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(-) Description

Title :  HYDROXYNITRILE LYASE FROM HEVEA BRASILIENSIS IN COMPLEX WITH THE NATURAL SUBSTRATE ACETONE CYANOHYDRIN
 
Authors :  K. Gruber, G. Gartler, B. Krammer, H. Schwab, C. Kratky
Date :  12 Feb 04  (Deposition) - 29 Jun 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (1x)
Keywords :  Alpha-Beta Hydrolase Fold, Substrate Complex, Catalytic Triad, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Gruber, G. Gartler, B. Krammer, H. Schwab, C. Kratky
Reaction Mechanism Of Hydroxynitrile Lyases Of The Alpha/Beta-Hydrolase Superfamily: The Three-Dimensional Structure Of The Transient Enzyme-Substrate Complex Certifies The Crucial Role Of Lys236
J. Biol. Chem. V. 279 20501 2004
PubMed-ID: 14998991  |  Reference-DOI: 10.1074/JBC.M401575200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - (S)-ACETONE-CYANOHYDRIN LYASE
    Chains: A
    EC Number: 4.1.2.39
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: BHIL-D2
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Gene: HNL
    Organism Scientific: HEVEA BRASILIENSIS
    Organism Taxid: 3981
    Synonym: HYDROXYNITRILE LYASE
    Tissue: LEAF

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A
Biological Unit 2 (1x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CNH1Ligand/Ion2-HYDROXY-2-METHYLPROPANENITRILE
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1CNH2Ligand/Ion2-HYDROXY-2-METHYLPROPANENITRILE
2SO44Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1CNH1Ligand/Ion2-HYDROXY-2-METHYLPROPANENITRILE
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:23 , LYS A:170 , HOH A:501 , HOH A:585 , HOH A:587 , HOH A:650 , HOH A:741BINDING SITE FOR RESIDUE SO4 A 400
2AC2SOFTWARETHR A:137 , LYS A:138 , ASP A:139 , GLY A:140 , GLY A:232 , GLY A:233 , LYS A:241 , HOH A:720 , HOH A:734 , HOH A:749BINDING SITE FOR RESIDUE SO4 A 401
3AC3SOFTWARETHR A:11 , SER A:80 , CYS A:81 , LEU A:157 , HIS A:235 , LYS A:236BINDING SITE FOR RESIDUE CNH A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SC9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SC9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SC9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1SC9)

(-) Exons   (0, 0)

(no "Exon" information available for 1SC9)

(-) 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:256
 aligned with HNL_HEVBR | P52704 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:256
                                    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      
            HNL_HEVBR     2 AFAHFVLIHTICHGAWIWHKLKPLLEALGHKVTALDLAASGVDPRQIEEIGSFDEYSEPLLTFLEALPPGEKVILVGESCGGLNIAIAADKYCEKIAAAVFHNSVLPDTEHCPSYVVDKLMEVFPDWKDTTYFTYTKDGKEITGLKLGFTLLRENLYTLCGPEEYELAKMLTRKGSLFQNILAKRPFFTKEGYGSIKKIYVWTDQDEIFLPEFQLWQIENYKPDKVYKVEGGDHKLQLTKTKEIAEILQEVADTYN 257
               SCOP domains d1sc9a_ A: Hydroxynitrile lyase                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1sc9A00 A:2-257  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                            CATH domains
               Pfam domains ----Abhydrolase_6-1sc9A01 A:6-248                                                                                                                                                                                                                      --------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhh...eeee...........hhhhh.hhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhh..eeeeeee...........hhhhhhhhhhh......eeeeeee..eeeeeee.hhhhhhhhh....hhhhhhhhhhhh..ee.hhhhhhh.......hhhhh.eeeee.......hhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sc9 A   2 AFAHFVLIHTICHGAWIWHKLKPLLEALGHKVTALDLAASGVDPRQIEEIGSFDEYSEPLLTFLEALPPGEKVILVGESCGGLNIAIAADKYCEKIAAAVFHNSVLPDTEHCPSYVVDKLMEVFPDWKDTTYFTYTKDGKEITGLKLGFTLLRENLYTLCGPEEYELAKMLTRKGSLFQNILAKRPFFTKEGYGSIKKIYVWTDQDEIFLPEFQLWQIENYKPDKVYKVEGGDHKLQLTKTKEIAEILQEVADTYN 257
                                    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
   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  (1, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: AB_hydrolase (347)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (HNL_HEVBR | P52704)
molecular function
    GO:0052891    aliphatic (S)-hydroxynitrile lyase activity    Catalysis of the reaction: an aliphatic (S)-hydroxynitrile = an aliphatic aldehyde or ketone + cyanide.
    GO:0052892    aromatic (S)-hydroxynitrile lyase activity    Catalysis of the reaction: an aromatic (S)-hydroxynitrile = an aromatic aldehyde + cyanide.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.

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  4.1.2.39
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 Related Entries

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

UniProtKB/Swiss-Prot
        HNL_HEVBR | P52704: 1qj4 1sci 1sck 1scq 1yas 1yb6 1yb7 2g4l 2yas 3c6x 3c6y 3c6z 3c70 3yas 4yas 5yas 6yas 7yas

(-) Related Entries Specified in the PDB File

1qj4
1sci THE SAME PROTEIN, K236L MUTANT
1sck THE SAME PROTEIN, K236L MUTANT COMPLEXED WITH ACETONE
1scq THE SAME PROTEIN, K236L MUTANT COMPLEXED WITH ACETONECYANOHYDRIN
1yas
2yas
3yas
4yas
5yas
6yas
7yas