1L3L | PD0298 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A BACTERIAL QUORUM-SENSING TRANSCRIPTION FACTOR COMPLEXED WITH PHEROMONE AND DNA

Authors :   R. Zhang, T. Pappas, J. L. Brace, P. C. Miller, T. Oulmassov, J. M. Molyneaux, J. C. Anderson, J. K. Bashkin, S. C. Winans, A. Joachimiak

Date :   27 Feb 02 (Deposition) - 03 Jul 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.66

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

Keywords :   Helix-Turn-Helix Dna Binding Motif, Alpha/Beta/Alpha Sandwich, Asymmetry Of The Protein-Dna Complex, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. G. Zhang, T. Pappas, J. L. Brace, P. C. Miller, T. Oulmassov, J. M. Molyneaux, J. C. Anderson, J. K. Bashkin, S. C. Winans, A. Joachimiak
Structure Of A Bacterial Quorum-Sensing Transcription Factor Complexed With Pheromone And Dna.
Nature V. 417 971 2002
PubMed-ID: 12087407 | Reference-DOI: 10.1038/NATURE00833
(for further references see the PDB file header)

*Molecule 1 - 5'- D(GPAPTPGPTPGPCPAPGPAPTPCPTPGPCPAPCPAPTP C)-3'*
	Chains	:	E, F, G, H
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - TRANSCRIPTIONAL ACTIVATOR PROTEIN TRAR
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PJZ358
	Expression System Strain	:	B21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	AGROBACTERIUM TUMEFACIENS
	Organism Taxid	:	358
	Synonym	:	QUORUM-SENSING TRANSCRIPTION FACTOR

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:		B		D	E		G
Biological Unit 2 (1x)	:	A		C			F		H

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 26)

No.	Name	Count	Type	Full Name
1	LAE	4	Ligand/Ion	3-OXO-OCTANOIC ACID (2-OXO-TETRAHYDRO-FURAN-3-YL)-AMIDE
2	MSE	22	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 13)

No.	Name	Count	Type	Full Name
1	LAE	2	Ligand/Ion	3-OXO-OCTANOIC ACID (2-OXO-TETRAHYDRO-FURAN-3-YL)-AMIDE
2	MSE	11	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 13)

No.	Name	Count	Type	Full Name
1	LAE	2	Ligand/Ion	3-OXO-OCTANOIC ACID (2-OXO-TETRAHYDRO-FURAN-3-YL)-AMIDE
2	MSE	11	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA B:38 , LEU B:40 , TYR B:53 , TRP B:57 , TYR B:61 , PHE B:62 , ASP B:70 , TRP B:85 , PHE B:101 , ALA B:105 , MSE B:127 , THR B:129 , HOH B:1027	BINDING SITE FOR RESIDUE LAE B 1001
2	AC2	SOFTWARE	ALA D:38 , LEU D:40 , TYR D:53 , TRP D:57 , TYR D:61 , PHE D:62 , ASP D:70 , VAL D:72 , TRP D:85 , PHE D:101 , TYR D:102 , ALA D:105 , ILE D:110 , MSE D:127 , THR D:129 , HOH D:1024	BINDING SITE FOR RESIDUE LAE D 1002
3	AC3	SOFTWARE	ALA A:38 , LEU A:40 , TYR A:53 , TRP A:57 , TYR A:61 , PHE A:62 , ASP A:70 , VAL A:72 , TRP A:85 , PHE A:101 , TYR A:102 , ALA A:105 , MSE A:127 , THR A:129 , HOH A:1049	BINDING SITE FOR RESIDUE LAE A 1003
4	AC4	SOFTWARE	ALA C:38 , LEU C:40 , TYR C:53 , TRP C:57 , TYR C:61 , PHE C:62 , ASP C:70 , TRP C:85 , PHE C:101 , TYR C:102 , ALA C:105 , MSE C:127 , THR C:129 , HOH C:1060	BINDING SITE FOR RESIDUE LAE C 1004

(no "SS Bond" information available for 1L3L)

