1H0M | PD0654 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   THREE-DIMENSIONAL STRUCTURE OF THE QUORUM SENSING PROTEIN TRAR BOUND TO ITS AUTOINDUCER AND TO ITS TARGET DNA

Authors :   A. Vannini, C. Volpari, C. Gargioli, E. Muraglia, R. Cortese, R. De Fra P. Neddermann, S. Di Marco

Date :   25 Jun 02 (Deposition) - 29 Aug 02 (Release) - 05 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Transcription/Dna, Luxr-Type Protein, Quorum Sensing, Transcriptional Regulator, Dna-Binding Protein, Homoserine Lactone, Trar, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Vannini, C. Volpari, C. Gargioli, E. Muraglia, R. Cortese, R. De Francesco, P. Neddermann, S. Di Marco
The Crystal Structure Of The Quorum Sensing Protein Trar Bound To Its Autoinducer And Target Dna
Embo J. V. 21 4393 2002
PubMed-ID: 12198141 | Reference-DOI: 10.1093/EMBOJ/CDF459
(for further references see the PDB file header)

Molecule 1 - TRANSCRIPTIONAL ACTIVATOR PROTEIN TRAR
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	B834-DE3
	Expression System Taxid	:	562
	Organism Scientific	:	AGROBACTERIUM TUMEFACIENS
	Organism Taxid	:	358
	Other Details	:	TRANSCRIPTIONAL ACTIVATOR PROTEIN TRAR FROM AGROBACTERIUM TUMEFACIENS
	Other Details - Source	:	ENCODED ON PLASMID PTIA6NC
	Strain	:	A348

*Molecule 2 - 5'-D(APTPGPTPGPCPAPGPAPTP CPTPGPCPAPCPAPT)-3'*
	Chains	:	E, F, G, H
	Engineered	:	YES
	Other Details	:	TRABOX
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 31)

No.	Name	Count	Type	Full Name
1	HSL	4	Ligand/Ion	HOMOSERINE LACTONE
2	MSE	23	Mod. Amino Acid	SELENOMETHIONINE
3	OOA	4	Ligand/Ion	3-OXOOCTANOIC ACID

Biological Unit 1 (3, 16)

No.	Name	Count	Type	Full Name
1	HSL	2	Ligand/Ion	HOMOSERINE LACTONE
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
3	OOA	2	Ligand/Ion	3-OXOOCTANOIC ACID

Biological Unit 2 (3, 15)

No.	Name	Count	Type	Full Name
1	HSL	2	Ligand/Ion	HOMOSERINE LACTONE
2	MSE	11	Mod. Amino Acid	SELENOMETHIONINE
3	OOA	2	Ligand/Ion	3-OXOOCTANOIC ACID

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:57 , TYR A:61 , ASP A:70 , VAL A:72 , PHE A:101 , TYR A:102 , ALA A:105 , ILE A:110 , OOA A:1236	BINDING SITE FOR RESIDUE HSL A1235
2	AC2	SOFTWARE	LEU A:40 , TYR A:53 , GLN A:58 , TYR A:61 , ASP A:70 , VAL A:72 , MSE A:127 , HSL A:1235	BINDING SITE FOR RESIDUE OOA A1236
3	AC3	SOFTWARE	TRP B:57 , TYR B:61 , ASP B:70 , VAL B:72 , TRP B:85 , PHE B:101 , TYR B:102 , ALA B:105 , ILE B:110 , OOA B:1236	BINDING SITE FOR RESIDUE HSL B1235
4	AC4	SOFTWARE	LEU B:40 , TYR B:53 , GLN B:58 , TYR B:61 , PHE B:62 , ASP B:70 , THR B:129 , HSL B:1235	BINDING SITE FOR RESIDUE OOA B1236
5	AC5	SOFTWARE	TYR C:53 , TRP C:57 , ASP C:70 , VAL C:72 , PHE C:101 , ALA C:105 , ILE C:110 , OOA C:1236	BINDING SITE FOR RESIDUE HSL C1235
6	AC6	SOFTWARE	LEU C:40 , TYR C:53 , TYR C:61 , VAL C:72 , TRP C:85 , MSE C:127 , THR C:129 , HSL C:1235	BINDING SITE FOR RESIDUE OOA C1236
7	AC7	SOFTWARE	TRP D:57 , TYR D:61 , ASP D:70 , VAL D:72 , TRP D:85 , ALA D:105 , ILE D:110 , OOA D:1236	BINDING SITE FOR RESIDUE HSL D1235
8	AC8	SOFTWARE	ALA D:38 , LEU D:40 , TYR D:53 , TYR D:61 , TRP D:85 , THR D:129 , HSL D:1235	BINDING SITE FOR RESIDUE OOA D1236

