1JWL | PD0250 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF THE DIMERIC LAC REPRESSOR/OPERATOR O1/ONPF COMPLEX

Authors :   C. E. Bell, M. Lewis

Date :   04 Sep 01 (Deposition) - 05 Oct 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   4.00

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

Keywords :   Lac Repressor, Gene Regulation, Dna-Bending, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. E. Bell, M. Lewis
Crystallographic Analysis Of Lac Repressor Bound To Natural Operator O1.
J. Mol. Biol. V. 312 921 2001
PubMed-ID: 11580238 | Reference-DOI: 10.1006/JMBI.2001.5024
(for further references see the PDB file header)

*Molecule 1 - 5'- D(APGPAPAPTTPGPTPGPAPGPCPGPGPAPTPAPAPCP* APAPTPT)-3'*
	Chains	:	D
	Engineered	:	YES
	Other Details	:	O1 TOP STRAND
	Synthetic	:	YES

*Molecule 2 - 5'- D(TPAPAPTPTPGPTPTPAPTPCPCPGPCPTPCPAPCPAP APTPTPC)-3'**
	Chains	:	E
	Engineered	:	YES
	Other Details	:	O1 BOTTOM STRAND
	Synthetic	:	YES

Molecule 3 - LACTOSE OPERON REPRESSOR
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL DELETION MUTANT
	Gene	:	LACI
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	NPF	3	Ligand/Ion	ORTHONITROPHENYL-BETA-D-FUCOPYRANOSIDE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	NPF	2	Ligand/Ion	ORTHONITROPHENYL-BETA-D-FUCOPYRANOSIDE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	NPF	2	Ligand/Ion	ORTHONITROPHENYL-BETA-D-FUCOPYRANOSIDE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA B:75 , ILE B:79 , LEU B:148 , ASP B:149 , PHE B:161 , ARG B:197 , ASN B:246 , ASP B:274 , GLN B:291 , PHE B:293	BINDING SITE FOR RESIDUE NPF B 334
2	AC2	SOFTWARE	ALA C:75 , ILE C:79 , LEU C:148 , PHE C:161 , ARG C:197 , ASN C:246 , ASP C:274 , GLN C:291 , PHE C:293 , LEU C:296	BINDING SITE FOR RESIDUE NPF C 334
3	AC3	SOFTWARE	ALA A:75 , ILE A:79 , ASN A:125 , PHE A:161 , ARG A:197 , TRP A:220 , ASN A:246 , ASP A:274 , PHE A:293	BINDING SITE FOR RESIDUE NPF A 334

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

Asymmetric Unit

No.	Residues
1	Ile A:283	-	Pro A:284
2	Ile B:283	-	Pro B:284
3	Ile C:283	-	Pro C:284

Asymmetric Unit (1, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LACI_ECOLI_001 *	Y	282	D	LACI_ECOLI	---	---	A/B/C	Y	282	D
	* 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_LACI_ECOLI_001 *	Y	282	D	LACI_ECOLI	---	---	A/B	Y	282	D
	* 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_LACI_ECOLI_001 *	Y	282	D	LACI_ECOLI	---	---	C	Y	282	D
	* ID not provided by source

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_LACI_2	PS50932	LacI-type HTH domain profile.	LACI_ECOLI	4-58	2	A:4-58 B:4-58
2	HTH_LACI_1	PS00356	LacI-type HTH domain signature.	LACI_ECOLI	6-24	2	A:6-24 B:6-24

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_LACI_2	PS50932	LacI-type HTH domain profile.	LACI_ECOLI	4-58	2	A:4-58 B:4-58
2	HTH_LACI_1	PS00356	LacI-type HTH domain signature.	LACI_ECOLI	6-24	2	A:6-24 B:6-24

Biological Unit 2 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_LACI_2	PS50932	LacI-type HTH domain profile.	LACI_ECOLI	4-58	0	- -
2	HTH_LACI_1	PS00356	LacI-type HTH domain signature.	LACI_ECOLI	6-24	0	- -

(no "Exon" information available for 1JWL)

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:329
 aligned with LACI_ECOLI | P03023 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:329
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321         
           LACI_ECOLI     2 KPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTL 330
               SCOP domains d1jwla1 A:2-60 Lac repressor (LacR), N-terminal domain     d1jwla2 A:61-330 Lac-repressor (lacR) core (C-terminal domain)                                                                                                                                                                                                                 SCOP domains
               CATH domains 1jwlA01 A:2-59 lambda repressor-like DNA-binding domains  1jwlA02 A:60-160,A:291-317  [code=3.40.50.2300, no name defined]                                     1jwlA03 A:161-290,A:318-330  [code=3.40.50.2300, no name defined]                                                                 1jwlA02 A:60-160,A:291-317 1jwlA03       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh...hhhhhhhhhh......hhhhhhhhhhhhhhh...hhhhhhhh.....eeeeeee...hhhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh....eee..........eeeehhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhh.........eeeeee..hhhhhh....eeee.hhhhhhhhhhhhhhhhhh......eeee..eee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --HTH_LACI_2  PDB: A:4-58 UniProt: 4-58                  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----HTH_LACI_1         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jwl A   2 KPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKTAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTL 330
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321