(no "Cis Peptide Bond" information available for 1L3L)

(no "SAP(SNP)/Variant" information available for 1L3L)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_LUXR_2	PS50043	LuxR-type HTH domain profile.	TRAR_RHIRD	167-232	4	A:167-232 B:167-232 C:172-232 D:172-232

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_LUXR_2	PS50043	LuxR-type HTH domain profile.	TRAR_RHIRD	167-232	2	- B:167-232 - D:172-232

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_LUXR_2	PS50043	LuxR-type HTH domain profile.	TRAR_RHIRD	167-232	2	A:167-232 - C:172-232 -

(no "Exon" information available for 1L3L)

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:233
 aligned with TRAR_RHIRD | P33905 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:233
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231   
           TRAR_RHIRD     2 QHWLDKLTDLAAIEGDECILKTGLADIADHFGFTGYAYLHIQHRHITAVTNYHRQWQSTYFDKKFEALDPVVKRARSRKHIFTWSGEHERPTLSKDERAFYDHASDFGIRSGITIPIKTANGFMSMFTMASDKPVIDLDREIDAVAAAATIGQIHARISFLRTTPTAEDAAWLDPKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKLI 234
               SCOP domains d1l3la2 A:2-169 Transcription factor TraR, N-terminal domain                                                                                                            d1l3la1 A:170-234                                                 SCOP domains
               CATH domains 1l3lA01 A:2-171  [code=3.30.450.80, no name defined]                                                                                                                      1l3lA02 A:172-234 'winged helix' repressor DNA binding domain   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh....hhhhhhhhhhhhhhhh...eeeeeeee..eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeehhhhh...hhhhhhhhhhhhh....eeeeeeee.hhh.eeeeeeee...........hhhhhhhhhhhhhhhhhhh.....ee.....hhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------HTH_LUXR_2  PDB: A:167-232 UniProt: 167-232                       -- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l3l A   2 QHWLDKLTDLAAIEGDECILKTGLADIADHFGFTGYAYLHIQHRHITAVTNYHRQWQSTYFDKKFEALDPVVKRARSRKHIFTWSGEHERPTLSKDERAFYDHASDFGIRSGITIPIKTANGFmSmFTmASDKPVIDLDREIDAVAAAATIGQIHARISFLRTTPTAEDAAWLDPKEATYLRWIAVGKTmEEIADVEGVKYNSVRVKLREAmKRFDVRSKAHLTALAIRRKLI 234
                                    11        21        31        41        51        61        71        81        91       101       111       121   | | 131       141       151       161       171       181       191       201       211 |     221       231   
                                                                                                                                                     125-MSE|                                                          191-MSE               213-MSE                 
                                                                                                                                                       127-MSE                                                                                                       
                                                                                                                                                          130-MSE

Chain B from PDB  Type:PROTEIN  Length:233
 aligned with TRAR_RHIRD | P33905 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:233
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231   
           TRAR_RHIRD     2 QHWLDKLTDLAAIEGDECILKTGLADIADHFGFTGYAYLHIQHRHITAVTNYHRQWQSTYFDKKFEALDPVVKRARSRKHIFTWSGEHERPTLSKDERAFYDHASDFGIRSGITIPIKTANGFMSMFTMASDKPVIDLDREIDAVAAAATIGQIHARISFLRTTPTAEDAAWLDPKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKLI 234
               SCOP domains d1l3lb2 B:2-169 Transcription factor TraR, N-terminal domain                                                                                                            d1l3lb1 B:170-234                                                 SCOP domains
               CATH domains 1l3lB01 B:2-171  [code=3.30.450.80, no name defined]                                                                                                                      1l3lB02 B:172-234 'winged helix' repressor DNA binding domain   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh....hhhhhhhhhhhhhhhh...eeeeeeee..eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeehhhhh...hhhhhhhhhhhhh....eeeeeeee.hhh.eeeeeeee...........hhhhhhhhhhhhhhhhhhh.....ee.....hhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------HTH_LUXR_2  PDB: B:167-232 UniProt: 167-232                       -- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l3l B   2 QHWLDKLTDLAAIEGDECILKTGLADIADHFGFTGYAYLHIQHRHITAVTNYHRQWQSTYFDKKFEALDPVVKRARSRKHIFTWSGEHERPTLSKDERAFYDHASDFGIRSGITIPIKTANGFmSmFTmASDKPVIDLDREIDAVAAAATIGQIHARISFLRTTPTAEDAAWLDPKEATYLRWIAVGKTmEEIADVEGVKYNSVRVKLREAmKRFDVRSKAHLTALAIRRKLI 234
                                    11        21        31        41        51        61        71        81        91       101       111       121   | | 131       141       151       161       171       181       191       201       211 |     221       231   
                                                                                                                                                     125-MSE|                                                          191-MSE               213-MSE                 
                                                                                                                                                       127-MSE                                                                                                       
                                                                                                                                                          130-MSE

