSEEELDYYANKFEQTGFTGAVNYYRALPINWELTAPWTGAQVKVPTKFIVGEFDLVYHIPGAKEYIHNGGFKKDVPLLEEVVVLEGAAHFVSQERPHEISKHIYDFIQKF 321
                                    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
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 3CXU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q41415_SOLTU | Q41415)
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: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.

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  3.3.2.10
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 Related Entries

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

UniProtKB/TrEMBL
        Q41415_SOLTU | Q41415: 2cjp 4ufn 4ufo 4ufp 4uhb 4y9s

(-) Related Entries Specified in the PDB File

2cjp STRUCTURE OF POTATO (SOLANUM TUBEROSUM) EPOXIDE HYDROLASE I (STEH1)