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(-) Description

Title :  CRYSTAL STRUCTURE OF B. SUBTILIS LUXS IN COMPLEX WITH A CATALYTIC 2-KETONE INTERMEDIATE
 
Authors :  R. Rajan, J. Zhu, X. Hu, D. Pei, C. E. Bell
Date :  22 Dec 04  (Deposition) - 15 Mar 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Quorum Sensing, Metalloenzyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Rajan, J. Zhu, X. Hu, D. Pei, C. E. Bell
Crystal Structure Of S-Ribosylhomocysteinase (Luxs) In Complex With A Catalytic 2-Ketone Intermediate.
Biochemistry V. 44 3745 2005
PubMed-ID: 15751951  |  Reference-DOI: 10.1021/BI0477384

(-) Compounds

Molecule 1 - S-RIBOSYLHOMOCYSTEINASE
    Chains: A
    EC Number: 3.13.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: LUXS
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: AUTOINDUCER-2 PRODUCTION PROTEIN LUXS, AI-2 SYNTHESIS PROTEIN

 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, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1CO1Ligand/IonCOBALT (II) ION
2KRI1Ligand/Ion(S)-2-AMINO-4-[(2S,3R)-2,3,5-TRIHYDROXY-4-OXO-PENTYL]MERCAPTO-BUTYRIC ACID
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2KRI2Ligand/Ion(S)-2-AMINO-4-[(2S,3R)-2,3,5-TRIHYDROXY-4-OXO-PENTYL]MERCAPTO-BUTYRIC ACID
3SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:54 , HIS A:58 , CYS A:126 , KRI A:401BINDING SITE FOR RESIDUE CO A 501
2AC2SOFTWAREHIS A:21 , LYS A:49 , THR A:97 , SER A:98 , HOH A:229 , HOH A:283BINDING SITE FOR RESIDUE SO4 A 601
3AC3SOFTWARESER A:6 , HIS A:11 , ARG A:39 , HIS A:54 , GLU A:57 , ARG A:65 , ASP A:78 , ILE A:79 , SER A:80 , ALA A:84 , CYS A:126 , GLY A:127 , HOH A:200 , HOH A:252 , CO A:501BINDING SITE FOR RESIDUE KRI A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:16 -Pro A:17

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YCL)

(-) 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:154
 aligned with LUXS_BACSU | O34667 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:154
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153    
           LUXS_BACSU     4 VESFELDHNAVVAPYVRHCGVHKVGTDGVVNKFDIRFCQPNKQAMKPDTIHTLEHLLAFTIRSHAEKYDHFDIIDISPMGCQTGYYLVVSGEPTSAEIVDLLEDTMKEAVEITEIPAANEKQCGQAKLHDLEGAKRLMRFWLSQDKEELLKVFG 157
               SCOP domains d1ycla_ A: Autoinducer-2 production protein LuxS                                                                                                           SCOP domains
               CATH domains 1yclA00 A:4-157  [code=3.30.1360.80, no name defined]                                                                                                      CATH domains
               Pfam domains LuxS-1yclA01 A:4-156                                                                                                                                     - Pfam domains
         Sec.struct. author hhhhhh........eeeeeeeeee...eeeeeeeee.........hhhhhhhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeeee..hhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhh.hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ycl A   4 VESFELDHNAVVAPYVRHCGVHKVGTDGVVNKFDIRFCQPNKQAMKPDTIHTLEHLLAFTIRSHAEKYDHFDIIDISPMGAQTGYYLVVSGEPTSAEIVDLLEDTMKEAVEITEIPAANEKQCGQAKLHDLEGAKRLMRFWLSQDKEELLKVFG 157
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153
   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) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Peptidase_ME (35)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (LUXS_BACSU | O34667)
molecular function
    GO:0043768    S-ribosylhomocysteine lyase activity    Catalysis of the reaction: S-(5-deoxy-D-ribos-5-yl)-L-homocysteine = (S)-4,5-dihydroxypentane-2,3-dione + L-homocysteine.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0009372    quorum sensing    The process in which single-celled organisms monitor their population density by detecting the concentration of small, diffusible signal molecules produced by the cells themselves.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LUXS_BACSU | O34667: 1ie0 1j98 1jqw 1jvi 2fqo 2fqt

(-) Related Entries Specified in the PDB File

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