Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF AUTOINDUCER-2 PRODUCTION PROTEIN (LUXS) FROM HEAMOPHILUS INFLUENZAE
 
Authors :  C. C. H. Chen, J. F. Parsons, K. Lim, C. Lehmann, A. Tempczyk, E. Eisenste O. Herzberg, Structure 2 Function Project (S2F)
Date :  27 Jul 01  (Deposition) - 08 Aug 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Luxs, Hi0491, Structural Genomics, Twinned Crystal, Structure 2 Function Project, S2F, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. C. H. Chen, J. F. Parsons, K. Lim, C. Lehmann, A. Tempczyk, E. Eisenstein, O. Herzberg
Crystal Structure Of Autoinducer-2 Production Protein (Luxs From Heamophilus Influenzae--A Case Of Twinned Crystal
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - AUTOINDUCER-2 PRODUCTION PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST14
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: HAEMOPHILUS INFLUENZAE RD
    Organism Taxid: 71421
    Strain: KW20
    Synonym: AI-2 SYNTHESIS PROTEIN, HI0491, LUXS

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1HG4Ligand/IonMERCURY (II) ION
2ZN4Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1HG-1Ligand/IonMERCURY (II) ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1HG-1Ligand/IonMERCURY (II) ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:40 , CYS A:41 , HOH A:216BINDING SITE FOR RESIDUE HG A 201
2AC2SOFTWARECYS B:41 , GLU B:46 , HOH B:213BINDING SITE FOR RESIDUE HG B 202
3AC3SOFTWARECYS C:41 , GLU C:46 , ILE C:142BINDING SITE FOR RESIDUE HG C 203
4AC4SOFTWARECYS D:41 , GLU D:46 , ASN D:145 , HOH D:237BINDING SITE FOR RESIDUE HG D 204
5AC5SOFTWAREHIS A:54 , HIS A:58 , CYS A:128 , HOH A:231BINDING SITE FOR RESIDUE ZN A 205
6AC6SOFTWAREHIS B:54 , HIS B:58 , CYS B:128 , HOH B:236BINDING SITE FOR RESIDUE ZN B 206
7AC7SOFTWAREHIS C:54 , HIS C:58 , CYS C:128BINDING SITE FOR RESIDUE ZN C 207
8AC8SOFTWAREHIS D:54 , HIS D:58 , CYS D:128BINDING SITE FOR RESIDUE ZN D 208

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:16 -Pro A:17
2Ala B:16 -Pro B:17
3Ala C:16 -Pro C:17
4Ala D:16 -Pro D:17

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1JOE)

(-) 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:148
 aligned with LUXS_HAEIN | P44007 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:148
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148        
           LUXS_HAEIN     9 VDHTKMNAPAVRIAKTMLTPKGDNITVFDLRFCIPNKEILSPKGIHTLEHLFAGFMRDHLNGDSIEIIDISPMGCRTGFYMSLIGTPNEQKVSEAWLASMQDVLGVQDQASIPELNIYQCGSYTEHSLEDAHEIAKNVIARGIGVNKN 156
               SCOP domains d1joea_ A: Autoinducer-2 production protein LuxS                                                                                                     SCOP domains
               CATH domains 1joeA00 A:9-156  [code=3.30.1360.80, no name defined]                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...eeeeeeeee.....eeeeeeee.........hhhhhhhhhhhhhhhhhh.......eeeeeee.....eeeeeee...hhhhhhhhhhhhhhhhh......................hhhhhhhhhhhhhhhh.eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1joe A   9 VDHTKMNAPAVRIAKTMLTPKGDNITVFDLRFCIPNKEILSPKGIHTLEHLFAGFMRDHLNGDSIEIIDISPMGCRTGFYMSLIGTPNEQKVSEAWLASMQDVLGVQDQASIPELNIYQCGSYTEHSLEDAHEIAKNVIARGIGVNKN 156
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148        


Chain B from PDB  Type:PROTEIN  Length:148
 aligned with LUXS_HAEIN | P44007 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:148
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148        
           LUXS_HAEIN     9 VDHTKMNAPAVRIAKTMLTPKGDNITVFDLRFCIPNKEILSPKGIHTLEHLFAGFMRDHLNGDSIEIIDISPMGCRTGFYMSLIGTPNEQKVSEAWLASMQDVLGVQDQASIPELNIYQCGSYTEHSLEDAHEIAKNVIARGIGVNKN 156
               SCOP domains d1joeb_ B: Autoinducer-2 production protein LuxS                                                                                                     SCOP domains
               CATH domains 1joeB00 B:9-156  [code=3.30.1360.80, no name defined]                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee.eeeeee.....eeeeeee............hhhhhhhhhhhhhhhhhh.....eeeeeee......eeeeee...hhhhhhhhhhhhhhhhhh..hhhhh..............hhhhhhhhhhhhhhhh.ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1joe B   9 VDHTKMNAPAVRIAKTMLTPKGDNITVFDLRFCIPNKEILSPKGIHTLEHLFAGFMRDHLNGDSIEIIDISPMGCRTGFYMSLIGTPNEQKVSEAWLASMQDVLGVQDQASIPELNIYQCGSYTEHSLEDAHEIAKNVIARGIGVNKN 156
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148        


