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(-) Description

Title :  ANOMALOUS SUBSTRUCTURE OF HYDROXYNITRILE LYASE
 
Authors :  C. Mueller-Dieckmann, M. S. Weiss
Date :  22 Feb 06  (Deposition) - 20 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Anomalous Substructure Of Hydroxynitrile Lyase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Mueller-Dieckmann, S. Panjikar, A. Schmidt, S. Mueller, J. Kuper, A. Geerlof, M. Wilmanns, R. K. Singh, P. A. Tucker, M. S. Weiss
On The Routine Use Of Soft X-Rays In Macromolecular Crystallography. Part Iv. Efficient Determination Of Anomalous Substructures In Biomacromolecules Using Longer X-Ray Wavelengths.
Acta Crystallogr. , Sect. D V. 63 366 2007
PubMed-ID: 17327674  |  Reference-DOI: 10.1107/S0907444906055624

(-) Compounds

Molecule 1 - (S)-ACETONE-CYANOHYDRIN LYASE
    Chains: A
    EC Number: 4.1.2.39
    Organism Scientific: HEVEA BRASILIENSIS
    Organism Taxid: 3981
    Synonym: S-HYDROXYNITRILE LYASE, S-HYDROXYNITRILASE, OXYNITRILASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2CME1Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
3SO45Ligand/IonSULFATE ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CME2Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
3SO410Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:23 , LYS A:170 , HOH A:336 , HOH A:350 , HOH A:456BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWARETHR A:137 , LYS A:138 , ASP A:139 , GLY A:140 , GLY A:233 , LYS A:241BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWARETYR A:116 , TRP A:217 , LYS A:229 , HOH A:394BINDING SITE FOR RESIDUE SO4 A 303
4AC4SOFTWARELYS A:141 , ASN A:181 , LYS A:185 , HOH A:390 , HOH A:453BINDING SITE FOR RESIDUE SO4 A 304
5AC5SOFTWARETHR A:110 , GLY A:195 , TYR A:222 , HOH A:407BINDING SITE FOR RESIDUE SO4 A 305
6AC6SOFTWARETHR A:190 , LYS A:191BINDING SITE FOR RESIDUE CL A 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2G4L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2G4L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2G4L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2G4L)

(-) Exons   (0, 0)

(no "Exon" information available for 2G4L)

(-) 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 d2g4la_ A: Hydroxynitrile lyase                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2g4lA00 A:2-257  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhh..eeee...........hhhhh.hhhhhhhhhhhhhhh......eeeeeeehhhhhhhhhhhhhh..eeeeeeeee.........hhhhhhhhhhh......eeeeeee..eeeeeee.hhhhhhhhh....hhhhhhhhhhhh.....hhhhhhhh......hhhhh.eeeee.......hhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g4l 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      
                                                                                                                       94-CME
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2G4L)

(-) 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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 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 2yas 3c6x 3c6y 3c6z 3c70 3yas 4yas 5yas 6yas 7yas

(-) Related Entries Specified in the PDB File

2g4h 2g4i 2g4j 2g4k 2g4m 2g4n 2g4o 2g4p 2g4q 2g4r 2g4s 2g4t 2g4u 2g4v 2g4w 2g4x 2g4y 2g4z 2g51 2g52 2g55