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Title :   UNPRECEDENTED QUATERNARY STRUCTURE OF E. COLI LAC REPRESSOR CORE TETRAMER: IMPLICATIONS FOR DNA LOOPING

Authors :   A. M. Friedman, T. O. Fischmann, T. A. Steitz

Date :   06 Mar 95 (Deposition) - 31 Jul 95 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. M. Friedman, T. O. Fischmann, T. A. Steitz
Crystal Structure Of Lac Repressor Core Tetramer And Its Implications For Dna Looping.
Science V. 268 1721 1995
PubMed-ID: 7792597
(for further references see the PDB file header)

Molecule 1 - LAC REPRESSOR
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System Vector Type	:	LAC
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 8)

No.	Name	Count	Type	Full Name
1	EMC	4	Ligand/Ion	ETHYL MERCURY ION
2	IPT	4	Ligand/Ion	ISOPROPYL-1-BETA-D-THIOGALACTOSIDE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:280 , CYS A:281 , MET B:223	BINDING SITE FOR RESIDUE EMC A 999
2	AC2	SOFTWARE	MET A:223 , SER B:280 , CYS B:281 , ARG B:326	BINDING SITE FOR RESIDUE EMC B 999
3	AC3	SOFTWARE	CYS C:281 , ARG C:326 , MET D:223	BINDING SITE FOR RESIDUE EMC C 999
4	AC4	SOFTWARE	ARG C:255 , ASP D:275 , GLU D:277 , CYS D:281 , LYS D:290	BINDING SITE FOR RESIDUE EMC D 999
5	AC5	SOFTWARE	ALA A:75 , PRO A:76 , LEU A:148 , ASP A:149 , SER A:193 , ARG A:197 , TRP A:220 , ASN A:246 , ASP A:274	BINDING SITE FOR RESIDUE IPT A 998
6	AC6	SOFTWARE	SER B:69 , ALA B:75 , PRO B:76 , ARG B:101 , ASN B:125 , ASP B:149 , SER B:193 , ARG B:197 , TRP B:220 , ASN B:246 , ASP B:274	BINDING SITE FOR RESIDUE IPT B 998
7	AC7	SOFTWARE	SER C:69 , ALA C:75 , PRO C:76 , ILE C:79 , ARG C:101 , ASP C:149 , SER C:193 , ARG C:197 , TRP C:220 , ASN C:246 , ASP C:274	BINDING SITE FOR RESIDUE IPT C 998
8	AC8	SOFTWARE	ALA D:75 , PRO D:76 , ARG D:101 , LEU D:148 , ASP D:149 , SER D:193 , ARG D:197 , TRP D:220 , ASN D:246 , ASP D:274	BINDING SITE FOR RESIDUE IPT D 998

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

Asymmetric/Biological Unit

No.	Residues
1	Ile A:283	-	Pro A:284
2	Ile B:283	-	Pro B:284
3	Ile C:283	-	Pro C:284
4	Ala C:331	-	Pro C:332
5	Ile D:283	-	Pro D:284

Asymmetric/Biological Unit (1, 4)

								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/D	Y	282	D
	* ID not provided by source

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

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

(no "Exon" information available for 1TLF)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:296
 aligned with LACI_ECOLI | P03023 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:296
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350      
           LACI_ECOLI    61 SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRL 356
               SCOP domains d1tlfa_ A: Lac-repressor (lacR) core (C-terminal domain)                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1tlfA01 A:61-161,A:291-320  [code=3.40.50.2300, no name defined]                                     1tlfA02 A:162-290,A:321-336  [code=3.40.50.2300, no name defined]                                                                1tlfA01 A:61-161,A:291-320    1tlfA02         -------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhh.....eeeeeee..hhhhhhhhhh.....eeeee........eeee.hhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhh......eeee..hhhhhhhhhhhhh.........eeeeee............eeee..hhhhhhhhhhhhhhhh.......eeee..eee..............hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D-------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tlf A  61 SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRL 356
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350

