2PUD | PDR046 - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES

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

Date :   04 Oct 97 (Deposition) - 06 May 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

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

Reference :   M. A. Schumacher, K. Y. Choi, H. Zalkin, R. G. Brennan
Crystal Structure Of Laci Member, Purr, Bound To Dna: Minor Groove Binding By Alpha Helices.
Science V. 266 763 1994
PubMed-ID: 7973627
(for further references see the PDB file header)

*Molecule 1 - DNA (5'- D(TPAPCPGPCPAPAPAPCPGPTPTPTPGPCPGPT )-3')**
	Chains	:	B
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - PROTEIN (PURINE REPRESSOR)
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PDNA100
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector	:	PET24A
	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 (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 , SER A:124 , THR A:192 , ARG A:196 , PHE A:221 , ASP A:275 , HOH A:755	BINDING SITE FOR RESIDUE HPA A 599

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

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 2PUD)

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 2PUD)

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: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 d2puda1 A:3-58                                          d2puda2 A:59-340 Purine repressor (PurR), C-terminal domain                                                                                                                                                                                                                                SCOP domains
               CATH domains 2pudA01 A:3-59 lambda repressor-like DNA-binding domains 2pudA02 A:60-161,A:292-323  [code=3.40.50.2300, no name defined]                                      2pudA03 A:162-291,A:324-340  [code=3.40.50.2300, no name defined]                                                                 2pudA02 A:60-161,A:292-323      2pudA03           CATH domains
               Pfam domains LacI-2pudA01 A:3-48                           -------------------------------------------------------------------------------------------------------------------------Peripla_BP_3-2pudA02 A:170-331                                                                                                                                    --------- Pfam domains
         Sec.struct. author .hhhhhhh....hhhhhhhhh......hhhhhhhhhhhhh......hhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhh....eeee......hhhhhhhhhh....eee............eee..hhhhhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhhhh.....hhh.......hhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhh........eeeeee....hhh.....eeee..hhhhhhhhhhhhhhhhh.......eee...eee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -HTH_LACI_1         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pud A   3 TIKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSAVARSLKVNHTKSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEYRHIPMVVMDWGEAKADFTDAVIDNAFEGGYMAGRYLIERGHREIGVIPGPLEANTGAGRLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYDNVRNARYFTPALTTIHQPKDSLGETAFNMLLDRIVNKREEPQSIEVHPRLIERRSVADGPFRDYR 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 B from PDB  Type:DNA  Length:17
                                                 
                 2pud B 699 TACGCAAACGTTTGCGT 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	2pudA03	A:162-291,A:324-340
1b	2pudA02	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)

2pudA01

A:3-59

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: LacI (35)

Escherichia coli (strain K12) (30)

LacI-2pudA01

A:3-48

Clan: Periplas_BP (97)

Family: Peripla_BP_3 (41)

Escherichia coli (strain K12) (28)

Peripla_BP_3-2pudA02

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

Description

Compounds

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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)

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Exons (0, 0)

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