1QP4 | PD0058 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   PURINE REPRESSOR-HYPOXANTHINE-PALINDROMIC OPERATOR COMPLEX

Authors :   A. Glasfeld, A. N. Koehler, M. A. Schumacher, R. G. Brennan

Date :   01 Jun 99 (Deposition) - 07 Jun 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A,M
Biol. Unit 1: A,M  (2x)

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

Reference :   A. Glasfeld, A. N. Koehler, M. A. Schumacher, R. G. Brennan
The Role Of Lysine 55 In Determining The Specificity Of The Purine Repressor For Its Operators Through Minor Groove Interactions.
J. Mol. Biol. V. 291 347 1999
PubMed-ID: 10438625 | Reference-DOI: 10.1006/JMBI.1999.2946
(for further references see the PDB file header)

*Molecule 1 - DNA (5'- D(TPAPCPGPCPAPAPTPCPGPAPTPTPGPCPGPT)-3')**
	Chains	:	M
	Engineered	:	YES
	Synonym	:	PURA
	Synthetic	:	YES

Molecule 2 - PROTEIN (PURINE NUCLEOTIDE SYNTHESIS REPRESSOR)
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Gene	:	PURR
	Expression System Plasmid	:	PDNA100:K55A
	Expression System Strain	:	BL21 LAMBDA DE3
	Expression System Taxid	:	562
	Expression System Vector	:	PET24A
	Expression System Vector Type	:	PLASMID
	Gene	:	PURR
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2
Asymmetric Unit	:	A	M
Biological Unit 1 (2x)	:	A	M

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	HPA	1	Ligand/Ion	HYPOXANTHINE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	HPA	2	Ligand/Ion	HYPOXANTHINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:73 , PHE A:74 , ARG A:190 , THR A:192 , ARG A:196 , PHE A:221 , ASP A:275	BINDING SITE FOR RESIDUE HPA A 599

(no "SS Bond" information available for 1QP4)

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 1QP4)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_LACI_1	PS00356	LacI-type HTH domain signature.	PURR_ECOLI	4-22	1	A:4-22

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_LACI_1	PS00356	LacI-type HTH domain signature.	PURR_ECOLI	4-22	2	A:4-22

(no "Exon" information available for 1QP4)

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
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Chain A from PDB  Type:PROTEIN  Length:338
 aligned with PURR_ECOLI | P0ACP7 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:338
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332        
           PURR_ECOLI     3 TIKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSAVARSLKVNHTKSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEYRHIPMVVMDWGEAKADFTDAVIDNAFEGGYMAGRYLIERGHREIGVIPGPLERNTGAGRLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYDNVRNARYFTPALTTIHQPKDSLGETAFNMLLDRIVNKREEPQSIEVHPRLIERRSVADGPFRDYR 340
               SCOP domains d1qp4a1 A:3-58                                          d1qp4a2 A:59-340 Purine repressor (PurR), C-terminal domain                                                                                                                                                                                                                                SCOP domains
               CATH domains 1qp4A01 A:3-59 lambda repressor-like DNA-binding domains 1qp4A02 A:60-161,A:292-323  [code=3.40.50.2300, no name defined]                                      1qp4A03 A:162-291,A:324-340  [code=3.40.50.2300, no name defined]                                                                 1qp4A02 A:60-161,A:292-323      1qp4A03           CATH domains
               Pfam domains LacI-1qp4A01 A:3-48                           -------------------------------------------------------------------------------------------------------------------------Peripla_BP_3-1qp4A02 A:170-331                                                                                                                                    --------- Pfam domains
         Sec.struct. author .hhhhhhhh...hhhhhhhhh......hhhhhhhhhhhhhh.....hhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhh....eeee......hhhhhhhhhh....eeeeee........eeee..hhhhhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhhhh.....hhh.......hhhhhhhhhhhh.......eeee..hhhhhhhhhhhhh.........eeeeee....hhh......eee..hhhhhhhhhhhhhhhhh.......eee...eee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -HTH_LACI_1         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qp4 A   3 TIKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSAVARSLKVNHTKSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEYRHIPMVVMDWGEAKADFTDAVIDNAFEGGYMAGRYLIERGHREIGVIPGPLERNTGAGRLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYDNVRNARYFTPALTTIHQPKDSLGETAFNMLLDRIVNKREEPQSIEVHPRLIERRSVADGPFRDYR 340
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332

Chain M from PDB  Type:DNA  Length:17
                                                 
                 1qp4 M 699 TACGCAATCGATTGCGT 715
                                   708

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	1qp4A03	A:162-291,A:324-340
1b	1qp4A02	A:60-161,A:292-323

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)

1qp4A01

A:3-59

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: LacI (35)

Escherichia coli (strain K12) (30)

LacI-1qp4A01

A:3-48

Clan: Periplas_BP (97)

Family: Peripla_BP_3 (41)

Escherichia coli (strain K12) (28)

Peripla_BP_3-1qp4A02

A:170-331

Asymmetric Unit(hide GO term definitions)

Chain A (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 Unit
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Thr A:284 - Pro A:285	[ RasMol ]
		Val A:265 - Pro A:266	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	1qp4
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 2)

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Pfam Domains (2, 2)

Gene Ontology (8, 8)

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