(no "SS Bond" information available for 1H0M)

Asymmetric Unit

No.	Residues
1	Glu A:15	-	Gly A:16
2	Glu B:15	-	Gly B:16
3	Glu C:15	-	Gly C:16
4	Glu D:15	-	Gly D:16

(no "SAP(SNP)/Variant" information available for 1H0M)

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:170-232 B:167-232 C:171-232 D:167-232

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	A:170-232 B:167-232 - -

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	- - C:171-232 D:167-232

(no "Exon" information available for 1H0M)

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:230
 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 d1h0ma2 A:1-165 Transcription factor TraR, N-terminal domain                                                                                                         ----d1h0ma1 A:170-234                                                 SCOP domains
               CATH domains -1h0mA01 A:2-170  [code=3.30.450.80, no name defined]                                                                                                                     1h0mA02 A:171-234 'winged helix' repressor DNA binding domain    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhh....hhhhhhhhhhhhhhhh...eeeeeeee..eeeeee..hhhhhhhhhhh.....hhhhhhhhhh...eee...........hhhhhhhhhhh....eeeeeeee.....eeeeeeee...........hhhhhhhhhhhhhhhhhhhh..----.....hhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------HTH_LUXR_2  PDB: A:170-232 UniProt: 167-232                       -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1h0m A   1 mQHWLDKLTDLAAIEGDECILKTGLADIADHFGFTGYAYLHIQHRHITAVTNYHRQWQSTYFDKKFEALDPVVKRARSRKHIFTWSGEHERPTLSKDERAFYDHASDFGIRSGITIPIKTANGFmSmFTmASDKPVIDLDREIDAVAAAATIGQIHARISFLRTT----DAAWLDPKEATYLRWIAVGKTmEEIADVEGVKYNSVRVKLREAmKRFDVRSKAHLTALAIRRKLI 234
                            |       10        20        30        40        50        60        70        80        90       100       110       120    | |130       140       150       160    |  170       180       190|      200       210  |    220       230    
                            |                                                                                                                         125-MSE|                                165  170                  191-MSE               213-MSE                 
                            1-MSE                                                                                                                       127-MSE                                                                                                       
                                                                                                                                                           130-MSE

Chain B from PDB  Type:PROTEIN  Length:230
 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 d1h0mb2 B:1-169 Transcription factor TraR, N-terminal domain                                                                                                             d1h0mb1 B:170-234                                                 SCOP domains
               CATH domains -1h0mB01 B:2-171  [code=3.30.450.80, no name defined]                                                                                                                      1h0mB02 B:172-234 'winged helix' repressor DNA binding domain   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhh....hhhhhhhhhhhhhhhhh..eeeeeee....eeeee..hhhhhhhhhhh.....hhhhhhhhh....eee..........hhhhhhhhhhhh....eeeeeeeee...eeeeeeeee......----.hhhhhhhhhhhhhhhhhhh............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
                 1h0m B   1 mQHWLDKLTDLAAIEGDECILKTGLADIADHFGFTGYAYLHIQHRHITAVTNYHRQWQSTYFDKKFEALDPVVKRARSRKHIFTWSGEHERPTLSKDERAFYDHASDFGIRSGITIPIKTANGFmSmFTmASDKPVID----IDAVAAAATIGQIHARISFLRTTPTAEDAAWLDPKEATYLRWIAVGKTmEEIADVEGVKYNSVRVKLREAmKRFDVRSKAHLTALAIRRKLI 234
                            |       10        20        30        40        50        60        70        80        90       100       110       120    | |130       | -  |    150       160       170       180       190|      200       210  |    220       230    
                            1-MSE                                                                                                                     125-MSE|     138  143                                             191-MSE               213-MSE                 
                                                                                                                                                        127-MSE                                                                                                       
                                                                                                                                                           130-MSE

