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Title :   CRYSTAL STRUCTURE OF THE LACTOSE REPRESSOR BOUND TO ANTI-INDUCER ONPF IN INDUCED STATE

Authors :   R. Daber

Date :   27 Mar 07 (Deposition) - 19 Jun 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.50

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

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

Reference :   R. Daber, S. Stayrook, A. Rosenberg, M. Lewis
Structural Analysis Of Lac Repressor Bound To Allosteric Effectors.
J. Mol. Biol. V. 370 609 2007
PubMed-ID: 17543986 | Reference-DOI: 10.1016/J.JMB.2007.04.028
(for further references see the PDB file header)

Molecule 1 - LACTOSE OPERON REPRESSOR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	HTUA
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	LACI
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

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

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA B:75 , ASN B:125 , LEU B:148 , ASP B:149 , ILE B:160 , PHE B:161 , ARG B:197 , TRP B:220 , ASN B:246 , ASP B:274 , GLN B:291	BINDING SITE FOR RESIDUE NPF B 901
2	AC2	SOFTWARE	ASN A:125 , LEU A:148 , ASP A:149 , PHE A:161 , SER A:193 , ARG A:197 , TRP A:220 , ASN A:246 , ASP A:274 , GLN A:291	BINDING SITE FOR RESIDUE NPF A 902

(no "SS Bond" information available for 2PAF)

Asymmetric/Biological Unit

No.	Residues
1	Asn A:142	-	Val A:143
2	Ile A:283	-	Pro A:284
3	Ile B:283	-	Pro B:284
4	Ala B:312	-	Val B:313

Asymmetric/Biological Unit (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)

(no "PROSITE Motif" information available for 2PAF)

(no "Exon" information available for 2PAF)

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: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 d2pafa1 A:62-330 Lac-repressor (lacR) core (C-terminal domain)                                                                                                                                                                                                                SCOP domains
               CATH domains 2pafA01 A:62-161,A:291-320  [code=3.40.50.2300, no name defined]                                    2pafA02 A:162-290,A:321-330  [code=3.40.50.2300, no name defined]                                                                2pafA01 A:62-161,A:291-320    2pafA02    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhh...........eeeee...hhhhhhhhhhhhh...eee..............hhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhh......ee....hhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhh........eee....hhhhhhh.....eee.hhhhhhhhhhhhhhhhh.............eee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2paf A  62 LLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTL 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 B 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 d2pafb1 B:62-330 Lac-repressor (lacR) core (C-terminal domain)                                                                                                                                                                                                                SCOP domains
               CATH domains 2pafB01 B:62-161,B:291-320  [code=3.40.50.2300, no name defined]                                    2pafB02 B:162-290,B:321-330  [code=3.40.50.2300, no name defined]                                                                2pafB01 B:62-161,B:291-320    2pafB02    CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------Peripla_BP_3-2pafB01 B:171-329                                                                                                                                 - Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------Peripla_BP_3-2pafB02 B:171-329                                                                                                                                 - Pfam domains (2)
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh....eee..........eeeehhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhh.......eee...hhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhh........eee....hhhhhhh.....eee.hhhhhhhhhhhhhhhhhhh.....eeee..eee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2paf B  62 LLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTL 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

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	d2pafa1	A:62-330
1b	d2pafb1	B:62-330

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. (30)

1a	2pafA02	A:162-290,A:321-330
1b	2pafB02	B:162-290,B:321-330
1c	2pafA01	A:62-161,A:291-320
1d	2pafB01	B:62-161,B: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_3-2pafB01	B:171-329
1b	Peripla_BP_3-2pafB02	B:171-329

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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 B:312 - Val B:313	[ RasMol ]
		Asn A:142 - Val A:143	[ RasMol ]
		Ile A:283 - Pro A:284	[ RasMol ]
		Ile B:283 - Pro B:284	[ RasMol ]

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	2paf
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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

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Exons (0, 0)

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