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(-) Description

Title :  CRYSTAL STRUCTURE OF HYDROXYNITRILE LYASE FROM SORGHUM BICOLOR IN COMPLEX WITH INHIBITOR BENZOIC ACID: A NOVEL CYANOGENIC ENZYME
 
Authors :  H. Lauble, B. Miehlich, S. Foerster, H. Wajant, F. Effenberger
Date :  11 Apr 02  (Deposition) - 01 Oct 02  (Release) - 26 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Lyase, Inhibitor Complex, Cyanogenesis Mechanism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Lauble, B. Miehlich, S. Foerster, H. Wajant, F. Effenberger
Crystal Structure Of Hydroxynitrile Lyase From Sorghum Bicolor In Complex With The Inhibitor Benzoic Acid: A Novel Cyanogenic Enzyme
Biochemistry V. 41 12043 2002
PubMed-ID: 12356304  |  Reference-DOI: 10.1021/BI020300O

(-) Compounds

Molecule 1 - P-(S)-HYDROXYMANDELONITRILE LYASE CHAIN A
    Chains: A, C
    EC Number: 4.1.2.11
    Organism Common: SORGHUM
    Organism Scientific: SORGHUM BICOLOR
    Organism Taxid: 4558
    Other Details: ISOENZYME II
    Synonym: HNL, HYDROXYNITRILE LYASE
    Tissue: PRIMARY LEAVES OF SEEDLINGS
 
Molecule 2 - P-(S)-HYDROXYMANDELONITRILE LYASE CHAIN B
    Chains: B, D
    EC Number: 4.1.2.11
    Organism Common: SORGHUM
    Organism Scientific: SORGHUM BICOLOR
    Organism Taxid: 4558
    Other Details: ISOENZYME II
    Synonym: HNL, HYDROXYNITRILE LYASE
    Tissue: PRIMARY LEAVES OF SEEDLINGS

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1BEZ2Ligand/IonBENZOIC ACID
2DKA2Ligand/IonDECANOIC ACID
3FUL2Ligand/IonBETA-L-FUCOSE
4NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:63 , PRO A:64 , ASP A:126 , SER A:158 , HIS A:160 , PHE A:161 , HOH A:2091BINDING SITE FOR RESIDUE BEZ A 601
2AC2SOFTWAREASN A:61 , GLY A:62 , GLU A:157 , ASN A:249 , TYR A:251 , TRP A:270 , HIS B:414BINDING SITE FOR RESIDUE DKA A 701
3AC3SOFTWAREGLY C:63 , PRO C:64 , ASP C:126 , SER C:158 , PHE C:161 , HOH C:2096BINDING SITE FOR RESIDUE BEZ C 602
4AC4SOFTWAREASN C:61 , GLY C:62 , GLU C:157 , ASN C:249 , TYR C:251 , TRP C:270 , HIS D:414 , LEU D:415BINDING SITE FOR RESIDUE DKA C 702
5AC5SOFTWAREGLY A:36 , TYR A:115 , ASN A:117 , SER B:312 , ILE B:314BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 117 RESIDUES 1117 TO 1119
6AC6SOFTWAREGLY A:112 , GLN B:304 , ASN B:310 , GLY B:313 , VAL B:315 , TYR B:317 , PRO B:318 , TRP B:319 , HOH B:2073BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 310 RESIDUES 1310 TO 1310
7AC7SOFTWAREGLY C:36 , TYR C:115 , ASN C:117 , HOH C:2009 , VAL D:311 , SER D:312 , ILE D:314BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 117 RESIDUES 1117 TO 1119
8AC8SOFTWAREPHE C:113 , GLN D:304 , ASN D:310 , GLY D:313 , VAL D:315 , TYR D:317 , PRO D:318 , TRP D:319 , HOH D:2071BINDING SITE FOR MONO-SACCHARIDE NAG D1310 BOUND TO ASN D 310

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:66 -B:322
2A:222 -A:234
3A:258 -B:289
4C:66 -D:322
5C:222 -C:234
6C:258 -D:289

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:63 -Pro A:64
2Ser A:107 -Pro A:108
3Gly C:63 -Pro C:64
4Ser C:107 -Pro C:108

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBOXYPEPT_SER_HISPS00560 Serine carboxypeptidases, histidine active site.HNLS_SORBI459-476
 		  2B:404-421
D:404-421

(-) Exons   (0, 0)

(no "Exon" information available for 1GXS)

(-) Sequences/Alignments

Asymmetric/Biological 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:267
 aligned with HNLS_SORBI | P52708 from UniProtKB/Swiss-Prot  Length:510

    Alignment length:267
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       
           HNLS_SORBI    59 QQEDDRIPGLPGQPNGVAFGMYGGYVTIDDNNGRALYYWFQEADTADPAAAPLVLWLNGGPGCSSIGLGAMQELGPFRVHTNGESLLLNEYAWNKAANILFAESPAGVVFSYSNTSSDLSMGDDKMAQDTYTFLVKWFERFPHYNYREFYIAGESGHFIPQLSQVVYRNRNNSPFINFQGLLVSSGLTNDHEDMIGMFELWWHHGLISDETRDSGLKVCPGTSFMHPTPECTEVWNKALAEQGNINPYTIYTPTCDREPSPYQRRFW 325
               SCOP domains d1gxs.1 A:,B: Hydroxynitrile lyase                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1gxsA00 A:4-270  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..............eeeeeeeee....eeeeeeee.....hhhhh.eeeeee......hhhhhhhhhhh.eee......eee...hhhhh.eeeee.........ee.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhh.......eeeeeeee....hhhhhhhhhhhhhhhh...hhhhhhhhhhhh........hhhhhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gxs A   4 QQEDDRILGLPGQPNGVAFGMYGGYVTIDDNNGRALYYWFQEADTADPAAAPLVLWLNGGPGCSSIGLGAMQELGAFRVHTNGESLLLNEYAWNKAANILFAESPAGVGFSYSNTSSDLSMGDDKMAQDTYTFLVKWFERFPHYNYREFYIAGESGHFIPQLSQVVYRNRNNSPFINFQGLLVSSGLTNDHEDMIGMFESWWHHGLISDETRDSGLKVCPGTSFMHPTPECTEVWNKALAEQGNINPYTIYTPTCDREPSPYQRRFW 270
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       


