1JHZ - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   PURINE REPRESSOR MUTANT COREPRESSOR BINDING DOMAIN STRUCTURE

Authors :   J. L. Huffman, F. Lu, H. Zalkin, R. G. Brennan

Date :   28 Jun 01 (Deposition) - 08 Feb 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

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

Reference :   J. L. Huffman, F. Lu, H. Zalkin, R. G. Brennan
Role Of Residue 147 In The Gene Regulatory Function Of The Escherichia Coli Purine Repressor.
Biochemistry V. 41 511 2002
PubMed-ID: 11781089 | Reference-DOI: 10.1021/BI0156660
(for further references see the PDB file header)

Molecule 1 - PURINE NUCLEOTIDE SYNTHESIS REPRESSOR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET24A
	Expression System Strain	:	BL21 LAMBDA DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	COREPRESSOR-FREE COREPRESSOR BINDING DOMAIN (RESIDUES 53-341)
	Gene	:	PURR
	Mutation	:	YES
	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:490 , GLU B:70	BINDING SITE FOR RESIDUE MG B 401
2	AC2	SOFTWARE	GLU A:320 , HOH A:464	BINDING SITE FOR RESIDUE MG A 402

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

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 1JHZ)

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

(no "Exon" information available for 1JHZ)

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 d1jhza_ A: Purine repressor (PurR), C-terminal domain                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1jhzA01 A:60-161,A:292-323  [code=3.40.50.2300, no name defined]                                      1jhzA02 A:162-291,A:324-34      0  [code=3.40.50.2300, no name defined]                                                           1jhzA01 A:60-161,A:292-323      1jhzA02          - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh....eeeee.........eeee.hhhhhhhhhhhhhhhh....eeee...------hhhhhhhhhhhhhh....hhhh......hhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhh........eee....hhhhhhh.....eee.hhhhhhhhhhhhhhhhhh.......eee...eee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jhz A  60 KSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEYRHIPMVVMDFGEAKADFTDAVIDNAFEGGYMAGRYLIERGHREIGVIPGP------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 d1jhzb_ B: Purine repressor (PurR), C-terminal domain                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1jhzB01 B:60-161,B:292-323  [code=3.40.50.2300, no name defined]                                      1jhzB02 B:162-291,B:324-34      0  [code=3.40.50.2300, no name defined]                                                           1jhzB01 B:60-161,B:292-323      1jhzB02          - CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------Peripla_BP_3-1jhzB      01 B:170-331                                                                                                                              ---------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------Peripla_BP_3-1jhzB      02 B:170-331                                                                                                                              ---------- Pfam domains (2)
         Sec.struct. author .eeeeee.......hhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh......ee....hhhhhhhhhhh......eeee.........eee.hhhhhhhhhhhhhhhh....eeee...------hhhhhhhhhhhhhh....hhhh......hhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhh........eeeeee.hhhhhhh....eeee....hhhhhhhhhhhhhhh........ee...eee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jhz B  60 KSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEYRHIPMVVMDFGEAKADFTDAVIDNAFEGGYMAGRYLIERGHREIGVIPGP------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	d1jhza_	A:
1b	d1jhzb_	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. (30)

1a	1jhzA02	A:162-291,A:324-340
1b	1jhzB02	B:162-291,B:324-340
1c	1jhzA01	A:60-161,A:292-323
1d	1jhzB01	B:60-161,B:292-323

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Periplas_BP (97)

Family: Peripla_BP_3 (41)

Escherichia coli (strain K12) (28)

1a	Peripla_BP_3-1jhzB01	B:170-331
1b	Peripla_BP_3-1jhzB02	B:170-331

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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	1jhz
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	PURR_ECOLI \| P0ACP7
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1jfs	PURINE REPRESSOR MUTANT-HYPOXANTHINE-PURF OPERATOR COMPLEX (W147F)
1jft	PURINE REPRESSOR MUTANT-HYPOXANTHINE-PURF OPERATOR COMPLEX (W147A)
1jh9	PURINE REPRESSOR MUTANT-HYPOXANTHINE-PURF OPERATOR COMPLEX (W147R)
1pnr	PURINE REPRESSOR-HYPOXANTHINE-PURF-OPERATOR COMPLEX
1qpz	PURINE REPRESSOR-HYPOXANTHINE-PALINDROMIC OPERATOR COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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SCOP Domains (1, 2)

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Gene Ontology (8, 8)

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