3JPU - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   LASR-TP4 COMPLEX

Authors :   Y. Zou, S. K. Nair

Date :   04 Sep 09 (Deposition) - 13 Oct 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C,D,E
Biol. Unit 1: A  (2x)
Biol. Unit 2: B,C  (1x)
Biol. Unit 3: D,E  (1x)

Keywords :   Quorum Sensing, Triphenyl Mimic, Activator, Dna-Binding, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Zou, S. K. Nair
Molecular Basis For The Recognition Of Structurally Distinc Autoinducer Mimics By The Pseudomonas Aeruginosa Lasr Quorum-Sensing Signaling Receptor.
Chem. Biol. V. 16 961 2009
PubMed-ID: 19778724 | Reference-DOI: 10.1016/J.CHEMBIOL.2009.09.001

Molecule 1 - TRANSCRIPTIONAL ACTIVATOR PROTEIN LASR
	Chains	:	A, B, C, D, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	LASR, PA1430
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (2x)	:	A
Biological Unit 2 (1x)	:		B	C
Biological Unit 3 (1x)	:				D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 5)

No.	Name	Count	Type	Full Name
1	TY4	5	Ligand/Ion	4-BROMO-2-({[(2-CHLOROPHENYL)CARBONYL]AMINO}METHYL)-6-METHYLPHENYL 2,4-DICHLOROBENZOATE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	TY4	2	Ligand/Ion	4-BROMO-2-({[(2-CHLOROPHENYL)CARBONYL]AMINO}METHYL)-6-METHYLPHENYL 2,4-DICHLOROBENZOATE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	TY4	2	Ligand/Ion	4-BROMO-2-({[(2-CHLOROPHENYL)CARBONYL]AMINO}METHYL)-6-METHYLPHENYL 2,4-DICHLOROBENZOATE

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	TY4	2	Ligand/Ion	4-BROMO-2-({[(2-CHLOROPHENYL)CARBONYL]AMINO}METHYL)-6-METHYLPHENYL 2,4-DICHLOROBENZOATE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:36 , GLY A:38 , ALA A:50 , ILE A:52 , TYR A:56 , TRP A:60 , TYR A:64 , ASP A:73 , THR A:75 , CYS A:79 , TRP A:88 , TYR A:93 , PHE A:101 , ALA A:105 , LEU A:125 , GLY A:126 , ALA A:127 , SER A:129	BINDING SITE FOR RESIDUE TY4 A 174
2	AC2	SOFTWARE	LEU B:36 , GLY B:38 , TYR B:47 , ALA B:50 , ILE B:52 , TYR B:56 , TRP B:60 , TYR B:64 , ASP B:73 , THR B:75 , VAL B:76 , CYS B:79 , TRP B:88 , TYR B:93 , PHE B:101 , LEU B:125 , ALA B:127 , SER B:129	BINDING SITE FOR RESIDUE TY4 B 174
3	AC3	SOFTWARE	LEU C:36 , GLY C:38 , TYR C:47 , TYR C:56 , TRP C:60 , TYR C:64 , ASP C:73 , THR C:75 , VAL C:76 , CYS C:79 , TRP C:88 , PHE C:101 , LEU C:125 , ALA C:127 , SER C:129	BINDING SITE FOR RESIDUE TY4 C 174
4	AC4	SOFTWARE	LEU D:36 , GLY D:38 , LEU D:39 , ALA D:50 , ILE D:52 , TYR D:56 , TRP D:60 , TYR D:64 , ASP D:73 , THR D:75 , VAL D:76 , CYS D:79 , TRP D:88 , LEU D:110 , LEU D:125 , GLY D:126 , ALA D:127 , SER D:129	BINDING SITE FOR RESIDUE TY4 D 174
5	AC5	SOFTWARE	LEU E:36 , GLY E:38 , LEU E:39 , TYR E:47 , ILE E:52 , TYR E:56 , TRP E:60 , TYR E:64 , ASP E:73 , THR E:75 , VAL E:76 , CYS E:79 , TRP E:88 , TYR E:93 , PHE E:101 , LEU E:125 , GLY E:126 , ALA E:127 , SER E:129	BINDING SITE FOR RESIDUE TY4 E 174

(no "SS Bond" information available for 3JPU)

(no "Cis Peptide Bond" information available for 3JPU)

