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(-) Description

Title :  OXIDIZED STRUCTURE OF THE FIRST GAF DOMAIN OF MYCOBACTERIUM TUBERCULOSIS DOSS
 
Authors :  B. S. Kang, H. Y. Cho, H. J. Cho
Date :  12 Nov 08  (Deposition) - 10 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Redox Sensor, Mycobacterium Tuberculosis, Heme, Kinase, Hypoxia, Gaf Domain, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Y. Cho, H. J. Cho, Y. M. Kim, J. I. Oh, B. S. Kang
Structural Insight Into The Heme-Based Redox Sensing By Doss From Mycobacterium Tuberculosis.
J. Biol. Chem. V. 284 13057 2009
PubMed-ID: 19276084  |  Reference-DOI: 10.1074/JBC.M808905200

(-) Compounds

Molecule 1 - TWO COMPONENT SENSOR HISTIDINE KINASE DEVS (GAF FAMILY PROTEIN)
    ChainsA, B
    EC Number2.7.3.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    FragmentGAF DOMAIN, RESIDUES 63-210
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid1773
    Other DetailsD63 TO K210 OF DOSS WITH ADDITIONAL GAMDP SEQUENCE AT THE N-TERMINUS DUE TO CLONING PROCEDURE
    SynonymDOSS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:83 , GLY A:84 , PHE A:98 , GLU A:101 , ILE A:103 , ILE A:111 , HIS A:113 , PRO A:115 , LYS A:116 , GLY A:117 , LEU A:118 , GLY A:119 , SER A:142 , ILE A:143 , GLY A:144 , PHE A:145 , PRO A:146 , HIS A:149 , MET A:152 , TYR A:171 , THR A:173 , HOH A:2134 , HOH A:2135 , HOH A:2136BINDING SITE FOR RESIDUE HEM A 500
2AC2SOFTWAREASP A:80 , ASP A:183 , HOH A:2026 , HOH A:2029 , HOH A:2119BINDING SITE FOR RESIDUE CA A 1206
3AC3SOFTWAREGLY B:84 , PHE B:98 , GLU B:101 , ILE B:103 , HIS B:113 , PRO B:115 , LYS B:116 , GLY B:117 , LEU B:118 , GLY B:119 , SER B:142 , ILE B:143 , GLY B:144 , PHE B:145 , PRO B:146 , HIS B:149 , MET B:152 , TYR B:171 , THR B:173 , HOH B:2020 , HOH B:2092 , HOH B:2123 , HOH B:2124BINDING SITE FOR RESIDUE HEM B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W3E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2W3E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W3E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W3E)

(-) Exons   (0, 0)

(no "Exon" information available for 2W3E)

(-) 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:148
 aligned with DEVS_MYCTO | P9WGK2 from UniProtKB/Swiss-Prot  Length:578

    Alignment length:193
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202   
           DEVS_MYCTO    13 AAMRPLRHTLSQLRLHELLVEVQDRVEQIVEGRDRLDGLVEAMLVVTAGLDLEATLRAIVHSATSLVDARYGAMEVHDRQHRVLHFVYEGIDEETVRRIGHLPKGLGVIGLLIEDPKPLRLDDVSAHPASIGFPPYHPPMRTFLGVPVRVRDESFGTLYLTDKTNGQPFSDDDEVLVQALAAAAGIAVANARL 205
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hh---------------------------------------------hhhhhhhhhhhhhhhhh.eeeeeeeee.hhh.eeeeeee..hhhhhhhhh......hhhhhhhhh...eee.hhhhh...............eeeeeeee..eeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w3e A  58 GAMDP---------------------------------------------DLEATLRAIVHSATSLVDARYGAMEVHDRQHRVLHFVYEGIDEETVRRIGHLPKGLGVIGLLIEDPKPLRLDDVSAHPASIGFPPYHPPMRTFLGVPVRVRDESFGTLYLTDKTNGQPFSDDDEVLVQALAAAAGIAVANARL 205
                                |    -         -         -         -         -|       72        82        92       102       112       122       132       142       152       162       172       182       192       202   
                               62                                            63                                                                                                                                              

Chain A from PDB  Type:PROTEIN  Length:148
 aligned with DEVS_MYCTU | P9WGK3 from UniProtKB/Swiss-Prot  Length:578

