2VZW - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   X-RAY STRUCTURE OF THE HEME-BOUND GAF DOMAIN OF SENSORY HISTIDINE KINASE DOST OF MYCOBACTERIUM TUBERCULOSIS

Authors :   L. M. Podust, A. Ioanoviciu, P. R. Ortiz De Montellano

Date :   06 Aug 08 (Deposition) - 17 Mar 09 (Release) - 06 Mar 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Transferase, Transferase, Oxygen Binding, Signal Transduction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. M. Podust, A. Ioanoviciu, P. R. Ortiz De Montellano
2. 3 A X-Ray Structure Of The Heme-Bound Gaf Domain Of Sensory Histidine Kinase Dost Of Mycobacterium Tuberculosis.
Biochemistry V. 47 12523 2008
PubMed-ID: 18980385 | Reference-DOI: 10.1021/BI8012356

Molecule 1 - PROBABLE HISTIDINE KINASE RESPONSE REGULATOR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET23A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	GAF SENSORY DOMAIN, RESIDUES 61-208
	Gene	:	RV2027C
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	83332
	Strain	:	H37RV
	Synonym	:	GAF FAMILY PROTEIN, DOST

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	OXY	1	Ligand/Ion	OXYGEN MOLECULE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	OXY	-1	Ligand/Ion	OXYGEN MOLECULE

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	OXY	1	Ligand/Ion	OXYGEN MOLECULE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:81 , GLY A:82 , GLU A:99 , ILE A:101 , ARG A:106 , ILE A:109 , SER A:111 , PRO A:113 , GLU A:114 , GLY A:115 , ARG A:116 , GLY A:117 , VAL A:118 , SER A:140 , VAL A:141 , GLY A:142 , PHE A:143 , PRO A:144 , HIS A:147 , MET A:150 , PHE A:153 , TYR A:169 , HOH A:2024	BINDING SITE FOR RESIDUE HEM A1206
2	AC2	SOFTWARE	GLY B:82 , PHE B:96 , GLU B:99 , ARG B:106 , ILE B:109 , GLY B:110 , SER B:111 , PRO B:113 , GLU B:114 , GLY B:115 , ARG B:116 , GLY B:117 , VAL B:118 , LEU B:119 , SER B:140 , VAL B:141 , GLY B:142 , PHE B:143 , PRO B:144 , HIS B:147 , TYR B:169 , THR B:171 , OXY B:1210	BINDING SITE FOR RESIDUE HEM B1209
3	AC3	SOFTWARE	PRO B:113 , LEU B:119 , TYR B:169 , HEM B:1209	BINDING SITE FOR RESIDUE OXY B1210
4	AC4	SOFTWARE	ARG A:87 , ARG A:92 , LEU A:93 , PRO A:113	BINDING SITE FOR RESIDUE ACT A1207
5	AC5	SOFTWARE	ARG B:87 , ARG B:92 , LEU B:93 , PRO B:113	BINDING SITE FOR RESIDUE ACT B1211

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

(no "Cis Peptide Bond" information available for 2VZW)

(no "SAP(SNP)/Variant" information available for 2VZW)

(no "PROSITE Motif" information available for 2VZW)

(no "Exon" information available for 2VZW)

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:146
 aligned with DOST_MYCTO | P9WGK0 from UniProtKB/Swiss-Prot  Length:573

    Alignment length:158
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197        
           DOST_MYCTO    48 GLIDAILAITSGLKLDATLRAIVHTAAELVDARYGALGVRGYDHRLVEFVYEGIDEETRHLIGSLPEGRGVLGALIEEPKPIRLDDISRHPASVGFPLHHPPMRTFLGVPVRIRDEVFGNLYLTEKADGQPFSDDDEVLVQALAAAAGIAVDNARLFE 205
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .------------hhhhhhhhhhhhhhhhhheeeeeeeee.....eeeeeee..hhhhhhhhh......hhhhhhhhh...eee.hhhhh...............eeeeeeee..eeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vzw A  60 G------------KLDATLRAIVHTAAELVDARYGALGVRGYDHRLVEFVYEGIDEETRHLIGSLPEGRGVLGALIEEPKPIRLDDISRHPASVGFPLHHPPMRTFLGVPVRIRDEVFGNLYLTEKADGQPFSDDDEVLVQALAAAAGIAVDNARLFE 205
                            |        -   |    67        77        87        97       107       117       127       137       147       157       167       177       187       197        
                            |           61                                                                                                                                                
                           60

Chain A from PDB  Type:PROTEIN  Length:146
 aligned with DOST_MYCTU | P9WGK1 from UniProtKB/Swiss-Prot  Length:573

    Alignment length:158
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197        
           DOST_MYCTU    48 GLIDAILAITSGLKLDATLRAIVHTAAELVDARYGALGVRGYDHRLVEFVYEGIDEETRHLIGSLPEGRGVLGALIEEPKPIRLDDISRHPASVGFPLHHPPMRTFLGVPVRIRDEVFGNLYLTEKADGQPFSDDDEVLVQALAAAAGIAVDNARLFE 205
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .------------hhhhhhhhhhhhhhhhhheeeeeeeee.....eeeeeee..hhhhhhhhh......hhhhhhhhh...eee.hhhhh...............eeeeeeee..eeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vzw A  60 G------------KLDATLRAIVHTAAELVDARYGALGVRGYDHRLVEFVYEGIDEETRHLIGSLPEGRGVLGALIEEPKPIRLDDISRHPASVGFPLHHPPMRTFLGVPVRIRDEVFGNLYLTEKADGQPFSDDDEVLVQALAAAAGIAVDNARLFE 205
                            |        -   |    67        77        87        97       107       117       127       137       147       157       167       177       187       197        
                           60           61

