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Title :   CRYSTAL STRUCTURE OF HAEMOPHILUS INFLUENZAE 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 :   2.10

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)

Molecule 1 - AUTOINDUCER-2 PRODUCTION PROTEIN LUXS
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	HAEMOPHILUS INFLUENZAE
	Organism Taxid	:	727
	Synonym	:	AI-2 SYNTHESIS PROTEIN, CONSERVED HYPOTHETICAL PROTEIN HI049

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 16)

No.	Name	Count	Type	Full Name
1	MET	2	Ligand/Ion	METHIONINE
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
3	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS B:54 , HIS B:58 , CYS B:128	BINDING SITE FOR RESIDUE ZN B 176
2	AC2	SOFTWARE	HIS A:54 , HIS A:58 , CYS A:128	BINDING SITE FOR RESIDUE ZN A 176
3	AC3	SOFTWARE	LEU A:4 , SER A:6 , PHE A:7 , ARG B:65 , ASP B:77 , ILE B:78 , SER B:79 , HOH B:517	BINDING SITE FOR RESIDUE MET B 501
4	AC4	SOFTWARE	ARG A:65 , ASP A:77 , ILE A:78 , SER A:79 , HOH A:622 , SER B:6 , TYR B:88	BINDING SITE FOR RESIDUE MET A 601

(no "SS Bond" information available for 1J6W)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:16	-	Pro A:17
2	Ala B:16	-	Pro B:17

(no "SAP(SNP)/Variant" information available for 1J6W)

(no "PROSITE Motif" information available for 1J6W)

(no "Exon" information available for 1J6W)

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:161
 aligned with LUXS_HAEIN | P44007 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:161
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162 
           LUXS_HAEIN     3 LLDSFKVDHTKMNAPAVRIAKTMLTPKGDNITVFDLRFCIPNKEILSPKGIHTLEHLFAGFMRDHLNGDSIEIIDISPMGCRTGFYMSLIGTPNEQKVSEAWLASMQDVLGVQDQASIPELNIYQCGSYTEHSLEDAHEIAKNVIARGIGVNKNEDLSLDN 163
               SCOP domains d1j6wa_ A: Autoinducer-2 production protein LuxS                                                                                                                  SCOP domains
               CATH domains 1j6wA00 A:3-163  [code=3.30.1360.80, no name defined]                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.hhhhh...eeeeeeeee.....eeeeeeee.........hhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee...hhhhhhhhhhhhhhhhhh..hhhhh..............hhhhhhhhhhhhhhhh.eeehhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j6w A   3 LLDSFKVDHTKmNAPAVRIAKTmLTPKGDNITVFDLRFCIPNKEILSPKGIHTLEHLFAGFmRDHLNGDSIEIIDISPmGCRTGFYmSLIGTPNEQKVSEAWLASmQDVLGVQDQASIPELNIYQCGSYTEHSLEDAHEIAKNVIARGIGVNKNEDLSLDN 163
                                    12 |      22  |     32        42        52        62 |      72        82      | 92       102     | 112       122       132       142       152       162 
                                      14-MSE     25-MSE                                 64-MSE           81-MSE  89-MSE            108-MSE

Chain B from PDB  Type:PROTEIN  Length:160
 aligned with LUXS_HAEIN | P44007 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:160
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162
           LUXS_HAEIN     3 LLDSFKVDHTKMNAPAVRIAKTMLTPKGDNITVFDLRFCIPNKEILSPKGIHTLEHLFAGFMRDHLNGDSIEIIDISPMGCRTGFYMSLIGTPNEQKVSEAWLASMQDVLGVQDQASIPELNIYQCGSYTEHSLEDAHEIAKNVIARGIGVNKNEDLSLD 162
               SCOP domains d1j6wb_ B: Autoinducer-2 production protein LuxS                                                                                                                 SCOP domains
               CATH domains 1j6wB00 B:3-162  [code=3.30.1360.80, no name defined]                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.hhhhh...eeeeeeeee.....eeeeeeee.........hhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee...hhhhhhhhhhhhhhhhhhh.hhhhh..............hhhhhhhhhhhhhhhh.ee.hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j6w B   3 LLDSFKVDHTKmNAPAVRIAKTmLTPKGDNITVFDLRFCIPNKEILSPKGIHTLEHLFAGFmRDHLNGDSIEIIDISPmGCRTGFYmSLIGTPNEQKVSEAWLASmQDVLGVQDQASIPELNIYQCGSYTEHSLEDAHEIAKNVIARGIGVNKNEDLSLD 162
                                    12 |      22  |     32        42        52        62 |      72        82      | 92       102     | 112       122       132       142       152       162
                                      14-MSE     25-MSE                                 64-MSE           81-MSE  89-MSE            108-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 '\|'

Asymmetric/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

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Organisms( (-)

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

Fold: LuxS/MPP-like metallohydrolase (89)

Superfamily: LuxS/MPP-like metallohydrolase (89)

Family: Autoinducer-2 production protein LuxS (15)

Protein domain: Autoinducer-2 production protein LuxS (15)

Haemophilus influenzae [TaxId: 727] (2)

1a	d1j6wa_	A:
1b	d1j6wb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Gyrase A; domain 2 (166)

Homologous Superfamily: [code=3.30.1360.80, no name defined] (15)

Haemophilus influenzae. Organism_taxid: 727. (1)

1a	1j6wB00	B:3-162
1b	1j6wA00	A:3-163

(no "Pfam Domain" information available for 1J6W)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:16 - Pro A:17	[ RasMol ]
		Ala B:16 - Pro B:17	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (3, 16)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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