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(-) Description

Title :  CRYSTAL STRUCTURE OF HELICOBACTER PYLORI LUXS
 
Authors :  H. A. Lewis, E. B. Furlong, M. G. Bergseid, W. E. Sanderson, S. G. Buchanan
Date :  14 May 01  (Deposition) - 08 Jun 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.38
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha-Beta Fold, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. A. Lewis, E. B. Furlong, B. Laubert, G. A. Eroshkina, Y. Batiyenko, J. M. Adams, M. G. Bergseid, C. D. Marsh, T. S. Peat, W. E. Sanderson, J. M. Sauder, S. G. Buchanan
A Structural Genomics Approach To The Study Of Quorum Sensing: Crystal Structures Of Three Luxs Orthologs.
Structure V. 9 527 2001
PubMed-ID: 11435117  |  Reference-DOI: 10.1016/S0969-2126(01)00613-X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AUTOINDUCER-2 PRODUCTION PROTEIN LUXS
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210
    Synonym: AI-2 SYNTHESIS PROTEIN, CONSERVED HYPOTHETICAL PROTEIN JHP0097

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric/Biological Unit (3, 16)
No.NameCountTypeFull Name
1MET2Ligand/IonMETHIONINE
2MSE12Mod. Amino AcidSELENOMETHIONINE
3ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:55 , HIS A:59 , CYS A:122BINDING SITE FOR RESIDUE ZN A 161
2AC2SOFTWAREHIS B:55 , HIS B:59 , CYS B:122 , HOH B:504BINDING SITE FOR RESIDUE ZN B 161
3AC3SOFTWAREVAL A:5 , SER A:7 , ARG B:66 , ASP B:74 , TRP B:75 , SER B:76 , HOH B:502 , HOH B:504BINDING SITE FOR RESIDUE MET B 501
4AC4SOFTWAREARG A:66 , ASP A:74 , TRP A:75 , SER A:76 , VAL B:5 , PHE B:8BINDING SITE FOR RESIDUE MET A 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J6X)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:17 -Pro A:18
2Ala B:17 -Pro B:18

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J6X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J6X)

(-) Exons   (0, 0)

(no "Exon" information available for 1J6X)

(-) 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:151
 aligned with LUXS_HELPJ | Q9ZMW8 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 
           LUXS_HELPJ     1 MKMNVESFNLDHTKVKAPYVRIADRKKGVNGDLIVKYDVRFKQPNRDHMDMPSLHSLEHLVAEIIRNHANYVVDWSPMGCQTGFYLTVLNHDNYTEILEVLEKTMQDVLKAKEVPASNEKQCGWAANHTLEGAQNLARAFLDKRAEWSEVG 151
               SCOP domains d1j6xa_ A: Autoinducer-2 production protein LuxS                                                                                                        SCOP domains
               CATH domains -1j6xA00 A:2-151  [code=3.30.1360.80, no name defined]                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh........eeeeeeeee.....eeeeeeee.........hhhhhhhhhhhhhhhhhhhh..eeeeee.....eeeeeee...hhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j6x A   1 mKmNVESFNLDHTKVKAPYVRIADRKKGVNGDLIVKYDVRFKQPNRDHmDmPSLHSLEHLVAEIIRNHANYVVDWSPmGCQTGFYLTVLNHDNYTEILEVLEKTmQDVLKAKEVPASNEKQCGWAANHTLEGAQNLARAFLDKRAEWSEVG 151
                            | |     10        20        30        40        50|       60        70       |80        90       100    |  110       120       130       140       150 
                            | |                                            49-MSE                       78-MSE                    105-MSE                                          
                            1-MSE                                            51-MSE                                                                                                
                              3-MSE                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:152
 aligned with LUXS_HELPJ | Q9ZMW8 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  
           LUXS_HELPJ     1 MKMNVESFNLDHTKVKAPYVRIADRKKGVNGDLIVKYDVRFKQPNRDHMDMPSLHSLEHLVAEIIRNHANYVVDWSPMGCQTGFYLTVLNHDNYTEILEVLEKTMQDVLKAKEVPASNEKQCGWAANHTLEGAQNLARAFLDKRAEWSEVGV 152
               SCOP domains d1j6xb_ B: Autoinducer-2 production protein LuxS                                                                                                         SCOP domains
               CATH domains -1j6xB00 B:2-152  [code=3.30.1360.80, no name defined]                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh........eeeeeeeee.....eeeeeeee.........hhhhhhhhhhhhhhhhhhhh..eeeeee.....eeeeeee...hhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j6x B   1 mKmNVESFNLDHTKVKAPYVRIADRKKGVNGDLIVKYDVRFKQPNRDHmDmPSLHSLEHLVAEIIRNHANYVVDWSPmGCQTGFYLTVLNHDNYTEILEVLEKTmQDVLKAKEVPASNEKQCGWAANHTLEGAQNLARAFLDKRAEWSEVGV 152
                            | |     10        20        30        40        50|       60        70       |80        90       100    |  110       120       130       140       150  
                            1-MSE                                          49-MSE                       78-MSE                    105-MSE                                           
                              3-MSE                                          51-MSE
   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) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J6X)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (LUXS_HELPJ | Q9ZMW8)
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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