Chain B from PDB  Type:PROTEIN  Length:158
 aligned with HNLS_SORBI | P52708 from UniProtKB/Swiss-Prot  Length:510

    Alignment length:158
                                   347       357       367       377       387       397       407       417       427       437       447       457       467       477       487        
           HNLS_SORBI   338 LPPYDPCAVFNSINYLNLPEVQTALHANVSGIVEYPWTVCSNTIFDQWGQAADDLLPVYRELIQAGLRVWVYSGDTDSVVPVSSTRRSLAALELPVKTSWYPWYMAPTEREVGGWSVQYEGLTYVSPSGAGHLVPVHRPAQAFLLFKQFLKGEPMPAE 495
               SCOP domains d1gxs.1 A:,B: Hydroxynitrile lyase                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhh.hhhhh........hhhhhhh.......hhhhhhhhhhh..eeeeeee......hhhhhhhhhhh....eeeeeeeee.......eeeeeeee..eeeeee.....hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------CARBOXYPEPT_SER_HI------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gxs B 283 LPPYDPCAVFNSINYLNLPEVQTALHANVSGIVEYPWTVCSNTIFDQWGQAADDLLPVYRELIQAGLRVWVYSGDTDSVVPVSSTRRSLAALELPVKTSWYPWYMAPTEREVGGWSVQYEGLTYVTVRGAGHLVPVHRPAQAFLLFKQFLKGEPMPAE 440
                                   292       302       312       322       332       342       352       362       372       382       392       402       412       422       432        


Chain C from PDB  Type:PROTEIN  Length:267
 aligned with HNLS_SORBI | P52708 from UniProtKB/Swiss-Prot  Length:510

    Alignment length:267
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       
           HNLS_SORBI    59 QQEDDRIPGLPGQPNGVAFGMYGGYVTIDDNNGRALYYWFQEADTADPAAAPLVLWLNGGPGCSSIGLGAMQELGPFRVHTNGESLLLNEYAWNKAANILFAESPAGVVFSYSNTSSDLSMGDDKMAQDTYTFLVKWFERFPHYNYREFYIAGESGHFIPQLSQVVYRNRNNSPFINFQGLLVSSGLTNDHEDMIGMFELWWHHGLISDETRDSGLKVCPGTSFMHPTPECTEVWNKALAEQGNINPYTIYTPTCDREPSPYQRRFW 325
               SCOP domains d1gxs.2 C:,D: Hydroxynitrile lyase                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1gxsC00 C:4-270  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh...............eeeeeeeee....eeeeeeee.....hhhhh.eeeee.......hhhhhhhhhh..eee......eee...hhhhh.eeeee.........ee.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhh.......eeeeeeee....hhhhhhhhhhhhhhhh...hhhhhhhhhhhh........hhhhhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gxs C   4 QQEDDRILGLPGQPNGVAFGMYGGYVTIDDNNGRALYYWFQEADTADPAAAPLVLWLNGGPGCSSIGLGAMQELGAFRVHTNGESLLLNEYAWNKAANILFAESPAGVGFSYSNTSSDLSMGDDKMAQDTYTFLVKWFERFPHYNYREFYIAGESGHFIPQLSQVVYRNRNNSPFINFQGLLVSSGLTNDHEDMIGMFESWWHHGLISDETRDSGLKVCPGTSFMHPTPECTEVWNKALAEQGNINPYTIYTPTCDREPSPYQRRFW 270
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       


Chain D from PDB  Type:PROTEIN  Length:158
 aligned with HNLS_SORBI | P52708 from UniProtKB/Swiss-Prot  Length:510

    Alignment length:158
                                   347       357       367       377       387       397       407       417       427       437       447       457       467       477       487        
           HNLS_SORBI   338 LPPYDPCAVFNSINYLNLPEVQTALHANVSGIVEYPWTVCSNTIFDQWGQAADDLLPVYRELIQAGLRVWVYSGDTDSVVPVSSTRRSLAALELPVKTSWYPWYMAPTEREVGGWSVQYEGLTYVSPSGAGHLVPVHRPAQAFLLFKQFLKGEPMPAE 495
               SCOP domains d1gxs.2 C:,D: Hydroxynitrile lyase                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhh.hhhhh........hhhhhhh.......hhhhhhhhhhh..eeeeeee......hhhhhhhhhhh....eeeeeeee..........eeeeee...eeeee.....hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------CARBOXYPEPT_SER_HI------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gxs D 283 LPPYDPCAVFNSINYLNLPEVQTALHANVSGIVEYPWTVCSNTIFDQWGQAADDLLPVYRELIQAGLRVWVYSGDTDSVVPVSSTRRSLAALELPVKTSWYPWYMAPTEREVGGWSVQYEGLTYVTVRGAGHLVPVHRPAQAFLLFKQFLKGEPMPAE 440
                                   292       302       312       322       332       342       352       362       372       382       392       402       412       422       432
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (HNLS_SORBI | P52708)
molecular function
    GO:0050419    hydroxymandelonitrile lyase activity    Catalysis of the reaction: 4-hydroxymandelonitrile = 4-hydroxybenzaldehyde + hydrocyanate.
    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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