Chain C from PDB  Type:PROTEIN  Length:225
 aligned with TRAR_RHIRD | P33905 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:234
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    
           TRAR_RHIRD     1 MQHWLDKLTDLAAIEGDECILKTGLADIADHFGFTGYAYLHIQHRHITAVTNYHRQWQSTYFDKKFEALDPVVKRARSRKHIFTWSGEHERPTLSKDERAFYDHASDFGIRSGITIPIKTANGFMSMFTMASDKPVIDLDREIDAVAAAATIGQIHARISFLRTTPTAEDAAWLDPKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKLI 234
               SCOP domains d1l3lc2 C:1-162 Transcription factor TraR, N-terminal domain                                                                                                      ---------d1l3lc1 C:172-234                                               SCOP domains
               CATH domains -1l3lC01 C:2-180  [code=3.30.450.80, no name defined]                                                                                                                               1l3lC02 C:181-234                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhh....hhhhhhhhhhhhhhhh...eeeeeee....eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhh....eeeeeeeeehhheeeeeeeee...........hhhhhhhhhhhhhhhhhh.---------...hhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------HTH_LUXR_2  PDB: C:172-232 UniProt: 167-232                       -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1l3l C   1 mQHWLDKLTDLAAIEGDECILKTGLADIADHFGFTGYAYLHIQHRHITAVTNYHRQWQSTYFDKKFEALDPVVKRARSRKHIFTWSGEHERPTLSKDERAFYDHASDFGIRSGITIPIKTANGFmSmFTmASDKPVIDLDREIDAVAAAATIGQIHARISFL---------AWLDPKEATYLRWIAVGKTmEEIADVEGVKYNSVRVKLREAmKRFDVRSKAHLTALAIRRKLI 234
                            |       10        20        30        40        50        60        70        80        90       100       110       120    | |130       140       150       160 |       - |     180       190|      200       210  |    220       230    
                            1-MSE                                                                                                                     125-MSE|                             162       172                191-MSE               213-MSE                 
                                                                                                                                                        127-MSE                                                                                                       
                                                                                                                                                           130-MSE

