2GQQ - JenaLib

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Biological Unit 1 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF E. COLI LEUCINE-RESPONSIVE REGULATORY PROTEIN (LRP)

Authors :   S. De Los Rios, J. J. Perona

Date :   21 Apr 06 (Deposition) - 06 Mar 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.20

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

Keywords :   Helix-Turn-Helix, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. De Los Rios, J. J. Perona
Structure Of The Escherichia Coli Leucine-Responsive Regulatory Protein Lrp Reveals A Novel Octameric Assembly.
J. Mol. Biol. V. 366 1589 2007
PubMed-ID: 17223133 | Reference-DOI: 10.1016/J.JMB.2006.12.032

Molecule 1 - LEUCINE-RESPONSIVE REGULATORY PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PJWD1
	Expression System Strain	:	JM105
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	LRP, ALSB, IHB, LIVR, OPPI
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2GQQ)

(no "Site" information available for 2GQQ)

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

(no "Cis Peptide Bond" information available for 2GQQ)

Asymmetric Unit (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LRP_ECOLI_001 *	D	114	E	LRP_ECOLI	---	---	A/B/C/D	D	114	E
	* ID not provided by source

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

Biological Unit 1 (1, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LRP_ECOLI_001 *	D	114	E	LRP_ECOLI	---	---	A/B/C/D	D	114	E
	* ID not provided by source

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

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_ASNC_2	PS50956	AsnC-type HTH domain profile.	LRP_ECOLI	12-73	4	A:12-73 B:12-73 C:12-73 D:12-73
2	HTH_ASNC_1	PS00519	AsnC-type HTH domain signature.	LRP_ECOLI	30-56	4	A:30-56 B:30-56 C:30-56 D:30-56

Biological Unit 1 (2, 16)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_ASNC_2	PS50956	AsnC-type HTH domain profile.	LRP_ECOLI	12-73	8	A:12-73 B:12-73 C:12-73 D:12-73
2	HTH_ASNC_1	PS00519	AsnC-type HTH domain signature.	LRP_ECOLI	30-56	8	A:30-56 B:30-56 C:30-56 D:30-56

(no "Exon" information available for 2GQQ)

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:153
 aligned with LRP_ECOLI | P0ACJ0 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:153
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161   
            LRP_ECOLI    12 LDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQGYTALLNPHYLDASLLVFVEITLNRGAPDVFEQFNTAVQKLEEIQECHLVSGDFDYLLKTRVPDMSAYRKLLGETLLRLPGVNDTRTYVVMEEVKQSNRLVIKTR 164
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -2gqqA01 A:13-64                                     ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.....hhhhh...........hhhhhhhhh.eeeeeeee.........eeeeeee......hhhhhhhhhhh....eeeeeee.....eeeeee..hhhhhhhhh...........eeeeeeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------E-------------------------------------------------- SAPs(SNPs)
                PROSITE (1) HTH_ASNC_2  PDB: A:12-73 UniProt: 12-73                       ------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------HTH_ASNC_1  PDB: A:30-56   ------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gqq A  12 LDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQGYTALLNPHYLDASLLVFVEITLNRGAPDVFEQFNTAVQKLEEIQECHLVSGDFDYLLKTRVPDMSAYRKLLGETLLRLPGVNDTRTYVVMEEVKQSNRLVIKTR 164
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain B from PDB  Type:PROTEIN  Length:151
 aligned with LRP_ECOLI | P0ACJ0 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:151
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161 
            LRP_ECOLI    12 LDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQGYTALLNPHYLDASLLVFVEITLNRGAPDVFEQFNTAVQKLEEIQECHLVSGDFDYLLKTRVPDMSAYRKLLGETLLRLPGVNDTRTYVVMEEVKQSNRLVIK 162
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -2gqqB01 B:13-64                                     -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...hhhhhhhhh........hhhhhhhhhh.eeeeeeee........eeeeeeeee.....hhhhhhhhhhh....eeeeeee.....eeeeeee.hhhhhhhhh..hhhhh..eeeeeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------E------------------------------------------------ SAPs(SNPs)
                PROSITE (1) HTH_ASNC_2  PDB: B:12-73 UniProt: 12-73                       ----------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------HTH_ASNC_1  PDB: B:30-56   ---------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gqq B  12 LDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQGYTALLNPHYLDASLLVFVEITLNRGAPDVFEQFNTAVQKLEEIQECHLVSGDFDYLLKTRVPDMSAYRKLLGETLLRLPGVNDTRTYVVMEEVKQSNRLVIK 162
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain C from PDB  Type:PROTEIN  Length:157
 aligned with LRP_ECOLI | P0ACJ0 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:157
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       
            LRP_ECOLI     8 PGKDLDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQGYTALLNPHYLDASLLVFVEITLNRGAPDVFEQFNTAVQKLEEIQECHLVSGDFDYLLKTRVPDMSAYRKLLGETLLRLPGVNDTRTYVVMEEVKQSNRLVIKTR 164
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----2gqqC01 C:13-64                                     ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhh.eeeeeeee........eeeeeeee......hhhhhhhh.......eeeeeee.....eeeeeee.hhhhhhhhhhhh........eeeeeeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------E-------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----HTH_ASNC_2  PDB: C:12-73 UniProt: 12-73                       ------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----------------------HTH_ASNC_1  PDB: C:30-56   ------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gqq C   8 PGKDLDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQGYTALLNPHYLDASLLVFVEITLNRGAPDVFEQFNTAVQKLEEIQECHLVSGDFDYLLKTRVPDMSAYRKLLGETLLRLPGVNDTRTYVVMEEVKQSNRLVIKTR 164
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157

