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(-) Description

Title :  HYDROXYNITRILE LYASE FROM HEVEA BRASILIENSIS COMPLEXED WITH RHODANIDE
 
Authors :  K. Gruber, M. Gugganig, C. Kratky
Date :  11 Mar 99  (Deposition) - 13 Oct 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.72
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Biol. Unit 3:  A  (2x)
Keywords :  Oxynitrilase, Cyanogenesis, Cyanhydrin Formation, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Zuegg, K. Gruber, M. Gugganig, U. G. Wagner, C. Kratky
Three-Dimensional Structures Of Enzyme-Substrate Complexes Of The Hydroxynitrile Lyase From Hevea Brasiliensis.
Protein Sci. V. 8 1990 1999
PubMed-ID: 10548044
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (HYDROXYNITRILE LYASE)
    Chains: A
    EC Number: 4.1.2.39
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Gene: HNL
    Expression System Plasmid: BHIL-D2
    Expression System Taxid: 4922
    Gene: HNL
    Organ: LEAF
    Organism Scientific: HEVEA BRASILIENSIS
    Organism Taxid: 3981
    Synonym: OXYNITRILE LYASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A
Biological Unit 3 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1SCN1Ligand/IonTHIOCYANATE ION
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1SCN1Ligand/IonTHIOCYANATE ION
2SO44Ligand/IonSULFATE ION
Biological Unit 2 (2, 10)
No.NameCountTypeFull Name
1SCN2Ligand/IonTHIOCYANATE ION
2SO48Ligand/IonSULFATE ION
Biological Unit 3 (2, 10)
No.NameCountTypeFull Name
1SCN2Ligand/IonTHIOCYANATE ION
2SO48Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:11 , SER A:80 , LEU A:157 , HIS A:235 , LYS A:236BINDING SITE FOR RESIDUE SCN A 300
2AC2SOFTWARETHR A:137 , ASP A:139 , GLY A:140 , GLY A:232 , GLY A:233 , LYS A:241 , HOH A:670 , HOH A:731 , HOH A:787BINDING SITE FOR RESIDUE SO4 A 400
3AC3SOFTWARELYS A:23 , LYS A:170 , HOH A:510 , HOH A:583 , HOH A:648 , HOH A:675BINDING SITE FOR RESIDUE SO4 A 401
4AC4SOFTWARELYS A:141 , ASN A:181 , LYS A:185 , HOH A:596 , HOH A:678 , HOH A:700 , HOH A:807BINDING SITE FOR RESIDUE SO4 A 402
5AC5SOFTWARETYR A:116 , TRP A:217 , LYS A:229 , HOH A:654 , HOH A:674 , HOH A:696 , HOH A:758BINDING SITE FOR RESIDUE SO4 A 403
6CATAUTHORSER A:80 , ASP A:207 , HIS A:235ACTIVE SITE

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YAS)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2YAS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YAS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YAS)

(-) Exons   (0, 0)

(no "Exon" information available for 2YAS)

(-) 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 d2yasa_ A: Hydroxynitrile lyase                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2yasA00 A:2-257  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                            CATH domains
               Pfam domains ----Abhydrolase_6-2yasA01 A:6-248                                                                                                                                                                                                                      --------- Pfam domains
         Sec.struct. author ...eeeee......hhhh..hhhhhhhh..eeee............hhh...hhhh.hhhhhhhh.......eeeeeehhhhhhhhhhhhhhhhheeeeeee............hhhhhhhhh.......eeeeeee..eeeeeee..hhhhhhh......hhhhhhhhhh.......hhhhhh........hhh..eeeee........hhhhhhhhhh....eeee.......hhhh.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yas 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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  2yas
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 Related Entries

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

UniProtKB/Swiss-Prot
        HNL_HEVBR | P52704: 1qj4 1sc9 1sci 1sck 1scq 1yas 1yb6 1yb7 2g4l 3c6x 3c6y 3c6z 3c70 3yas 4yas 5yas 6yas 7yas

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