3ZXO - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE MUTANT ATP-BINDING DOMAIN OF MYCOBACTERIUM TUBERCULOSIS DOSS

Authors :   H. Y. Cho, H. J. Cho, B. S. Kang

Date :   13 Aug 11 (Deposition) - 24 Aug 11 (Release) - 22 May 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Y. Cho, Y. H. Lee, Y. S. Bae, E. Kim, B. S. Kang
Activation Of Atp Binding For The Autophosphorylation Of Doss, A Mycobacterium Tuberculosis Histidine Kinase Lacking An Atp-Lid Motif.
J. Biol. Chem. V. 288 12437 2013
PubMed-ID: 23486471 | Reference-DOI: 10.1074/JBC.M112.442467
(for further references see the PDB file header)

Molecule 1 - REDOX SENSOR HISTIDINE KINASE RESPONSE REGULATOR DEVS
	Chains	:	A, B
	EC Number	:	2.7.3.-, 2.7.13.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	B834
	Expression System Taxid	:	562
	Fragment	:	ATP-BINDING DOMAIN, RESIDUES 454-578
	Mutation	:	YES
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	83332
	Strain	:	H37RV
	Synonym	:	TWO COMPONENT SENSOR HISTIDINE KINASE DEVS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 13)

No.	Name	Count	Type	Full Name
1	ACT	4	Ligand/Ion	ACETATE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
4	OCS	2	Mod. Amino Acid	CYSTEINESULFONIC ACID
5	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (4, 11)

No.	Name	Count	Type	Full Name
1	ACT	4	Ligand/Ion	ACETATE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
4	OCS	2	Mod. Amino Acid	CYSTEINESULFONIC ACID
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (4, 6)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
4	OCS	1	Mod. Amino Acid	CYSTEINESULFONIC ACID
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:505 , HIS A:507 , ASP A:529 , GLU A:537 , HOH A:2062	BINDING SITE FOR RESIDUE ZN A1579
2	AC2	SOFTWARE	LYS A:518 , ASP A:521 , ASP A:522 , HOH A:2078	BINDING SITE FOR RESIDUE ACT A1580
3	AC3	SOFTWARE	GLU A:499 , ASN A:503 , PHE A:538 , GLY A:542 , LEU A:543 , LEU A:546	BINDING SITE FOR RESIDUE ACT A1581
4	AC4	SOFTWARE	VAL B:505 , HIS B:507 , ASP B:529 , GLU B:537 , HOH B:2042	BINDING SITE FOR RESIDUE ZN B1578
5	AC5	SOFTWARE	ASP B:521 , ASP B:522	BINDING SITE FOR RESIDUE ACT B1579
6	AC6	SOFTWARE	ASN B:503 , PHE B:538 , GLY B:542 , LEU B:543 , LEU B:546 , HOH B:2041	BINDING SITE FOR RESIDUE ACT B1580
7	AC7	SOFTWARE	GLU A:494 , MSE B:534 , ASP B:536 , HOH B:2068	BINDING SITE FOR RESIDUE GOL B1581

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

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

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

(no "PROSITE Motif" information available for 3ZXO)

(no "Exon" information available for 3ZXO)

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:125
 aligned with DEVS_MYCTO | P9WGK2 from UniProtKB/Swiss-Prot  Length:578

    Alignment length:125
                                   463       473       483       493       503       513       523       533       543       553       563       573     
           DEVS_MYCTO   454 TRLRQRIDAAVAQFADSGLRTSVQFVGPLSVVDSALADQAEAVVREAVSNAVRHAKASTLTVRVKVDDDLCIEVTDNGRGLPDEFTGSGLTNLRQRAEQAGGEFTLASVPGASGTVLRWSAPLSQ 578
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeee..eeeeeeee..........hhhhhhhhhhhhhh..eeeeee......eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zxo A 454 TRLRQRIDAAVAQFADSGLRTSVQFVGPLSVVDSALADQAEAVVREAVSNAVRHAAASTLTVRVKVDDDLcIEVTDNGRGmPDEFTGSGLTNLRQRAEQAGGEFTLASmPGASGTVLRWSAPLSQ 578
                                   463       473       483       493       503       513       523|      533|      543       553       563       573     
                                                                                                524-OCS   534-MSE                     562-MSE

Chain A from PDB  Type:PROTEIN  Length:125
 aligned with DEVS_MYCTU | P9WGK3 from UniProtKB/Swiss-Prot  Length:578

    Alignment length:125
                                   463       473       483       493       503       513       523       533       543       553       563       573     
           DEVS_MYCTU   454 TRLRQRIDAAVAQFADSGLRTSVQFVGPLSVVDSALADQAEAVVREAVSNAVRHAKASTLTVRVKVDDDLCIEVTDNGRGLPDEFTGSGLTNLRQRAEQAGGEFTLASVPGASGTVLRWSAPLSQ 578
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeee..eeeeeeee..........hhhhhhhhhhhhhh..eeeeee......eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zxo A 454 TRLRQRIDAAVAQFADSGLRTSVQFVGPLSVVDSALADQAEAVVREAVSNAVRHAAASTLTVRVKVDDDLcIEVTDNGRGmPDEFTGSGLTNLRQRAEQAGGEFTLASmPGASGTVLRWSAPLSQ 578
                                   463       473       483       493       503       513       523|      533|      543       553       563       573     
                                                                                                524-OCS   534-MSE                     562-MSE

