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(-) Description

Title :  CRYSTAL STRUCTURE OF HYDROXYNITRILE LYASE FROM MANIHOT ESCULENTA AT 2.2 ANGSTROM RESOLUTION
 
Authors :  H. Lauble, U. Wagner, C. Kratky, B. Mielich, H. Wajant, S. Forster, F. Effenberger
Date :  10 Dec 99  (Deposition) - 07 Dec 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Hydroxynitrile Lyase, Cyanogenesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Lauble, S. Forster, B. Miehlich, H. Wajant, F. Effenberger
Structure Of Hydroxynitrile Lyase From Manihot Esculenta In Complex With Substrates Acetone And Chloroacetone: Implications For The Mechanism Of Cyanogenesis
Acta Crystallogr. , Sect. D V. 57 194 2001
PubMed-ID: 11173464  |  Reference-DOI: 10.1107/S0907444900015766

(-) Compounds

Molecule 1 - HYDROXYNITRILE LYASE
    Chains: A, B
    EC Number: 4.2.1.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: CASSAVA
    Organism Scientific: MANIHOT ESCULENTA
    Organism Taxid: 3983
    Other Details: ACETATE COMPLEX
    Other Details - Source: RECOMBINANT PROTEIN
    Synonym: (S)-ACETONE-CYANOHYDRIN LYASE, (S)-HYDROXYNITRILASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:80 , CYS A:81BINDING SITE FOR RESIDUE ACT A1259
2AC2SOFTWARESER B:80 , CYS B:81 , MET B:147BINDING SITE FOR RESIDUE ACT B1259

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1DWP)

(-) 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:262
 aligned with HNL_MANES | P52705 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:262
                                1                                                                                                                                                                                                                                                                 
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256  
            HNL_MANES     - ----MVTAHFVLIHTICHGAWIWHKLKPALERAGHKVTALDMAASGIDPRQIEQINSFDEYSEPLLTFLEKLPQGEKVIIVGESCAGLNIAIAADRYVDKIAAGVFHNSLLPDTVHSPSYTVEKLLESFPDWRDTEYFTFTNITGETITTMKLGFVLLRENLFTKCTDGEYELAKMVMRKGSLFQNVLAQRPKFTEKGYGSIKKVYIWTDQDKIFLPDFQRWQIANYKPDKVYQVQGGDHKLQLTKTEEVAHILQEVADAYA 258
               SCOP domains d1dwpa_ A: Hydroxynitrile lyase                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1dwpA00 A:-4-258  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee.....hhhhhhhhhhhhhhh..eeeee..........hhhhh.hhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhh..eeeeeee...........hhhhhhhhhhh......eeeeee.....eeeeee.hhhhhhhh.....hhhhhhhhhhhh.....hhhhhhhh......hhhhh.eeeeee......hhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dwp A  -4 PISKMVTAHFVLIHTICHGAWIWHKLKPALERAGHKVTALDMAASGIDPRQIEQINSFDEYSEPLLTFLEKLPQGEKVIIVGESCAGLNIAIAADRYVDKIAAGVFHNSLLPDTVHSPSYTVEKLLESFPDWRDTEYFTFTNITGETITTMKLGFVLLRENLFTKCTDGEYELAKMVMRKGSLFQNVLAQRPKFTEKGYGSIKKVYIWTDQDKIFLPDFQRWQIANYKPDKVYQVQGGDHKLQLTKTEEVAHILQEVADAYA 258
                               ||    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256  
                              -1|                                                                                                                                                                                                                                                                 
                                1                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:258
 aligned with HNL_MANES | P52705 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:258
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250        
            HNL_MANES     1 MVTAHFVLIHTICHGAWIWHKLKPALERAGHKVTALDMAASGIDPRQIEQINSFDEYSEPLLTFLEKLPQGEKVIIVGESCAGLNIAIAADRYVDKIAAGVFHNSLLPDTVHSPSYTVEKLLESFPDWRDTEYFTFTNITGETITTMKLGFVLLRENLFTKCTDGEYELAKMVMRKGSLFQNVLAQRPKFTEKGYGSIKKVYIWTDQDKIFLPDFQRWQIANYKPDKVYQVQGGDHKLQLTKTEEVAHILQEVADAYA 258
               SCOP domains d1dwpb_ B: Hydroxynitrile lyase                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1dwpB00 B:1-258  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhhhhhh..eeeee..........hhhhh.hhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhh..eeeeeee...........hhhhhhhhhhh......eeeeee.....eeeeee.hhhhhhhh.....hhhhhhhhhhhh.....hhhhhhhh......hhhhh.eeeee.......hhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1dwp B   1 MVTAHFVLIHTICHGAWIWHKLKPALERAGHKVTALDMAASGIDPRQIEQINSFDEYSEPLLTFLEKLPQGEKVIIVGESCAGLNIAIAADRYVDKIAAGVFHNSLLPDTVHSPSYTVEKLLESFPDWRDTEYFTFTNITGETITTMKLGFVLLRENLFTKCTDGEYELAKMVMRKGSLFQNVLAQRPKFTEKGYGSIKKVYIWTDQDKIFLPDFQRWQIANYKPDKVYQVQGGDHKLQLTKTEEVAHILQEVADAYA 258
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HNL_MANES | P52705)
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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  4.2.1.37
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 Related Entries

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

UniProtKB/Swiss-Prot
        HNL_MANES | P52705: 1dwo 1dwq 1e89 1e8d 1eb8 1eb9 3rks 3x3h 4yk7

(-) Related Entries Specified in the PDB File

1dwo CRYSTAL STRUCTURE OF HYDROXYNITRILE LYASE FROM MANIHOT ESCULENTA IN COMPLEX WITH SUBSTRATES ACETONE AND CHLOROACETONE:IMPLICATIONS FOR THE MECHANISM OF CYANOGENESIS
1dwq CRYSTAL STRUCTURE OF HYDROXYNITRILE LYASE FROM MANIHOT ESCULENTA IN COMPLEX WITH SUBSTRATES ACETONE AND CHLOROACETONE:IMPLICATIONS FOR THE MECHANISM OF CYANOGENESIS