    Alignment length:193
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202   
           DEVS_MYCTU    13 AAMRPLRHTLSQLRLHELLVEVQDRVEQIVEGRDRLDGLVEAMLVVTAGLDLEATLRAIVHSATSLVDARYGAMEVHDRQHRVLHFVYEGIDEETVRRIGHLPKGLGVIGLLIEDPKPLRLDDVSAHPASIGFPPYHPPMRTFLGVPVRVRDESFGTLYLTDKTNGQPFSDDDEVLVQALAAAAGIAVANARL 205
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hh---------------------------------------------hhhhhhhhhhhhhhhhh.eeeeeeeee.hhh.eeeeeee..hhhhhhhhh......hhhhhhhhh...eee.hhhhh...............eeeeeeee..eeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w3e A  58 GAMDP---------------------------------------------DLEATLRAIVHSATSLVDARYGAMEVHDRQHRVLHFVYEGIDEETVRRIGHLPKGLGVIGLLIEDPKPLRLDDVSAHPASIGFPPYHPPMRTFLGVPVRVRDESFGTLYLTDKTNGQPFSDDDEVLVQALAAAAGIAVANARL 205
                                |    -         -         -         -         -|       72        82        92       102       112       122       132       142       152       162       172       182       192       202   
                               62                                            63                                                                                                                                              

Chain B from PDB  Type:PROTEIN  Length:145
 aligned with DEVS_MYCTO | P9WGK2 from UniProtKB/Swiss-Prot  Length:578

    Alignment length:145
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202     
           DEVS_MYCTO    63 DLEATLRAIVHSATSLVDARYGAMEVHDRQHRVLHFVYEGIDEETVRRIGHLPKGLGVIGLLIEDPKPLRLDDVSAHPASIGFPPYHPPMRTFLGVPVRVRDESFGTLYLTDKTNGQPFSDDDEVLVQALAAAAGIAVANARLYQ 207
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) GAF-2w3eB01 B:63-200                                                                                                                      ------- Pfam domains (1)
           Pfam domains (2) GAF-2w3eB02 B:63-200                                                                                                                      ------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhheeeeeeeee.....eeeeeee..hhhhhhhhh.....hhhhhhhhhh...eee.hhhhh...............eeeeeeee..eeeeeeeeeee.hhh..hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w3e B  63 DLEATLRAIVHSATSLVDARYGAMEVHDRQHRVLHFVYEGIDEETVRRIGHLPKGLGVIGLLIEDPKPLRLDDVSAHPASIGFPPYHPPMRTFLGVPVRVRDESFGTLYLTDKTNGQPFSDDDEVLVQALAAAAGIAVANARLYQ 207
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202     

Chain B from PDB  Type:PROTEIN  Length:145
 aligned with DEVS_MYCTU | P9WGK3 from UniProtKB/Swiss-Prot  Length:578

    Alignment length:145
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202     
           DEVS_MYCTU    63 DLEATLRAIVHSATSLVDARYGAMEVHDRQHRVLHFVYEGIDEETVRRIGHLPKGLGVIGLLIEDPKPLRLDDVSAHPASIGFPPYHPPMRTFLGVPVRVRDESFGTLYLTDKTNGQPFSDDDEVLVQALAAAAGIAVANARLYQ 207
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) GAF-2w3eB01 B:63-200                                                                                                                      ------- Pfam domains (1)
           Pfam domains (2) GAF-2w3eB02 B:63-200                                                                                                                      ------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhheeeeeeeee.....eeeeeee..hhhhhhhhh.....hhhhhhhhhh...eee.hhhhh...............eeeeeeee..eeeeeeeeeee.hhh..hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w3e B  63 DLEATLRAIVHSATSLVDARYGAMEVHDRQHRVLHFVYEGIDEETVRRIGHLPKGLGVIGLLIEDPKPLRLDDVSAHPASIGFPPYHPPMRTFLGVPVRVRDESFGTLYLTDKTNGQPFSDDDEVLVQALAAAAGIAVANARLYQ 207
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202     

   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  (0, 0)

(no "SCOP Domain" information available for 2W3E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2W3E)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: GAF (44)

(-) Gene Ontology  (27, 41)

Asymmetric/Biological Unit(hide GO term definitions)
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.

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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DEVS_MYCTO | P9WGK22w3d 2w3f 2w3g 2w3h 2y79 3zxo 4ynr 4yof
        DEVS_MYCTU | P9WGK32w3d 2w3f 2w3g 2w3h 2y79 3zxo 4ynr 4yof

(-) Related Entries Specified in the PDB File

2w3d 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