1JH9 | PD0226 - JenaLib

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Title :   PURINE REPRESSOR MUTANT-HYPOXANTHINE-PURF OPERATOR COMPLEX

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

Date :   27 Jun 01 (Deposition) - 08 Feb 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.55

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

Keywords :   Transcription Regulation, Dna-Binding, Repressor, Purine Biosynthesis, Complex (Dna-Binding Protein/Dna), Allosteric Regulation, Transcription/Dna Complex (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 - 5'- D(APAPCPGPAPAPAPAPCPGPTPTPTPTPCPGPT)-3'**
	Chains	:	B
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - PURINE NUCLEOTIDE SYNTHESIS REPRESSOR
	Chains	:	A
	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
	Gene	:	PURR
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	HPA	1	Ligand/Ion	HYPOXANTHINE
2	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	HPA	2	Ligand/Ion	HYPOXANTHINE
2	PO4	4	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:291 , GLN A:292 , PRO A:293 , LYS A:294 , ASP A:295 , SER A:296	BINDING SITE FOR RESIDUE PO4 A 799
2	AC2	SOFTWARE	ARG A:52 , HIS A:58 , LYS A:60 , HOH A:880	BINDING SITE FOR RESIDUE PO4 A 800
3	AC3	SOFTWARE	TYR A:73 , PHE A:74 , ARG A:190 , THR A:192 , ARG A:196 , PHE A:221 , ASP A:275 , HOH A:808 , HOH A:832	BINDING SITE FOR RESIDUE HPA A 599

(no "SS Bond" information available for 1JH9)

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 1JH9)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_LACI_2	PS50932	LacI-type HTH domain profile.	PURR_ECOLI	2-56	1	A:2-56
2	HTH_LACI_1	PS00356	LacI-type HTH domain signature.	PURR_ECOLI	4-22	1	A:4-22

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_LACI_2	PS50932	LacI-type HTH domain profile.	PURR_ECOLI	2-56	2	A:2-56
2	HTH_LACI_1	PS00356	LacI-type HTH domain signature.	PURR_ECOLI	4-22	2	A:4-22

(no "Exon" information available for 1JH9)

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:339
 aligned with PURR_ECOLI | P0ACP7 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:339
                                    11        21        31        41        51        61        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       331         
           PURR_ECOLI     2 ATIKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSAVARSLKVNHTKSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEYRHIPMVVMDWGEAKADFTDAVIDNAFEGGYMAGRYLIERGHREIGVIPGPLERNTGAGRLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYDNVRNARYFTPALTTIHQPKDSLGETAFNMLLDRIVNKREEPQSIEVHPRLIERRSVADGPFRDYR 340
               SCOP domains d1jh9a1 A:2-58 Purine repressor (PurR), N-terminal domaind1jh9a2 A:59-340 Purine repressor (PurR), C-terminal domain                                                                                                                                                                                                                                SCOP domains
               CATH domains -1jh9A01 A:3-59 lambda repressor-like DNA-binding domains 1jh9A02 A:60-161,A:292-323  [code=3.40.50.2300, no name defined]                                      1jh9A03 A:162-291,A:324-340  [code=3.40.50.2300, no name defined]                                                                 1jh9A02 A:60-161,A:292-323      1jh9A03           CATH domains
               Pfam domains -LacI-1jh9A01 A:3-48                           -------------------------------------------------------------------------------------------------------------------------Peripla_BP_3-1jh9A02 A:170-331                                                                                                                                    --------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhhh...hhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhh.eee...........eeee..hhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhh....hhhh......hhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhh........eeeeee...hhhhh....eeee..hhhhhhhhhhhhhhhhhh......eee...eee.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) HTH_LACI_2  PDB: A:2-56 UniProt: 2-56                  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --HTH_LACI_1         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jh9 A   2 ATIKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSAVARSLKVNHTKSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEYRHIPMVVMDRGEAKADFTDAVIDNAFEGGYMAGRYLIERGHREIGVIPGPLERNTGAGRLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYDNVRNARYFTPALTTIHQPKDSLGETAFNMLLDRIVNKREEPQSIEVHPRLIERRSVADGPFRDYR 340
                                    11        21        31        41        51        61        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       331

Chain B from PDB  Type:DNA  Length:17
                                                 
                 1jh9 B 699 AACGAAAACGTTTTCGT 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	1jh9A03	A:162-291,A:324-340
1b	1jh9A02	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)

1jh9A01

A:3-59

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: LacI (35)

Escherichia coli (strain K12) (30)

LacI-1jh9A01

A:3-48

Clan: Periplas_BP (97)

Family: Peripla_BP_3 (41)

Escherichia coli (strain K12) (28)

Peripla_BP_3-1jh9A02

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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	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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	1jh9
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1jfs	PURINE REPRESSOR MUTANT-HYPOXANTHINE-PURF OPERATOR COMPLEX (W147F)
1jft	PURINE REPRESSOR MUTANT-HYPOXANTHINE-PURF OPERATOR COMPLEX (W147A)
1jhz	PURINE REPRESSOR MUTANT COREPRESSOR BINDING DOMAIN STRUCTURE
1pnr	PURINE REPRESSOR-HYPOXANTHINE-PURF-OPERATOR COMPLEX
1qpz	PURINE REPRESSOR-HYPOXANTHINE-PALINDROMIC OPERATOR COMPLEX

Description

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Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

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