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(-) Description

Title :  CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE PUTATIVE HISTIDINE KINASE VPHK1S-Z8
 
Authors :  Z. Zhang, W. A. Hendrickson
Date :  24 Jan 10  (Deposition) - 05 May 10  (Release) - 11 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Pdc Fold, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Zhang, W. A. Hendrickson
Structural Characterization Of The Predominant Family Of Histidine Kinase Sensor Domains.
J. Mol. Biol. V. 400 335 2010
PubMed-ID: 20435045  |  Reference-DOI: 10.1016/J.JMB.2010.04.049

(-) Compounds

Molecule 1 - PUTATIVE SENSORY BOX/GGDEF FAMILY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B+
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: EXTRACELLULAR DOMAIN (UNP RESIDUES 28-313)
    Gene: VP0354
    Organism Scientific: VIBRIO PARAHAEMOLYTICUS
    Organism Taxid: 670

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EDO9Ligand/Ion1,2-ETHANEDIOL
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 3 (2, 11)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO9Ligand/Ion1,2-ETHANEDIOL
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:106 , ARG A:108 , LYS A:138 , ARG A:141 , TYR A:143 , GLU A:163 , ARG A:164 , ARG A:178 , ASN A:196 , HOH A:334BINDING SITE FOR RESIDUE PO4 A 321
02AC2SOFTWARELYS A:138 , ARG A:141 , GLY A:167BINDING SITE FOR RESIDUE CL A 350
03AC3SOFTWARETYR A:78 , PRO A:82 , ASP A:111 , LYS A:117 , HOH A:382 , HOH A:515BINDING SITE FOR RESIDUE EDO A 2
04AC4SOFTWAREHOH A:25 , TYR A:171 , ILE A:238 , PRO A:240 , HOH A:570BINDING SITE FOR RESIDUE EDO A 3
05AC5SOFTWARETYR A:146 , ALA A:157 , HOH A:535 , HOH A:571BINDING SITE FOR RESIDUE EDO A 4
06AC6SOFTWAREILE A:160 , LYS A:220 , TYR A:235 , ASP A:237BINDING SITE FOR RESIDUE EDO A 5
07AC7SOFTWARELEU A:79 , ARG A:80 , VAL A:185 , GLN A:190 , SER B:149BINDING SITE FOR RESIDUE EDO A 9
08AC8SOFTWAREGLN B:106 , ARG B:108 , LYS B:138 , ARG B:141 , TYR B:143 , GLU B:163 , ARG B:164 , ARG B:178 , ASN B:196 , HOH B:366BINDING SITE FOR RESIDUE PO4 B 321
09AC9SOFTWARELYS B:138 , ARG B:141 , LYS B:166 , GLY B:167BINDING SITE FOR RESIDUE CL B 351
10BC1SOFTWAREILE B:160 , LYS B:220 , ILE B:226 , TYR B:235 , ASP B:237BINDING SITE FOR RESIDUE EDO B 1
11BC2SOFTWAREASP A:60 , GLN B:47 , TYR B:50 , SER B:209 , ARG B:212BINDING SITE FOR RESIDUE EDO B 6
12BC3SOFTWAREGLY B:159 , ILE B:160 , LYS B:220 , SER B:282 , HOH B:431BINDING SITE FOR RESIDUE EDO B 7
13BC4SOFTWAREARG A:257 , HOH A:345 , TYR B:78 , LEU B:79 , LYS B:117BINDING SITE FOR RESIDUE EDO B 8

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Tyr A:171 -Pro A:172
2Ile A:309 -Gln A:310
3Tyr B:171 -Pro B:172

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LID)

(-) 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:279
 aligned with Q87SR8_VIBPA | Q87SR8 from UniProtKB/TrEMBL  Length:626

