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(-) Description

Title :  CRYSTAL STRUCTURE OF A AUTOINDUCER-2 SYNTHESIS PROTEIN
 
Authors :  Structural Genomix
Date :  03 Nov 03  (Deposition) - 25 Nov 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Badger, J. M. Sauder, J. M. Adams, S. Antonysamy, K. Bain, M. G. Bergseid, S. G. Buchanan, M. D. Buchanan, Y. Batiyenko, J. A. Christopher, S. Emtage, A. Eroshkina, I. Feil, E. B. Furlong, K. S. Gajiwala, X. Gao, D. He, J. Hendle, A. Huber, K. Hoda, P. Kearins, C. Kissinger, B. Laubert, H. A. Lewis, J. Lin, K. Loomis, D. Lorimer, G. Louie, M. Maletic, C. D. Marsh, I. Miller, J. Molinari, H. J. Muller-Dieckmann, J. M. Newman, B. W. Noland, B. Pagarigan, F. Park, T. S. Peat, K. W. Post, S. Radojicic, A. Ramos, R. Romero, M. E. Rutter, W. E. Sanderson, K. D. Schwinn, J. Tresser, J. Winhoven, T. A. Wright, L. Wu, J. Xu, T. J. Harris
Structural Analysis Of A Set Of Proteins Resulting From A Bacterial Genomics Project
Proteins V. 60 787 2005
PubMed-ID: 16021622  |  Reference-DOI: 10.1002/PROT.20541

(-) Compounds

Molecule 1 - S-RIBOSYLHOMOCYSTEINASE
    Chains: A, B
    EC Number: 3.13.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LUXS, DR2387
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299
    Synonym: AUTOINDUCER-2 PRODUCTION PROTEIN LUXS, AI-2 SYNTHESIS PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CSD2Mod. Amino Acid3-SULFINOALANINE
2ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:57 , HIS A:61 , CYS A:125 , HOH B:190BINDING SITE FOR RESIDUE ZN A 167
2AC2SOFTWAREHIS B:57 , HIS B:61 , CYS B:125 , HOH B:184BINDING SITE FOR RESIDUE ZN B 167

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:19 -Pro A:20
2Ala B:19 -Pro B:20

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VGX)

(-) 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:149
 aligned with LUXS_DEIRA | Q9RRU8 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:149
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147         
           LUXS_DEIRA     8 ESFDLDHTKVKAPYVRLAGVKTTPKGDQISKYDLRFLQPNQGAIDPAAIHTLEHLLAGYMRDHLEGVVDVSPMGCRTGMYMAVIGEPDEQGVMKAFEAALKDTAGHDQPIPGVSELECGNYRDHDLAAARQHARDVLDQGLKVQETILL 156
               SCOP domains d1vgxa_ A: Autoinducer-2 production protein LuxS                                                                                                      SCOP domains
               CATH domains 1vgxA00 A:8-156  [code=3.30.1360.80, no name defined]                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeeeee.....eeeeeeee.........hhhhhhhhhhhhhhhhhhhh..eeeeee.....eeeeeee...hhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vgx A   8 ESFDLDHTKVKAPYVRLAGVKTTPKGDQISKYDLRFLQPNQGAIDPAAIHTLEHLLAGYMRDHLEGVVDVSPMGcRTGMYMAVIGEPDEQGVMKAFEAALKDTAGHDQPIPGVSELECGNYRDHDLAAARQHARDVLDQGLKVQETILL 156
                                    17        27        37        47        57        67        77    |   87        97       107       117       127       137       147         
                                                                                                     82-CSD                                                                      


Chain B from PDB  Type:PROTEIN  Length:151
 aligned with LUXS_DEIRA | Q9RRU8 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:151
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155 
           LUXS_DEIRA     6 NVESFDLDHTKVKAPYVRLAGVKTTPKGDQISKYDLRFLQPNQGAIDPAAIHTLEHLLAGYMRDHLEGVVDVSPMGCRTGMYMAVIGEPDEQGVMKAFEAALKDTAGHDQPIPGVSELECGNYRDHDLAAARQHARDVLDQGLKVQETILL 156
               SCOP domains d1vgxb_ B: Autoinducer-2 production protein LuxS                                                                                                        SCOP domains
               CATH domains 1vgxB00 B:6-156  [code=3.30.1360.80, no name defined]                                                                                                   CATH domains
           Pfam domains (1) LuxS-1vgxB01 B:6-156                                                                                                                                    Pfam domains (1)
           Pfam domains (2) LuxS-1vgxB02 B:6-156                                                                                                                                    Pfam domains (2)
         Sec.struct. author ...............eeeeeeeee.....eeeeeeee.........hhhhhhhhhhhhhhhhhhhh..eeeeee.....eeeeeee...hhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vgx B   6 NVESFDLDHTKVKAPYVRLAGVKTTPKGDQISKYDLRFLQPNQGAIDPAAIHTLEHLLAGYMRDHLEGVVDVSPMGcRTGMYMAVIGEPDEQGVMKAFEAALKDTAGHDQPIPGVSELECGNYRDHDLAAARQHARDVLDQGLKVQETILL 156
                                    15        25        35        45        55        65        75      | 85        95       105       115       125       135       145       155 
                                                                                                       82-CSD
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_ME (35)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (LUXS_DEIRA | Q9RRU8)
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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  1vgx
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 Related Entries

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

UniProtKB/Swiss-Prot
        LUXS_DEIRA | Q9RRU8: 1inn 1j6v 1vh2 1vje

(-) Related Entries Specified in the PDB File

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