Chain D from PDB  Type:PROTEIN  Length:225
 aligned with TRAR_RHIRD | P33905 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:234
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    
           TRAR_RHIRD     1 MQHWLDKLTDLAAIEGDECILKTGLADIADHFGFTGYAYLHIQHRHITAVTNYHRQWQSTYFDKKFEALDPVVKRARSRKHIFTWSGEHERPTLSKDERAFYDHASDFGIRSGITIPIKTANGFMSMFTMASDKPVIDLDREIDAVAAAATIGQIHARISFLRTTPTAEDAAWLDPKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKLI 234
               SCOP domains d1l3ld2 D:1-162 Transcription factor TraR, N-terminal domain                                                                                                      ---------d1l3ld1 D:172-234                                               SCOP domains
               CATH domains -1l3lD01 D:2-180  [code=3.30.450.80, no name defined]                                                                                                                               1l3lD02 D:181-234                                      CATH domains
           Pfam domains (1) ----------------Autoind_bind-1l3lD01 D:17-159                                                                                                                  ------------GerE-1l3lD05 D:172-228                                   ------ Pfam domains (1)
           Pfam domains (2) ----------------Autoind_bind-1l3lD02 D:17-159                                                                                                                  ------------GerE-1l3lD06 D:172-228                                   ------ Pfam domains (2)
           Pfam domains (3) ----------------Autoind_bind-1l3lD03 D:17-159                                                                                                                  ------------GerE-1l3lD07 D:172-228                                   ------ Pfam domains (3)
           Pfam domains (4) ----------------Autoind_bind-1l3lD04 D:17-159                                                                                                                  ------------GerE-1l3lD08 D:172-228                                   ------ Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhh....hhhhhhhhhhhhhhhh...eeeeeee....eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeehhhhh...hhhhhhhhhhhhh....eeeeeeeeehhheeeeeeeee...........hhhhhhhhhhhhhhhhhh.---------...hhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------HTH_LUXR_2  PDB: D:172-232 UniProt: 167-232                       -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1l3l D   1 mQHWLDKLTDLAAIEGDECILKTGLADIADHFGFTGYAYLHIQHRHITAVTNYHRQWQSTYFDKKFEALDPVVKRARSRKHIFTWSGEHERPTLSKDERAFYDHASDFGIRSGITIPIKTANGFmSmFTmASDKPVIDLDREIDAVAAAATIGQIHARISFL---------AWLDPKEATYLRWIAVGKTmEEIADVEGVKYNSVRVKLREAmKRFDVRSKAHLTALAIRRKLI 234
                            |       10        20        30        40        50        60        70        80        90       100       110       120    | |130       140       150       160 |       - |     180       190|      200       210  |    220       230    
                            1-MSE                                                                                                                     125-MSE|                             162       172                191-MSE               213-MSE                 
                                                                                                                                                        127-MSE                                                                                                       
                                                                                                                                                           130-MSE

Chain E from PDB  Type:DNA  Length:20
                                                    
                 1l3l E   1 GATGTGCAGATCTGCACATC  20
                                    10        20

Chain F from PDB  Type:DNA  Length:20
                                                    
                 1l3l F 101 GATGTGCAGATCTGCACATC 120
                                   110       120

Chain G from PDB  Type:DNA  Length:20
                                                    
                 1l3l G   1 GATGTGCAGATCTGCACATC  20
                                    10        20

Chain H from PDB  Type:DNA  Length:20
                                                    
                 1l3l H 101 GATGTGCAGATCTGCACATC 120
                                   110       120

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 Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Beta-Lactamase (202)

Homologous Superfamily: [code=3.30.450.80, no name defined] (2)

[unclassified] (1)

1a	1l3lA01	A:2-171
1b	1l3lB01	B:2-171
1c	1l3lC01	C:2-180
1d	1l3lD01	D:2-180

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: 'winged helix' repressor DNA binding domain (507)

[unclassified] (77)

2a	1l3lA02	A:172-234
2b	1l3lB02	B:172-234
2c	1l3lC02	C:181-234
2d	1l3lD02	D:181-234

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GAF (44)

Family: Autoind_bind (5)

Rhizobium radiobacter (Agrobacterium tumefaciens) (Agrobacterium radiobacter) (1)

1a	Autoind_bind-1l3lD01	D:17-159
1b	Autoind_bind-1l3lD02	D:17-159
1c	Autoind_bind-1l3lD03	D:17-159
1d	Autoind_bind-1l3lD04	D:17-159

Clan: HTH (544)

Family: GerE (15)

Rhizobium radiobacter (Agrobacterium tumefaciens) (Agrobacterium radiobacter) (1)

2a	GerE-1l3lD05	D:172-228
2b	GerE-1l3lD06	D:172-228
2c	GerE-1l3lD07	D:172-228
2d	GerE-1l3lD08	D:172-228

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (TRAR_RHIRD | P33905)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
	GO:0000746	conjugation	The union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms.
	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: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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(no "Related Entries Specified in the PDB File" available for 1L3L)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 26)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

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