Chain C from PDB  Type:PROTEIN  Length:228
 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 d1h0mc2 C:1-164 Transcription factor TraR, N-terminal domain                                                                                                        ------d1h0mc1 C:171-234                                                SCOP domains
               CATH domains -1h0mC01 C:2-180  [code=3.30.450.80, no name defined]                                                                                                                               1h0mC02 C:181-234                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhh....hhhhhhhhhhhhhhhh...eeeeeee....eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh...eee..........hhhhhhhhhhhh....eeeeeeee.....eeeeeeee...........hhhhhhhhhhhhhhhhhhh..------....hhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------HTH_LUXR_2  PDB: C:171-232 UniProt: 167-232                       -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1h0m C   1 mQHWLDKLTDLAAIEGDECILKTGLADIADHFGFTGYAYLHIQHRHITAVTNYHRQWQSTYFDKKFEALDPVVKRARSRKHIFTWSGEHERPTLSKDERAFYDHASDFGIRSGITIPIKTANGFmSmFTmASDKPVIDLDREIDAVAAAATIGQIHARISFLRT------AAWLDPKEATYLRWIAVGKTmEEIADVEGVKYNSVRVKLREAmKRFDVRSKAHLTALAIRRKLI 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|                               164    171                 191-MSE               213-MSE                 
                                                                                                                                                        127-MSE                                                                                                       
                                                                                                                                                           130-MSE

Chain D from PDB  Type:PROTEIN  Length:229
 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 d1h0md2 D:2-169 Transcription factor TraR, N-terminal domain                                                                                                            d1h0md1 D:170-234                                                 SCOP domains
               CATH domains 1h0mD01 D:2-171  [code=3.30.450.80, no name defined]                                                                                                                      1h0mD02 D:172-234 'winged helix' repressor DNA binding domain   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh....hhhhhhhhhhhhhhhhh..eeeeeee....eeeee..hhhhhhhhhhh.....hhhhhhhhh....eee..........hhhhhhhhhhhh....eeeeeeeee...eeeeeeeee......----.hhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------HTH_LUXR_2  PDB: D:167-232 UniProt: 167-232                       -- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h0m D   2 QHWLDKLTDLAAIEGDECILKTGLADIADHFGFTGYAYLHIQHRHITAVTNYHRQWQSTYFDKKFEALDPVVKRARSRKHIFTWSGEHERPTLSKDERAFYDHASDFGIRSGITIPIKTANGFmSmFTmASDKPVID----IDAVAAAATIGQIHARISFLRTTPTAEDAAWLDPKEATYLRWIAVGKTmEEIADVEGVKYNSVRVKLREAmKRFDVRSKAHLTALAIRRKLI 234
                                    11        21        31        41        51        61        71        81        91       101       111       121   | | 131      |  - |     151       161       171       181       191       201       211 |     221       231   
                                                                                                                                                     125-MSE|     138  143                                             191-MSE               213-MSE                 
                                                                                                                                                       127-MSE                                                                                                       
                                                                                                                                                          130-MSE

Chain E from PDB  Type:DNA  Length:18
                                                  
                 1h0m E   1 ATGTGCAGATCTGCACAT  18
                                    10

Chain F from PDB  Type:DNA  Length:18
                                                  
                 1h0m F   1 ATGTGCAGATCTGCACAT  18
                                    10

Chain G from PDB  Type:DNA  Length:18
                                                  
                 1h0m G   1 ATGTGCAGATCTGCACAT  18
                                    10

Chain H from PDB  Type:DNA  Length:18
                                                  
                 1h0m H   1 ATGTGCAGATCTGCACAT  18
                                    10

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)

Agrobacterium tumefaciens. Organism_taxid: 358. Strain: a348. (1)

1a	1h0mB01	B:2-171
1b	1h0mD01	D:2-171
1c	1h0mA01	A:2-170
1d	1h0mC01	C: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)

Agrobacterium tumefaciens. Organism_taxid: 358. Strain: a348. (1)

2a	1h0mA02	A:171-234
2b	1h0mB02	B:172-234
2c	1h0mD02	D:172-234
2d	1h0mC02	C:181-234

(no "Pfam Domain" information available for 1H0M)

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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	Cis Peptide Bonds
		Glu A:15 - Gly A:16	[ RasMol ]
		Glu B:15 - Gly B:16	[ RasMol ]
		Glu C:15 - Gly C:16	[ RasMol ]
		Glu D:15 - Gly D:16	[ RasMol ]

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	TRAR_RHIRD \| P33905	:	1l3l

1l3l	CRYSTAL STRUCTURE OF A BACTERIAL QUORUM- SENSINGTRANSCRIPTION FACTOR COMPLEXED WITH PHEROMONE AND DNA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 31)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

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SCOP Domains (2, 8)

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