    Alignment length:279
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302         
         Q87SR8_VIBPA    33 LANNVENTAKEALHQLAYTGREYNNIQDQIETISDLLGHSQSLYDYLREPSKANLTILENMWSSVARNQKLYKQIRFLDTSGTEKVRIKYDFKTSIAGPSLILRDKSAREYFKYAQSLDNEQISAWGIELERDKGELVYPLSPSLRILMPISVNDVRQGYLVLNVDIEYLSSLLNYSPVRDFHIELVKHKGFYIASPDESRLYGDIIPERSQFNFSNMYPDIWPRVVSEQAGYSYSGEHLIAFSSIKFVSNEPLHLIIDLSNEQLSKRATRDINDLIQE 311
               SCOP domains d3lida1 A:33-206 GGDEF family protein VP0354                                                                                                                                  d3lida2 A:207-311 GGDEF family protein VP0354                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.eeeeeeee....eeeeeeee....eeee.........hhhhhhhhhh.....ee...ee.ee..ee.....eeeeeeeeeee..eeeeeeeeeeehhhhhhhhhee....ee.eeee....eee..hhhhh....hhhhh..hhhhhh..hhhhhhh...eeee...eeeeeeee.......eeeeeeeehhhhhhh...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lid A  33 LANNVENTAKEALHQLAYTGREYNNIQDQIETISDLLGHSQSLYDYLREPSKANLTILENMWSSVARNQKLYKQIRFLDTSGTEKVRIKYDFKTSIAGPSLILRDKSAREYFKYAQSLDNEQISAWGIELERDKGELVYPLSPSLRILMPISVNDVRQGYLVLNVDIEYLSSLLNYSPVRDFHIELVKHKGFYIASPDESRLYGDIIPERSQFNFSNMYPDIWPRVVSEQAGYSYSGEHLIAFSSIKFVSNEPLHLIIDLSNEQLSKRATRDINDLIQE 311
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302         


Chain B from PDB  Type:PROTEIN  Length:276
 aligned with Q87SR8_VIBPA | Q87SR8 from UniProtKB/TrEMBL  Length:626

    Alignment length:276
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305      
         Q87SR8_VIBPA    36 NVENTAKEALHQLAYTGREYNNIQDQIETISDLLGHSQSLYDYLREPSKANLTILENMWSSVARNQKLYKQIRFLDTSGTEKVRIKYDFKTSIAGPSLILRDKSAREYFKYAQSLDNEQISAWGIELERDKGELVYPLSPSLRILMPISVNDVRQGYLVLNVDIEYLSSLLNYSPVRDFHIELVKHKGFYIASPDESRLYGDIIPERSQFNFSNMYPDIWPRVVSEQAGYSYSGEHLIAFSSIKFVSNEPLHLIIDLSNEQLSKRATRDINDLIQE 311
               SCOP domains d3lidb1 B:36-206 GGDEF family protein VP0354                                                                                                                               d3lidb2 B:207-311 GGDEF family protein VP0354                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.eeeeeeee....eeeeeeee....eeee.........hhhhhhhhhh.....ee...ee.ee..ee.....eeeeeeeeeee..eeeeeeeeeeehhhhhhhhhee....ee.eeee....eee..hhhhh....hhhhh..hhhhhh..hhhhhh...eeeee...eeeeeeee.......eeeeeeeehhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lid B  36 NVENTAKEALHQLAYTGREYNNIQDQIETISDLLGHSQSLYDYLREPSKANLTILENMWSSVARNQKLYKQIRFLDTSGTEKVRIKYDFKTSIAGPSLILRDKSAREYFKYAQSLDNEQISAWGIELERDKGELVYPLSPSLRILMPISVNDVRQGYLVLNVDIEYLSSLLNYSPVRDFHIELVKHKGFYIASPDESRLYGDIIPERSQFNFSNMYPDIWPRVVSEQAGYSYSGEHLIAFSSIKFVSNEPLHLIIDLSNEQLSKRATRDINDLIQE 311
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric 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: 2p7j 3lie

(-) Related Entries Specified in the PDB File

3li8 3li9 3lia 3lib 3lic 3lie 3lif