Chain B from PDB  Type:PROTEIN  Length:125
 aligned with DEVS_MYCTO | P9WGK2 from UniProtKB/Swiss-Prot  Length:578

    Alignment length:125
                                   462       472       482       492       502       512       522       532       542       552       562       572     
           DEVS_MYCTO   453 ITRLRQRIDAAVAQFADSGLRTSVQFVGPLSVVDSALADQAEAVVREAVSNAVRHAKASTLTVRVKVDDDLCIEVTDNGRGLPDEFTGSGLTNLRQRAEQAGGEFTLASVPGASGTVLRWSAPLS 577
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhhhhhhhhhhhhhh........eeeeeeee..eeeeeeee..........hhhhhhhhhhhhhh..eeeeee......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zxo B 453 VTRLRQRIDAAVAQFADSGLRTSVQFVGPLSVVDSALADQAEAVVREAVSNAVRHAAASTLTVRVKVDDDLcIEVTDNGRGmPDEFTGSGLTNLRQRAEQAGGEFTLASmPGASGTVLRWSAPLS 577
                                   462       472       482       492       502       512       522 |     532 |     542       552       562       572     
                                                                                                 524-OCS   534-MSE                     562-MSE

Chain B from PDB  Type:PROTEIN  Length:125
 aligned with DEVS_MYCTU | P9WGK3 from UniProtKB/Swiss-Prot  Length:578

    Alignment length:125
                                   462       472       482       492       502       512       522       532       542       552       562       572     
           DEVS_MYCTU   453 ITRLRQRIDAAVAQFADSGLRTSVQFVGPLSVVDSALADQAEAVVREAVSNAVRHAKASTLTVRVKVDDDLCIEVTDNGRGLPDEFTGSGLTNLRQRAEQAGGEFTLASVPGASGTVLRWSAPLS 577
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhhhhhhhhhhhhhh........eeeeeeee..eeeeeeee..........hhhhhhhhhhhhhh..eeeeee......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zxo B 453 VTRLRQRIDAAVAQFADSGLRTSVQFVGPLSVVDSALADQAEAVVREAVSNAVRHAAASTLTVRVKVDDDLcIEVTDNGRGmPDEFTGSGLTNLRQRAEQAGGEFTLASmPGASGTVLRWSAPLS 577
                                   462       472       482       492       502       512       522 |     532 |     542       552       562       572     
                                                                                                 524-OCS   534-MSE                     562-MSE

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 '\|'

(no "SCOP Domain" information available for 3ZXO)

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (DEVS_MYCTO | P9WGK2)

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.

Chain A,B (DEVS_MYCTU | P9WGK3)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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:0051776	detection of redox state	The series of events in which a chemical stimulus indicating redox state is received and converted into a molecular signal. Redox state refers to the balance of oxidized versus reduced forms of electron donors and acceptors in an organelle, cell or organ; plastoquinone, glutathione (GSH/GSSG), and nicotinamide nucleotides (NAD+/NADH and NADP+/NADPH) are among the most important.
	GO:0040007	growth	The increase in size or mass of an entire organism, a part of an organism or a cell.
	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:0051775	response to redox state	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 redox state. Redox state refers to the balance of oxidized versus reduced forms of electron donors and acceptors in an organelle, cell or organ; plastoquinone, glutathione (GSH/GSSG), and nicotinamide nucleotides (NAD+/NADH and NADP+/NADPH) are among the most important.
	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: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: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.
	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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	Cis Peptide Bonds
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	3zxo
		Family and Domain Information	:	ProDom \| SYSTERS
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Access by UniProt ID/Accession number
	DEVS_MYCTO \| P9WGK2
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	DEVS_MYCTU \| P9WGK3
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	2.7.13.3
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	2.7.3.-
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2w3d	STRUCTURE OF THE FIRST GAF DOMAIN OF MYCOBACTERIUM TUBERCULOSIS DOSS
2w3e	OXIDIZED STRUCTURE OF THE FIRST GAF DOMAIN OF MYCOBACTERIUM TUBERCULOSIS DOSS
2w3f	REDUCED STRUCTURE OF THE FIRST GAF DOMAIN OF MYCOBACTERIUM TUBERCULOSIS DOSS
2w3g	AIR-OXIDIZED STRUCTURE OF THE FIRST GAF DOMAIN OF MYCOBACTERIUM TUBERCULOSIS DOSS
2w3h	CYANIDE BOUND STRUCTURE OF THE FIRST GAF DOMAIN OF MYCOBACTERIUM TUBERCULOSIS DOSS
2y79	STRUCTURE OF THE FIRST GAF DOMAIN E87A MUTANT OF MYCOBACTERIUM TUBERCULOSIS DOSS
3zxq	CRYSTAL STRUCTURE OF THE ATP-BINDING DOMAIN OF MYCOBACTERIUM TUBERCULOSIS DOST

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 13)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (0, 0)

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Gene Ontology (27, 41)

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