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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DOMAIN OF PUTATIVE SENSORY BOX/GGDEF FAMILY PROTEIN FROM VIBRIO PARAHAEMOLYTICUS
 
Authors :  R. Wu, A. James, A. Joachimiak, Midwest Center For Structural Geno (Mcsg)
Date :  20 Mar 07  (Deposition) - 01 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Sensory Box/Ggdef Family Protein, Structural Genomics, Mcsg, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Wu, A. James, A. Joachimiak
The Crystal Structure Of The Domain Of Putative Sensory Box/Ggdef Family Protein From Vibrio Parahaemolyticus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE SENSORY BOX/GGDEF FAMILY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PDM68
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 27-312
    Gene: VP0354
    Organism Scientific: VIBRIO PARAHAEMOLYTICUS RIMD 2210633
    Organism Taxid: 223926
    Strain: 223926

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2MSE6Mod. Amino AcidSELENOMETHIONINE
3NA1Ligand/IonSODIUM ION
4SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS B:112 , ARG B:115 , GLY B:141BINDING SITE FOR RESIDUE NA B 401
2AC2SOFTWAREGLN A:80 , ARG A:82 , LYS A:112 , ARG A:115 , TYR A:117 , GLU A:137 , ARG A:138 , ARG A:152 , ASN A:170 , HOH A:530BINDING SITE FOR RESIDUE SO4 A 501
3AC3SOFTWAREGLN B:80 , ARG B:82 , LYS B:112 , ARG B:115 , TYR B:117 , GLU B:137 , ARG B:138 , ARG B:152 , ASN B:170 , HOH B:703BINDING SITE FOR RESIDUE SO4 B 502
4AC4SOFTWAREGLN B:80 , GLU B:90 , ARG B:93 , ILE B:108 , ARG B:110 , LYS B:112 , ARG B:138 , ASP B:139 , HOH B:703BINDING SITE FOR RESIDUE ACY B 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P7J)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:145 -Pro A:146
2Ala B:8 -Asn B:9
3Tyr B:145 -Pro B:146
4Ser B:242 -Gly B:243

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P7J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P7J)

(-) Exons   (0, 0)

(no "Exon" information available for 2P7J)

(-) 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:265
 aligned with Q87SR8_VIBPA | Q87SR8 from UniProtKB/TrEMBL  Length:626

    Alignment length:265
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294     
         Q87SR8_VIBPA    35 NNVENTAKEALHQLAYTGREYNNIQDQIETISDLLGHSQSLYDYLREPSKANLTILENMWSSVARNQKLYKQIRFLDTSGTEKVRIKYDFKTSIAGPSLILRDKSAREYFKYAQSLDNEQISAWGIELERDKGELVYPLSPSLRILMPISVNDVRQGYLVLNVDIEYLSSLLNYSPVRDFHIELVKHKGFYIASPDESRLYGDIIPERSQFNFSNMYPDIWPRVVSEQAGYSYSGEHLIAFSSIKFVSNEPLHLIIDLSNEQLSK 299
               SCOP domains d2p7ja2 A:9-180 GGDEF family protein VP0354                                                                                                                                 d2p7ja1 A:181-273 GGDEF family protein VP0354                                                 SCOP domains
               CATH domains 2p7jA01 A:9-46                        2p7jA02 A:47-180  [code=3.30.450.20, no name defined]                                                                                 2p7jA03 A:181-273  [code=3.30.450.20, no name defined]                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.eeeeeee.....eeeeeeee....eeee.........hhhhhhhhh......eeeeeee.ee..ee.....eeeeeeeeeee..eeeeeeeeeeehhhhhhhhhee....eeeeee.....eee..hhhhh...........hhhhhh..hhhhhhh...eeee...eeeeeeeee.....eeeeeeeeehhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p7j A   9 NNVENTAKEALHQLAYTGREYNNIQDQIETISDLLGHSQSLYDYLREPSKANLTILENmWSSVARNQKLYKQIRFLDTSGTEKVRIKYDFKTSIAGPSLILRDKSAREYFKYAQSLDNEQISAWGIELERDKGELVYPLSPSLRILmPISVNDVRQGYLVLNVDIEYLSSLLNYSPVRDFHIELVKHKGFYIASPDESRLYGDIIPERSQFNFSNmYPDIWPRVVSEQAGYSYSGEHLIAFSSIKFVSNEPLHLIIDLSNEQLSK 273
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148      |158       168       178       188       198       208       218     | 228       238       248       258       268     
                                                                                     67-MSE                                                                                 155-MSE                                                              224-MSE                                             


Chain B from PDB  Type:PROTEIN  Length:274
 aligned with Q87SR8_VIBPA | Q87SR8 from UniProtKB/TrEMBL  Length:626

    Alignment length:274
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303    
         Q87SR8_VIBPA    34 ANNVENTAKEALHQLAYTGREYNNIQDQIETISDLLGHSQSLYDYLREPSKANLTILENMWSSVARNQKLYKQIRFLDTSGTEKVRIKYDFKTSIAGPSLILRDKSAREYFKYAQSLDNEQISAWGIELERDKGELVYPLSPSLRILMPISVNDVRQGYLVLNVDIEYLSSLLNYSPVRDFHIELVKHKGFYIASPDESRLYGDIIPERSQFNFSNMYPDIWPRVVSEQAGYSYSGEHLIAFSSIKFVSNEPLHLIIDLSNEQLSKRATRDIND 307
               SCOP domains d2p7jb2 B:8-180 GGDEF family protein VP0354                                                                                                                                  d2p7jb1 B:181-281 GGDEF family protein VP0354                                                         SCOP domains
               CATH domains 2p7jB01 B:8-46                         2p7jB02 B:47-180  [code=3.30.450.20, no name defined]                                                                                 2p7jB03 B:181-275  [code=3.30.450.20, no name defined]                                         ------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.eeeeeeee....eeeeeeee....eeee.........hhhhhhhhh......eeeeeee.ee..ee.....eeeeeeeeeee..eeeeeeeeeeehhhhhhhhhee....eeeeee.....eee..hhhhh....hhhhh..hhhhhh..hhhhhhhh.eeeee...eeeeeeeee.....eeeeeeeeehhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p7j B   8 ANNVENTAKEALHQLAYTGREYNNIQDQIETISDLLGHSQSLYDYLREPSKANLTILENmWSSVARNQKLYKQIRFLDTSGTEKVRIKYDFKTSIAGPSLILRDKSAREYFKYAQSLDNEQISAWGIELERDKGELVYPLSPSLRILmPISVNDVRQGYLVLNVDIEYLSSLLNYSPVRDFHIELVKHKGFYIASPDESRLYGDIIPERSQFNFSNmYPDIWPRVVSEQAGYSYSGEHLIAFSSIKFVSNEPLHLIIDLSNEQLSKRATRDIND 281
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217      |227       237       247       257       267       277    
                                                                                      67-MSE                                                                                 155-MSE                                                              224-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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2P7J)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q87SR8_VIBPA | Q87SR8)
molecular function
    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.
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: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: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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 Related Entries

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UniProtKB/TrEMBL
        Q87SR8_VIBPA | Q87SR8: 3lid 3lie

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