Asymmetric Unit (1, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LASR_PSEAE_001 *	M	144	I	LASR_PSEAE	---	---	A/B/C/D/E	M	144	I
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LASR_PSEAE_001 *	M	144	I	LASR_PSEAE	---	---	A	M	144	I
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LASR_PSEAE_001 *	M	144	I	LASR_PSEAE	---	---	B/C	M	144	I
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LASR_PSEAE_001 *	M	144	I	LASR_PSEAE	---	---	D/E	M	144	I
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 3JPU)

(no "Exon" information available for 3JPU)

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:161
 aligned with LASR_PSEAE | P25084 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:161
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165 
           LASR_PSEAE     6 GFLELERSSGKLEWSAILQKMASDLGFSKILFGLLPKDSQDYENAFIVGNYPAAWREHYDRAGYARVDPTVSHCTQSVLPIFWEPSIYQTRKQHEFFEEASAAGLVYGLTMPLHGARGELGALSLSVEAENRAEANRFMESVLPTLWMLKDYALQSGAGLA 166
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..hhhhhhhhhhhhhhhh....eeeeee.....hhhhheeee..hhhhhhhhhhhhhhhhhhhhhhhhhh...ee.hhhhh.hhhhhhhhhhhhhh...eeeeeeee.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------I---------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jpu A   6 GFLELERSSGKLEWSAILQKMASDLGFSKILFGLLPKDSQDYENAFIVGNYPAAWREHYDRAGYARVDPTVSHCTQSVLPIFWEPSIYQTRKQHEFFEEASAAGLVYGLTMPLHGARGELGALSLSVEAENRAEANRFMESVLPTLWMLKDYALQSGAGLA 166
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165

Chain B from PDB  Type:PROTEIN  Length:161
 aligned with LASR_PSEAE | P25084 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:161
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165 
           LASR_PSEAE     6 GFLELERSSGKLEWSAILQKMASDLGFSKILFGLLPKDSQDYENAFIVGNYPAAWREHYDRAGYARVDPTVSHCTQSVLPIFWEPSIYQTRKQHEFFEEASAAGLVYGLTMPLHGARGELGALSLSVEAENRAEANRFMESVLPTLWMLKDYALQSGAGLA 166
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh..hhhhhhhhhhhhhhhhh...eeeeee.....hhhhheeee..hhhhhhhhhhhhhhhhhhhhhhhhhh...ee.hhhhh.hhhhhhhhhhhhhh...eeeeeeee.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------I---------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jpu B   6 GFLELERSSGKLEWSAILQKMASDLGFSKILFGLLPKDSQDYENAFIVGNYPAAWREHYDRAGYARVDPTVSHCTQSVLPIFWEPSIYQTRKQHEFFEEASAAGLVYGLTMPLHGARGELGALSLSVEAENRAEANRFMESVLPTLWMLKDYALQSGAGLA 166
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165

Chain C from PDB  Type:PROTEIN  Length:163
 aligned with LASR_PSEAE | P25084 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:163
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163   
           LASR_PSEAE     4 VDGFLELERSSGKLEWSAILQKMASDLGFSKILFGLLPKDSQDYENAFIVGNYPAAWREHYDRAGYARVDPTVSHCTQSVLPIFWEPSIYQTRKQHEFFEEASAAGLVYGLTMPLHGARGELGALSLSVEAENRAEANRFMESVLPTLWMLKDYALQSGAGLA 166
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh..hhhhhhhhhhhhhhhhh..eeeeeee..........eeee..hhhhhhhhhhhhhhhhhhhhhhhh.....ee.hhhhh.hhhhhhhhhhhhhh....eeeeeee.....eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------I---------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jpu C   4 VDGFLELERSSGKLEWSAILQKMASDLGFSKILFGLLPKDSQDYENAFIVGNYPAAWREHYDRAGYARVDPTVSHCTQSVLPIFWEPSIYQTRKQHEFFEEASAAGLVYGLTMPLHGARGELGALSLSVEAENRAEANRFMESVLPTLWMLKDYALQSGAGLA 166
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163