Chain B from PDB  Type:PROTEIN  Length:149
 aligned with DOST_MYCTO | P9WGK0 from UniProtKB/Swiss-Prot  Length:573

    Alignment length:161
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207 
           DOST_MYCTO    48 GLIDAILAITSGLKLDATLRAIVHTAAELVDARYGALGVRGYDHRLVEFVYEGIDEETRHLIGSLPEGRGVLGALIEEPKPIRLDDISRHPASVGFPLHHPPMRTFLGVPVRIRDEVFGNLYLTEKADGQPFSDDDEVLVQALAAAAGIAVDNARLFEESR 208
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------GAF-2vzwB01 B:61-198                                                                                                                      ---------- Pfam domains (1)
           Pfam domains (2) -------------GAF-2vzwB02 B:61-198                                                                                                                      ---------- Pfam domains (2)
         Sec.struct. author .------------hhhhhhhhhhhhhhhhh.eeeeeeeee.....eeeeeee..hhhhhhhhh......hhhhhhhhh...eee.hhhhh...............eeeeeeee..eeeeeeeeeee.hhh..hhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vzw B  60 G------------KLDATLRAIVHTAAELVDARYGALGVRGYDHRLVEFVYEGIDEETRHLIGSLPEGRGVLGALIEEPKPIRLDDISRHPASVGFPLHHPPMRTFLGVPVRIRDEVFGNLYLTEKADGQPFSDDDEVLVQALAAAAGIAVDNARLFEESR 208
                            |        -   |    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207 
                           60           61

Chain B from PDB  Type:PROTEIN  Length:149
 aligned with DOST_MYCTU | P9WGK1 from UniProtKB/Swiss-Prot  Length:573

    Alignment length:161
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207 
           DOST_MYCTU    48 GLIDAILAITSGLKLDATLRAIVHTAAELVDARYGALGVRGYDHRLVEFVYEGIDEETRHLIGSLPEGRGVLGALIEEPKPIRLDDISRHPASVGFPLHHPPMRTFLGVPVRIRDEVFGNLYLTEKADGQPFSDDDEVLVQALAAAAGIAVDNARLFEESR 208
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------GAF-2vzwB01 B:61-198                                                                                                                      ---------- Pfam domains (1)
           Pfam domains (2) -------------GAF-2vzwB02 B:61-198                                                                                                                      ---------- Pfam domains (2)
         Sec.struct. author .------------hhhhhhhhhhhhhhhhh.eeeeeeeee.....eeeeeee..hhhhhhhhh......hhhhhhhhh...eee.hhhhh...............eeeeeeee..eeeeeeeeeee.hhh..hhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vzw B  60 G------------KLDATLRAIVHTAAELVDARYGALGVRGYDHRLVEFVYEGIDEETRHLIGSLPEGRGVLGALIEEPKPIRLDDISRHPASVGFPLHHPPMRTFLGVPVRIRDEVFGNLYLTEKADGQPFSDDDEVLVQALAAAAGIAVDNARLFEESR 208
                            |        -   |    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207 
                           60           61

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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 '\|'

(no "SCOP Domain" information available for 2VZW)

(no "CATH Domain" information available for 2VZW)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GAF (44)

Family: GAF (30)

Mycobacterium tuberculosis (6)

1a	GAF-2vzwB01	B:61-198
1b	GAF-2vzwB02	B:61-198

Asymmetric Unit(hide GO term definitions)

Chain A,B (DOST_MYCTU | P9WGK1)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0070025	carbon monoxide binding	Interacting selectively and non-covalently with carbon monoxide (CO).
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0070026	nitric oxide binding	Interacting selectively and non-covalently with nitric oxide (NO).
	GO:0019825	oxygen binding	Interacting selectively and non-covalently with oxygen (O2).
	GO:0019826	oxygen sensor activity	Interacting selectively and non-covalently with and responding, e.g. by conformational change, to changes in the cellular level of oxygen (O2).
	GO:0000155	phosphorelay sensor kinase activity	Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response.
	GO:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
	GO:0004673	protein histidine kinase activity	Catalysis of the reaction: ATP + protein L-histidine = ADP + protein phospho-L-histidine.
	GO:0004672	protein kinase activity	Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0070483	detection of hypoxia	The series of events in which a stimulus indicating lowered oxygen tension is received by a cell and converted into a molecular signal. 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:0018106	peptidyl-histidine phosphorylation	The phosphorylation of peptidyl-histidine to form peptidyl-1'-phospho-L-histidine (otherwise known as tau-phosphohistidine, tele-phosphohistidine) or peptidyl-3'-phospho-L-histidine (otherwise known as pi-phosphohistidine, pros-phosphohistidine).
	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:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0046777	protein autophosphorylation	The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
	GO:0023014	signal transduction by protein phosphorylation	A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.

Chain A,B (DOST_MYCTO | P9WGK0)

molecular function
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000155	phosphorelay sensor kinase activity	Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response.
	GO:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
	GO:0004673	protein histidine kinase activity	Catalysis of the reaction: ATP + protein L-histidine = ADP + protein phospho-L-histidine.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0070483	detection of hypoxia	The series of events in which a stimulus indicating lowered oxygen tension is received by a cell and converted into a molecular signal. 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:0018106	peptidyl-histidine phosphorylation	The phosphorylation of peptidyl-histidine to form peptidyl-1'-phospho-L-histidine (otherwise known as tau-phosphohistidine, tele-phosphohistidine) or peptidyl-3'-phospho-L-histidine (otherwise known as pi-phosphohistidine, pros-phosphohistidine).
	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:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0046777	protein autophosphorylation	The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
	GO:0023014	signal transduction by protein phosphorylation	A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.

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