Chain B from PDB  Type:PROTEIN  Length:296
 aligned with LACI_ECOLI | P03023 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:296
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350      
           LACI_ECOLI    61 SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRL 356
               SCOP domains d1tlfb_ B: Lac-repressor (lacR) core (C-terminal domain)                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1tlfB01 B:61-161,B:291-320  [code=3.40.50.2300, no name defined]                                     1tlfB02 B:162-290,B:321-336  [code=3.40.50.2300, no name defined]                                                                1tlfB01 B:61-161,B:291-320    1tlfB02         -------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhh.....eeeeeee..hhhhhhhhhh.....eeeee........eeee.hhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhh......eeee..hhhhhhhhhhhhh.........eeeeee............eeee..hhhhhhhhhhhhhhhh.......eeee..eee..............hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D-------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tlf B  61 SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRL 356
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350

Chain C from PDB  Type:PROTEIN  Length:296
 aligned with LACI_ECOLI | P03023 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:296
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350      
           LACI_ECOLI    61 SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRL 356
               SCOP domains d1tlfc_ C: Lac-repressor (lacR) core (C-terminal domain)                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1tlfC01 C:61-161,C:291-320  [code=3.40.50.2300, no name defined]                                     1tlfC02 C:162-290,C:321-336  [code=3.40.50.2300, no name defined]                                                                1tlfC01 C:61-161,C:291-320    1tlfC02         -------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhh.....eeeeeee..hhhhhhhhhh.....eeeee........eeee.hhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhh......eeee..hhhhhhhhhhhhh.........eeeeee............eeee..hhhhhhhhhhhhhhhh.......eeee..eee..............hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D-------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tlf C  61 SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRL 356
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350

Chain D from PDB  Type:PROTEIN  Length:296
 aligned with LACI_ECOLI | P03023 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:296
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350      
           LACI_ECOLI    61 SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRL 356
               SCOP domains d1tlfd_ D: Lac-repressor (lacR) core (C-terminal domain)                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1tlfD01 D:61-161,D:291-320  [code=3.40.50.2300, no name defined]                                     1tlfD02 D:162-290,D:321-336  [code=3.40.50.2300, no name defined]                                                                1tlfD01 D:61-161,D:291-320    1tlfD02         -------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------Peripla_BP_3-1tlfD01 D:171-329                                                                                                                                 --------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------Peripla_BP_3-1tlfD02 D:171-329                                                                                                                                 --------------------------- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------Peripla_BP_3-1tlfD03 D:171-329                                                                                                                                 --------------------------- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------Peripla_BP_3-1tlfD04 D:171-329                                                                                                                                 --------------------------- Pfam domains (4)
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhh.....eeeeeee..hhhhhhhhhh.....eeeee........eeee.hhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhh......eeee..hhhhhhhhhhhhh.........eeeeee............eeee..hhhhhhhhhhhhhhhh.......eeee..eee..............hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D-------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tlf D  61 SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRL 356
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Periplasmic binding protein-like I (179)

Superfamily: Periplasmic binding protein-like I (179)

Family: L-arabinose binding protein-like (114)

Protein domain: Lac-repressor (lacR) core (C-terminal domain) (11)

Escherichia coli [TaxId: 562] (11)

1a	d1tlfa_	A:
1b	d1tlfb_	B:
1c	d1tlfc_	C:
1d	d1tlfd_	D:

Asymmetric/Biological 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)

Escherichia coli. Organism_taxid: 562. Expression_system_vector_type:lac (1)

1a	1tlfA02	A:162-290,A:321-336
1b	1tlfB02	B:162-290,B:321-336
1c	1tlfC02	C:162-290,C:321-336
1d	1tlfD02	D:162-290,D:321-336
1e	1tlfA01	A:61-161,A:291-320
1f	1tlfB01	B:61-161,B:291-320
1g	1tlfC01	C:61-161,C:291-320
1h	1tlfD01	D:61-161,D:291-320

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Periplas_BP (97)

Family: Peripla_BP_3 (41)

Escherichia coli (strain K12) (28)

1a	Peripla_BP_3-1tlfD01	D:171-329
1b	Peripla_BP_3-1tlfD02	D:171-329
1c	Peripla_BP_3-1tlfD03	D:171-329
1d	Peripla_BP_3-1tlfD04	D:171-329

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (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/Biological Unit
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	Cis Peptide Bonds
		Ala C:331 - Pro C:332	[ RasMol ]
		Ile A:283 - Pro A:284	[ RasMol ]
		Ile B:283 - Pro B:284	[ RasMol ]
		Ile C:283 - Pro C:284	[ RasMol ]
		Ile D:283 - Pro D:284	[ RasMol ]

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	1tlf
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(no "Related Entries Specified in the PDB File" available for 1TLF)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 4)

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