1ZLK | PD0651 - JenaLib

Title :   CRYSTAL STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS HYPOXIC RESPONSE REGULATOR DOSR C-TERMINAL DOMAIN-DNA COMPLEX

Authors :   G. Wisedchaisri, M. Wu, A. E. Rice, D. M. Roberts, D. R. Sherman, W. G. J. Hol

Date :   06 May 05 (Deposition) - 31 Jan 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

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

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

Reference :   G. Wisedchaisri, M. Wu, A. E. Rice, D. M. Roberts, D. R. Sherman, W. G. J. Hol
Structures Of Mycobacterium Tuberculosis Dosr And Dosr-Dna Complex Involved In Gene Activation During Adaptation To Hypoxic Latency.
J. Mol. Biol. V. 354 630 2005
PubMed-ID: 16246368 | Reference-DOI: 10.1016/J.JMB.2005.09.048
(for further references see the PDB file header)

Compounds

*Molecule 1 - 5'- D(GPGPCPCPCPGPCPGPCPTPTPTPGPGPGPGPAPCPTP APAPAPGPTPCPCPCPTPAPAPCPCPCPTPGPGPCPCPA PCPGPAPT)-3'**
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - 5'- D(CPGPTPGPGPCPCPAPGPGPGPTPTPAPGPGPGPAPCP TPTPTPAPGPTPCPCPCPCPAPAPAPGPCPGPCPGPGPG PCPCPAPT)-3'**
	Chains	:	D
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - DORMANCY SURVIVAL REGULATOR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28(+)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL DOMAIN
	Gene	:	DOSR, DEVR, RV3133C
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Synonym	:	DOSR

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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:65
 aligned with DEVR_MYCTU | P9WMF9 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:65
                                   154       164       174       184       194       204     
           DEVR_MYCTU   145 DPLSGLTDQERTLLGLLSEGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMERRTQAAVFATELKR 209
               SCOP domains d1zlka_ A: automated matches                                      SCOP domains
               CATH domains 1zlkA00 A:145-209 'winged helix' repressor DNA binding domain     CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhh.hhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------HTH_LUXR_1  PDB: A:164-191  ------------------ PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                 1zlk A 145 DPLSGLTDQERTLLGLLSEGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMERRTQAAVFATELKR 209
                                   154       164       174       184       194       204

Chain B from PDB  Type:PROTEIN  Length:65
 aligned with DEVR_MYCTU | P9WMF9 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:65
                                   154       164       174       184       194       204     
           DEVR_MYCTU   145 DPLSGLTDQERTLLGLLSEGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMERRTQAAVFATELKR 209
               SCOP domains d1zlkb_ B: automated matches                                      SCOP domains
               CATH domains 1zlkB00 B:145-209 'winged helix' repressor DNA binding domain     CATH domains
           Pfam domains (1) --GerE-1zlkB01 B:147-204                                    ----- Pfam domains (1)
           Pfam domains (2) --GerE-1zlkB02 B:147-204                                    ----- Pfam domains (2)
         Sec.struct. author ..........hhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------HTH_LUXR_1  PDB: B:164-191  ------------------ PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                 1zlk B 145 DPLSGLTDQERTLLGLLSEGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMERRTQAAVFATELKR 209
                                   154       164       174       184       194       204

Chain C from PDB  Type:DNA  Length:24
                                                        
                 1zlk C   8 GCTTTGGGGACTAAAGTCCCTAAC  31
                                    17        27

Chain D from PDB  Type:DNA  Length:25
                                                         
                 1zlk D   7 AGGGTTAGGGACTTTAGTCCCCAAA  31
                                    16        26

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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (DEVR_MYCTU | P9WMF9)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:0022611	dormancy process	A developmental process in which dormancy (sometimes called a dormant state) is induced, maintained or broken. Dormancy is a suspension of most physiological activity and growth that can be reactivated.
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	GO:0000160	phosphorelay signal transduction system	A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
	GO:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0019217	regulation of fatty acid metabolic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving fatty acids.
	GO:0080134	regulation of response to stress	Any process that modulates the frequency, rate or extent of a response to stress. Response to stress is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0001666	response to hypoxia	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005618	cell wall	The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0044161	host cell cytoplasmic vesicle	A vesicle formed of membrane or protein, found in the cytoplasm of a host cell.
	GO:0072493	host cell endosome lumen	The volume enclosed by the membranes of the host cell endosome.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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	1zlk
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