Chain D from PDB  Type:PROTEIN  Length:162
 aligned with LASR_PSEAE | P25084 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:162
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164  
           LASR_PSEAE     5 DGFLELERSSGKLEWSAILQKMASDLGFSKILFGLLPKDSQDYENAFIVGNYPAAWREHYDRAGYARVDPTVSHCTQSVLPIFWEPSIYQTRKQHEFFEEASAAGLVYGLTMPLHGARGELGALSLSVEAENRAEANRFMESVLPTLWMLKDYALQSGAGLA 166
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhh..hhhhhhhhhhhhhhhh....eeeeee..........eeee..hhhhhhhhhhhhhhhhhhhhhhhh.....ee.hhhhh.hhhhhhhhhhhhhh...eeeeeeee.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------I---------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3jpu D   5 DGFLELERSSGKLEWSAILQKMASDLGFSKILFGLLPKDSQDYENAFIVGNYPAAWREHYDRAGYARVDPTVSHCTQSVLPIFWEPSIYQTRKQHEFFEEASAAGLVYGLTMPLHGARGELGALSLSVEAENRAEANRFMESVLPTLWMLKDYALQSGAGLA 166
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164

Chain E from PDB  Type:PROTEIN  Length:161
 aligned with LASR_PSEAE | P25084 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:161
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165 
           LASR_PSEAE     6 GFLELERSSGKLEWSAILQKMASDLGFSKILFGLLPKDSQDYENAFIVGNYPAAWREHYDRAGYARVDPTVSHCTQSVLPIFWEPSIYQTRKQHEFFEEASAAGLVYGLTMPLHGARGELGALSLSVEAENRAEANRFMESVLPTLWMLKDYALQSGAGLA 166
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------Autoind_bind-3jpuE01 E:16-161                                                                                                                     ----- Pfam domains (1)
           Pfam domains (2) ----------Autoind_bind-3jpuE02 E:16-161                                                                                                                     ----- Pfam domains (2)
           Pfam domains (3) ----------Autoind_bind-3jpuE03 E:16-161                                                                                                                     ----- Pfam domains (3)
           Pfam domains (4) ----------Autoind_bind-3jpuE04 E:16-161                                                                                                                     ----- Pfam domains (4)
           Pfam domains (5) ----------Autoind_bind-3jpuE05 E:16-161                                                                                                                     ----- Pfam domains (5)
         Sec.struct. author hhhhhhh..hhhhhhhhhhhhhhhhh...eeeeee..........eeee..hhhhhhhhhhhhhhhhhhhhhhhhhh...ee.hhhhh....hhhhhhhhh.....eeeeeeee.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------I---------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jpu E   6 GFLELERSSGKLEWSAILQKMASDLGFSKILFGLLPKDSQDYENAFIVGNYPAAWREHYDRAGYARVDPTVSHCTQSVLPIFWEPSIYQTRKQHEFFEEASAAGLVYGLTMPLHGARGELGALSLSVEAENRAEANRFMESVLPTLWMLKDYALQSGAGLA 166
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165

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 '\|'

(no "SCOP Domain" information available for 3JPU)

(no "CATH Domain" information available for 3JPU)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GAF (44)

Family: Autoind_bind (5)

Pseudomonas aeruginosa (2)

1a	Autoind_bind-3jpuE01	E:16-161
1b	Autoind_bind-3jpuE02	E:16-161
1c	Autoind_bind-3jpuE03	E:16-161
1d	Autoind_bind-3jpuE04	E:16-161
1e	Autoind_bind-3jpuE05	E:16-161

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (LASR_PSEAE | P25084)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	GO:0051544	positive regulation of elastin biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of elastin.
	GO:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	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.
	GO:0060310	regulation of elastin catabolic process	Any process that modulates the rate, frequency or extent of elastin catabolism, the chemical reactions and pathways resulting in the breakdown of elastin.
	GO:0010468	regulation of gene expression	Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3jpu)

Biological Units
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	3jpu
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	LASR_PSEAE \| P25084
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UniProtKB/Swiss-Prot
	LASR_PSEAE \| P25084	:	2uv0 3ix3 3ix4 3ix8 4ng2

3ix3	SAME PROTEIN WITH NATIVE LIGAND
3ix4	SMAE PROTEIN WITH DIFFERENT TRIPHENYL LIGAND
3ix8	SAME PROTEIN WITH DIFFERENT TRIPHENT LIGAND

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 5)

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Related Entries Specified in the PDB File