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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   DNA-BINDING REGULATORY PROTEIN

Authors :   M. A. Schumacher, K. Y. Choi, F. Lu, H. Zalkin, R. G. Brennan

Date :   13 Feb 96 (Deposition) - 07 Dec 96 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Transcription Regulation, Dna-Binding Regulatory Protein, Purine Repressor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. A. Schumacher, K. Y. Choi, F. Lu, H. Zalkin, R. G. Brennan
Mechanism Of Corepressor-Mediated Specific Dna Binding By The Purine Repressor.
Cell(Cambridge, Mass. ) V. 83 147 1995
PubMed-ID: 7553867 | Reference-DOI: 10.1016/0092-8674(95)90243-0
(for further references see the PDB file header)

Molecule 1 - PURINE REPRESSOR
	Chains	:	A, B
	Fragment	:	COREPRESSOR-FREE COREPRESSOR-BINDING DOMAIN
	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, 3)

No.	Name	Count	Type	Full Name
1	MG	3	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:409	BINDING SITE FOR RESIDUE MG A 2
2	AC2	SOFTWARE	HOH B:393	BINDING SITE FOR RESIDUE MG B 3

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

Asymmetric/Biological Unit

No.	Residues
1	Val A:265	-	Pro A:266
2	Thr A:284	-	Pro A:285
3	Val B:265	-	Pro B:266
4	Thr B:284	-	Pro B:285

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

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

(no "Exon" information available for 1DBQ)

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:276
 aligned with PURR_ECOLI | P0ACP7 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:282
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339  
           PURR_ECOLI    60 KSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEYRHIPMVVMDWGEAKADFTDAVIDNAFEGGYMAGRYLIERGHREIGVIPGPLERNTGAGRLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYDNVRNARYFTPALTTIHQPKDSLGETAFNMLLDRIVNKREEPQSIEVHPRLIERRSVADGPFRDYRR 341
               SCOP domains d1dbqa_ A: Purine repressor (PurR), C-terminal domain                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1dbqA01 A:60-161,A:292-323  [code=3.40.50.2300, no name defined]                                      1dbqA02 A:162-291,A:324-34      0  [code=3.40.50.2300, no name defined]                                                           1dbqA01 A:60-161,A:292-323      1dbqA02          - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhh....eeeee.....hhhhhhhhhh....eeee...........eeee.hhhhhhhhhhhhhh.....eeee...------.hhhhhhhhhhhhh.....hhh.......hhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhh........eeeeee....hhh.....eeee...hhhhhhhhhhhhhhhh.......eeee..eee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1dbq A  60 KSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEYRHIPMVVMDWGEAKADFTDAVIDNAFEGGYMAGRYLIERGHREIGVIPGP------AGRLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYDNVRNARYFTPALTTIHQPKDSLGETAFNMLLDRIVNKREEPQSIEVHPRLIERRSVADGPFRDYRR 341
                                    69        79        89        99       109       119       129       139       149       159       169       179       | -    |  199       209       219       229       239       249       259       269       279       289       299       309       319       329       339  
                                                                                                                                                         187    194

Chain B from PDB  Type:PROTEIN  Length:276
 aligned with PURR_ECOLI | P0ACP7 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:282
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339  
           PURR_ECOLI    60 KSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEYRHIPMVVMDWGEAKADFTDAVIDNAFEGGYMAGRYLIERGHREIGVIPGPLERNTGAGRLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYDNVRNARYFTPALTTIHQPKDSLGETAFNMLLDRIVNKREEPQSIEVHPRLIERRSVADGPFRDYRR 341
               SCOP domains d1dbqb_ B: Purine repressor (PurR), C-terminal domain                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1dbqB01 B:60-161,B:292-323  [code=3.40.50.2300, no name defined]                                      1dbqB02 B:162-291,B:324-34      0  [code=3.40.50.2300, no name defined]                                                           1dbqB01 B:60-161,B:292-323      1dbqB02          - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.........hhhhhhhhhhhhh..eeeeee......hhhhhhhhhhh..............hhhhhhhhh........eee........eee...hhhhhhhhhhhhhh.....eeee...------.hhhhhhhhhhhhh.....hhh.......hhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhh........eeeeee....hhh.....eeee.....hhhhhhhhhhhhh..............eee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1dbq B  60 KSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEYRHIPMVVMDWGEAKADFTDAVIDNAFEGGYMAGRYLIERGHREIGVIPGP------AGRLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYDNVRNARYFTPALTTIHQPKDSLGETAFNMLLDRIVNKREEPQSIEVHPRLIERRSVADGPFRDYRR 341
                                    69        79        89        99       109       119       129       139       149       159       169       179       | -    |  199       209       219       229       239       249       259       269       279       289       299       309       319       329       339  
                                                                                                                                                         187    194

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: Purine repressor (PurR), C-terminal domain (24)

Escherichia coli [TaxId: 562] (24)

1a	d1dbqa_	A:
1b	d1dbqb_	B:

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 (14)

1a	1dbqA02	A:162-291,A:324-340
1b	1dbqB02	B:162-291,B:324-340
1c	1dbqA01	A:60-161,A:292-323
1d	1dbqB01	B:60-161,B:292-323

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PURR_ECOLI | P0ACP7)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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: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: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:0006164	purine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	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
		Thr A:284 - Pro A:285	[ RasMol ]
		Thr B:284 - Pro B:285	[ RasMol ]
		Val A:265 - Pro A:266	[ RasMol ]
		Val B:265 - Pro B:266	[ RasMol ]

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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

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