3C57 - JenaLib

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

Authors :   G. Wisedchaisri, M. Wu, D. R. Sherman, W. G. J. Hol

Date :   30 Jan 08 (Deposition) - 22 Apr 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (1x)

Keywords :   Response Regulator, Two-Component Regulatory System, Dna-Binding Protein, Tuberculosis, Transcription Regulation, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Wisedchaisri, M. Wu, D. R. Sherman, W. G. Hol
Crystal Structures Of The Response Regulator Dosr From Mycobacterium Tuberculosis Suggest A Helix Rearrangement Mechanism For Phosphorylation Activation
J. Mol. Biol. V. 378 227 2008
PubMed-ID: 18353359 | Reference-DOI: 10.1016/J.JMB.2008.02.029

Molecule 1 - TWO COMPONENT TRANSCRIPTIONAL REGULATORY PROTEIN DEVR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-28(+)
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL DOMAIN RESIDUES 144-217
	Gene	:	DEVR
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Synonym	:	PROBABLY LUXR/UHPA-FAMILY, DEVR, DNA-BINDING RESPONSE REGULATOR, LUXR FAMILY

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:	A
Biological Unit 3 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3C57)

(no "Site" information available for 3C57)

(no "SS Bond" information available for 3C57)

(no "Cis Peptide Bond" information available for 3C57)

(no "SAP(SNP)/Variant" information available for 3C57)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_LUXR_1	PS00622	LuxR-type HTH domain signature.	DEVR_MYCTO	164-191	2	A:164-191 B:164-191
1	HTH_LUXR_1	PS00622	LuxR-type HTH domain signature.	DEVR_MYCTU	164-191	2	A:164-191 B:164-191

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_LUXR_1	PS00622	LuxR-type HTH domain signature.	DEVR_MYCTO	164-191	2	A:164-191 B:164-191
1	HTH_LUXR_1	PS00622	LuxR-type HTH domain signature.	DEVR_MYCTU	164-191	2	A:164-191 B:164-191

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_LUXR_1	PS00622	LuxR-type HTH domain signature.	DEVR_MYCTO	164-191	1	A:164-191 -
1	HTH_LUXR_1	PS00622	LuxR-type HTH domain signature.	DEVR_MYCTU	164-191	1	A:164-191 -

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_LUXR_1	PS00622	LuxR-type HTH domain signature.	DEVR_MYCTO	164-191	1	- B:164-191
1	HTH_LUXR_1	PS00622	LuxR-type HTH domain signature.	DEVR_MYCTU	164-191	1	- B:164-191

(no "Exon" information available for 3C57)

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:51
 aligned with DEVR_MYCTO | P9WMF8 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:51
                                   158       168       178       188       198 
           DEVR_MYCTO   149 GLTDQERTLLGLLSEGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMERRTQ 199
               SCOP domains d3c57a_ A: automated matches                        SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------HTH_LUXR_1  PDB: A:164-191  -------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                 3c57 A 149 GLTDQERTLLGLLSEGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMERRTQ 199
                                   158       168       178       188       198

Chain A from PDB  Type:PROTEIN  Length:51
 aligned with DEVR_MYCTU | P9WMF9 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:51
                                   158       168       178       188       198 
           DEVR_MYCTU   149 GLTDQERTLLGLLSEGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMERRTQ 199
               SCOP domains d3c57a_ A: automated matches                        SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------HTH_LUXR_1  PDB: A:164-191  -------- PROSITE (2)
                 Transcript --------------------------------------------------- Transcript
                 3c57 A 149 GLTDQERTLLGLLSEGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMERRTQ 199
                                   158       168       178       188       198

Chain B from PDB  Type:PROTEIN  Length:49
 aligned with DEVR_MYCTO | P9WMF8 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:49
                                   160       170       180       190         
           DEVR_MYCTO   151 TDQERTLLGLLSEGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMERRTQ 199
               SCOP domains d3c57b_ B: automated matches                      SCOP domains
               CATH domains ------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------HTH_LUXR_1  PDB: B:164-191  -------- PROSITE
                 Transcript ------------------------------------------------- Transcript
                 3c57 B 151 TDQERTLLGLLSEGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMERRTQ 199
                                   160       170       180       190

Chain B from PDB  Type:PROTEIN  Length:49
 aligned with DEVR_MYCTU | P9WMF9 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:49
                                   160       170       180       190         
           DEVR_MYCTU   151 TDQERTLLGLLSEGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMERRTQ 199
               SCOP domains d3c57b_ B: automated matches                      SCOP domains
               CATH domains ------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------HTH_LUXR_1  PDB: B:164-191  -------- PROSITE (2)
                 Transcript ------------------------------------------------- Transcript
                 3c57 B 151 TDQERTLLGLLSEGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMERRTQ 199
                                   160       170       180       190

Legend:		→ Mismatch	(orange background)
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	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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All alpha proteins (14657)

Fold: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: C-terminal effector domain of the bipartite response regulators (45)

Family: automated matches (19)

Protein domain: automated matches (19)

Mycobacterium tuberculosis [TaxId: 1773] (3)

1a	d3c57a_	A:
1b	d3c57b_	B:

(no "CATH Domain" information available for 3C57)

(no "Pfam Domain" information available for 3C57)

Asymmetric Unit(hide GO term definitions)

Chain A,B (DEVR_MYCTO | P9WMF8)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
	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: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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0044161	host cell cytoplasmic vesicle	A vesicle formed of membrane or protein, found in the cytoplasm of a host cell.

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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	3c57
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	DEVR_MYCTO \| P9WMF8
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	DEVR_MYCTU \| P9WMF9
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	DEVR_MYCTO \| P9WMF8
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UniProtKB/Swiss-Prot
	DEVR_MYCTO \| P9WMF8	:	3c3w
	DEVR_MYCTU \| P9WMF9	:	1zlj 1zlk 3c3w

1zlj	CRYSTAL STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS HYPOXIC RESPONSE REGULATOR DOSR C-TERMINAL DOMAIN
1zlk	CRYSTAL STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS HYPOXIC RESPONSE REGULATOR DOSR C-TERMINAL DOMAIN-DNA COMPLEX
3c3w	CRYSTAL STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS HYPOXIC RESPONSE REGULATOR DOSR

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Gene Ontology (18, 24)

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