Chain D from PDB  Type:PROTEIN  Length:153
 aligned with LRP_ECOLI | P0ACJ0 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:153
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161   
            LRP_ECOLI    12 LDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQGYTALLNPHYLDASLLVFVEITLNRGAPDVFEQFNTAVQKLEEIQECHLVSGDFDYLLKTRVPDMSAYRKLLGETLLRLPGVNDTRTYVVMEEVKQSNRLVIKTR 164
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -2gqqD01 D:13-64                                     ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eeeeeeee........eeeeeeeee.....hhhhhhhh.......eeeeeee.....eeeeeee.hhhhhhhhhhhh......eeeeeeeeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------E-------------------------------------------------- SAPs(SNPs)
                PROSITE (1) HTH_ASNC_2  PDB: D:12-73 UniProt: 12-73                       ------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------HTH_ASNC_1  PDB: D:30-56   ------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gqq D  12 LDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQGYTALLNPHYLDASLLVFVEITLNRGAPDVFEQFNTAVQKLEEIQECHLVSGDFDYLLKTRVPDMSAYRKLLGETLLRLPGVNDTRTYVVMEEVKQSNRLVIKTR 164
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

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 '\|'

(no "SCOP Domain" information available for 2GQQ)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

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

Escherichia coli. Organism_taxid: 562. (11)

1a	2gqqA01	A:13-64
1b	2gqqB01	B:13-64
1c	2gqqC01	C:13-64
1d	2gqqD01	D:13-64

(no "Pfam Domain" information available for 2GQQ)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (LRP_ECOLI | P0ACJ0)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
	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.
biological process
	GO:0009098	leucine biosynthetic process	The chemical reactions and pathways resulting in the formation of leucine, 2-amino-4-methylpentanoic acid.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0043201	response to leucine	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a leucine stimulus.
	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.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2gqq)

	Sites
(no "Sites" information available for 2gqq)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2gqq)

Biological Unit
	Complete Structure
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	2gqq
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	LRP_ECOLI \| P0ACJ0	:	2l4a

(no "Related Entries Specified in the PDB File" available for 2GQQ)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 4)

PROSITE Motifs (2, 8)

Exons (0, 0)

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