Chain C from PDB  Type:PROTEIN  Length:148
 aligned with LUXS_HAEIN | P44007 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:148
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148        
           LUXS_HAEIN     9 VDHTKMNAPAVRIAKTMLTPKGDNITVFDLRFCIPNKEILSPKGIHTLEHLFAGFMRDHLNGDSIEIIDISPMGCRTGFYMSLIGTPNEQKVSEAWLASMQDVLGVQDQASIPELNIYQCGSYTEHSLEDAHEIAKNVIARGIGVNKN 156
               SCOP domains d1joec_ C: Autoinducer-2 production protein LuxS                                                                                                     SCOP domains
               CATH domains 1joeC00 C:9-156  [code=3.30.1360.80, no name defined]                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee...eeee.....eeeeeeee...........hhhhhhhhhhhhhhhhhh.....eeeeeee.....eeeeeee...hhhhhhhhhhhhhhhhhhh.hhhhh..............hhhhhhhhhhhhhhhh.ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1joe C   9 VDHTKMNAPAVRIAKTMLTPKGDNITVFDLRFCIPNKEILSPKGIHTLEHLFAGFMRDHLNGDSIEIIDISPMGCRTGFYMSLIGTPNEQKVSEAWLASMQDVLGVQDQASIPELNIYQCGSYTEHSLEDAHEIAKNVIARGIGVNKN 156
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148        


Chain D from PDB  Type:PROTEIN  Length:148
 aligned with LUXS_HAEIN | P44007 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:148
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148        
           LUXS_HAEIN     9 VDHTKMNAPAVRIAKTMLTPKGDNITVFDLRFCIPNKEILSPKGIHTLEHLFAGFMRDHLNGDSIEIIDISPMGCRTGFYMSLIGTPNEQKVSEAWLASMQDVLGVQDQASIPELNIYQCGSYTEHSLEDAHEIAKNVIARGIGVNKN 156
               SCOP domains d1joed_ D: Autoinducer-2 production protein LuxS                                                                                                     SCOP domains
               CATH domains 1joeD00 D:9-156  [code=3.30.1360.80, no name defined]                                                                                                CATH domains
           Pfam domains (1) LuxS-1joeD01 D:9-156                                                                                                                                 Pfam domains (1)
           Pfam domains (2) LuxS-1joeD02 D:9-156                                                                                                                                 Pfam domains (2)
           Pfam domains (3) LuxS-1joeD03 D:9-156                                                                                                                                 Pfam domains (3)
           Pfam domains (4) LuxS-1joeD04 D:9-156                                                                                                                                 Pfam domains (4)
         Sec.struct. author .........eeeeeeeee.....eeeeeeee.........hhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee...hhhhhhhhhhhhhhhhhhh.hhhhh..............hhhhhhhhhhhhhhhh.ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1joe D   9 VDHTKMNAPAVRIAKTMLTPKGDNITVFDLRFCIPNKEILSPKGIHTLEHLFAGFMRDHLNGDSIEIIDISPMGCRTGFYMSLIGTPNEQKVSEAWLASMQDVLGVQDQASIPELNIYQCGSYTEHSLEDAHEIAKNVIARGIGVNKN 156
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148
   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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Peptidase_ME (35)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (LUXS_HAEIN | P44007)
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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    HG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:16 - Pro A:17   [ RasMol ]  
    Ala B:16 - Pro B:17   [ RasMol ]  
    Ala C:16 - Pro C:17   [ RasMol ]  
    Ala D:16 - Pro D:17   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1joe
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  LUXS_HAEIN | P44007
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  LUXS_HAEIN | P44007
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        LUXS_HAEIN | P44007: 1j6w

(-) Related Entries Specified in the PDB File

1j6w IJ6W IS THE CRYSTAL STRUCTURE OF HAEMOPHILUS INFLUENZAE LUXS RELATED ID: HI0491 RELATED DB: TARGETDB