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(-) Description

Title :  KINA PAS-A DOMAIN, HOMODIMER
 
Authors :  J. Lee, D. R. Tomchick, C. A. Brautigam, M. Machius, R. Kort, K. J. Hellingwerf, K. H. Gardner
Date :  14 Jan 08  (Deposition) - 18 Mar 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Histidine Kinase, Two-Component Regulatory System, Two-Component Signal Transduction, Transferase, Sporulation, Phosphorylation, Scod, Scob, Gsic, Spoiij, Kinase, Spoiif, Pas Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Lee, D. R. Tomchick, C. A. Brautigam, M. Machius, R. Kort, K. J. Hellingwerf, K. H. Gardner
Changes At The Kina Pas-A Dimerization Interface Influence Histidine Kinase Function.
Biochemistry V. 47 4051 2008
PubMed-ID: 18324779  |  Reference-DOI: 10.1021/BI7021156

(-) Compounds

Molecule 1 - SPORULATION KINASE A
    ChainsA, B, C, D
    EC Number2.7.13.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHIS6GBETA1KINA
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPHIS6GBETA1
    FragmentPAS-A, RESIDUES 10-117
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid1423
    Other DetailsBACILLUS GENETIC STOCK CENTER, COLUMBUS, OH, U.S.A.
    StrainSTRAIN 1A40
    SynonymSTAGE II SPORULATION PROTEIN J, KINA PAS-A

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A  D
Biological Unit 2 (1x) BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL4Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA C:19 , VAL C:20 , ILE C:108 , HOH C:2004 , HOH C:2084 , ALA D:19 , VAL D:20 , ILE D:108BINDING SITE FOR RESIDUE ACT C1117
2AC2SOFTWAREALA C:92 , GLU C:94 , ILE C:108 , LYS C:110BINDING SITE FOR RESIDUE ACT C1118
3AC3SOFTWAREGLU A:69 , HIS A:71 , HOH D:2039BINDING SITE FOR RESIDUE CL D1115
4AC4SOFTWARETYR A:29 , HOH A:2006 , TYR B:29BINDING SITE FOR RESIDUE CL B1115
5AC5SOFTWAREHOH D:2074BINDING SITE FOR RESIDUE CL C1115

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VLG)

(-) Sequences/Alignments

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:93
 aligned with KINA_BACSU | P16497 from UniProtKB/Swiss-Prot  Length:606

    Alignment length:100
                                    24        34        44        54        64        74        84        94       104       114
           KINA_BACSU    15 TDIHAVLASNGRIIYISANSKLHLGYLQGEMIGSFLKTFLHEEDQFLVESYFYNEHHLMPCTFRFIKKDHTIVWVEAAVEIVTTRAERTEREIILKMKVL 114
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....eeee..hhhhhhh.hhhhhh...hhhh.hhhhhhhhhhhhhh......eeeeee.....eeeeeeeeee.-------...eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 2vlg A  15 TDIHAVLASNGRIIYISANSKLHLGYLQGEMIGSFLKTFLHEEDQFLVESYFYNEHHLMPCTFRFIKKDHTIVWVEAAVEIV-------EREIILKMKVL 114
                                    24        34        44        54        64        74        84        94 |     104       114
                                                                                                            96     104          

Chain B from PDB  Type:PROTEIN  Length:93
 aligned with KINA_BACSU | P16497 from UniProtKB/Swiss-Prot  Length:606

    Alignment length:100
                                    24        34        44        54        64        74        84        94       104       114
           KINA_BACSU    15 TDIHAVLASNGRIIYISANSKLHLGYLQGEMIGSFLKTFLHEEDQFLVESYFYNEHHLMPCTFRFIKKDHTIVWVEAAVEIVTTRAERTEREIILKMKVL 114
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....eeee..hhhhhhh.hhhhhh...hhhh.hhhhhhhhhhhhhh......eeeeee.....eeeeeeeeee..-------..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 2vlg B  15 TDIHAVLASNGRIIYISANSKLHLGYLQGEMIGSFLKTFLHEEDQFLVESYFYNEHHLMPCTFRFIKKDHTIVWVEAAVEIVT-------REIILKMKVL 114
                                    24        34        44        54        64        74        84        94  |      -|      114
                                                                                                             97     105         

Chain C from PDB  Type:PROTEIN  Length:102
 aligned with KINA_BACSU | P16497 from UniProtKB/Swiss-Prot  Length:606

    Alignment length:102
                                    24        34        44        54        64        74        84        94       104       114  
           KINA_BACSU    15 TDIHAVLASNGRIIYISANSKLHLGYLQGEMIGSFLKTFLHEEDQFLVESYFYNEHHLMPCTFRFIKKDHTIVWVEAAVEIVTTRAERTEREIILKMKVLEE 116
               SCOP domains ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee....eeee..hhhhhhh.hhhhhh...hhhh.hhhhhh.hhhhhhh......eeeeee.....eeeeeeeeeeeeee...eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 2vlg C  15 TDIHAVLASNGRIIYISANSKLHLGYLQGEMIGSFLKTFLHEEDQFLVESYFYNEHHLMPCTFRFIKKDHTIVWVEAAVEIVTTRAERTEREIILKMKVLEE 116
                                    24        34        44        54        64        74        84        94       104       114  

Chain D from PDB  Type:PROTEIN  Length:101
 aligned with KINA_BACSU | P16497 from UniProtKB/Swiss-Prot  Length:606

    Alignment length:103
                                    24        34        44        54        64        74        84        94       104       114   
           KINA_BACSU    15 TDIHAVLASNGRIIYISANSKLHLGYLQGEMIGSFLKTFLHEEDQFLVESYFYNEHHLMPCTFRFIKKDHTIVWVEAAVEIVTTRAERTEREIILKMKVLEEE 117
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeee..hhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhh..--....eeeeee.....eeeeeeeeeeeeee...eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 2vlg D  15 TDIHAVLASNGRIIYISANSKLHLGYLQGEMIGSFLKTFLHEEDQFLVESYFYN--HLMPCTFRFIKKDHTIVWVEAAVEIVTTRAERTEREIILKMKVLEEE 117
                                    24        34        44        54        64   |  | 74        84        94       104       114   
                                                                                68 71                                              

   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 2VLG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2VLG)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (KINA_BACSU | P16497)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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.
    GO:0016772    transferase activity, transferring phosphorus-containing groups    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
biological process
    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:0043938    positive regulation of sporulation    Any process that activates, maintains or increases the frequency, rate or extent of sporulation, the process whose specific outcome is the progression of a spore over time, from its initiation to the mature structure.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    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.
    GO:0030435    sporulation resulting in formation of a cellular spore    The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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