Chain B from PDB  Type:PROTEIN  Length:329
 aligned with LACI_ECOLI | P03023 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:329
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321         
           LACI_ECOLI     2 KPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTL 330
               SCOP domains d1jwlb1 B:2-60 Lac repressor (LacR), N-terminal domain     d1jwlb2 B:61-330 Lac-repressor (lacR) core (C-terminal domain)                                                                                                                                                                                                                 SCOP domains
               CATH domains 1jwlB01 B:2-59 lambda repressor-like DNA-binding domains  1jwlB02 B:60-160,B:291-317  [code=3.40.50.2300, no name defined]                                     1jwlB03 B:161-290,B:318-330  [code=3.40.50.2300, no name defined]                                                                 1jwlB02 B:60-160,B:291-317 1jwlB03       CATH domains
           Pfam domains (1) ---LacI-1jwlB01 B:5-50                           ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---LacI-1jwlB02 B:5-50                           ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .....hhhhhh...hhhhhhhhhh......hhhhhhhhhhhhhhh...hhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh....eee..........eeeehhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhh.........eeeeee..hhhhhh....eeee.hhhhhhhhhhhhhhhhhh......eeee..eee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --HTH_LACI_2  PDB: B:4-58 UniProt: 4-58                  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----HTH_LACI_1         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jwl B   2 KPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKTAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTL 330
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321

Chain C from PDB  Type:PROTEIN  Length:269
 aligned with LACI_ECOLI | P03023 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:269
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321         
           LACI_ECOLI    62 LLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTL 330
               SCOP domains d1jwlc_ C: Lac-repressor (lacR) core (C-terminal domain)                                                                                                                                                                                                                      SCOP domains
               CATH domains 1jwlC01 C:62-161,C:291-320  [code=3.40.50.2300, no name defined]                                    1jwlC02 C:162-290,C:321-330  [code=3.40.50.2300, no name defined]                                                                1jwlC01 C:62-161,C:291-320    1jwlC02    CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------Peripla_BP_3-1jwlC01 C:171-329                                                                                                                                 - Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------Peripla_BP_3-1jwlC02 C:171-329                                                                                                                                 - Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------Peripla_BP_3-1jwlC03 C:171-329                                                                                                                                 - Pfam domains (3)
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh....eee..........eeeehhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhh.........eeeeee..hhhhhh....eeee.hhhhhhhhhhhhhhhhhh......eeee..eee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jwl C  62 LLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKTAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTL 330
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321

Chain D from PDB  Type:DNA  Length:14
                                              
                 1jwl D   6 TGTGAGCGGATAAC  19
                                    15

Chain E from PDB  Type:DNA  Length:14
                                              
                 1jwl E   6 GTTATCCGCTCACA  19
                                    15

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: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.2300, no name defined] (308)

[unclassified] (27)

1a	1jwlC02	C:162-290,C:321-330
1b	1jwlB02	B:60-160,B:291-317
1c	1jwlA03	A:161-290,A:318-330
1d	1jwlB03	B:161-290,B:318-330
1e	1jwlC01	C:62-161,C:291-320
1f	1jwlA02	A:60-160,A:291-317

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: 434 Repressor (Amino-terminal Domain) (116)

Homologous Superfamily: lambda repressor-like DNA-binding domains (100)

[unclassified] (45)

2a	1jwlA01	A:2-59
2b	1jwlB01	B:2-59

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: LacI (35)

Escherichia coli (strain K12) (30)

1a	LacI-1jwlB01	B:5-50
1b	LacI-1jwlB02	B:5-50

Clan: Periplas_BP (97)

Family: Peripla_BP_3 (41)

Escherichia coli (strain K12) (28)

2a	Peripla_BP_3-1jwlC01	C:171-329
2b	Peripla_BP_3-1jwlC02	C:171-329
2c	Peripla_BP_3-1jwlC03	C:171-329

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (LACI_ECOLI | P03023)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000986	bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase.
	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.
	GO:0001141	transcriptional repressor activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase in order to stop, prevent, or reduce the frequency, rate or extent of transcription from a bacterial-type RNA polymerase promoter.
biological process
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	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.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
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		Ile A:283 - Pro A:284	[ RasMol ]
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		Ile C:283 - Pro C:284	[ RasMol ]

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	1jwl
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 3)

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Exons (0, 0)

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