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The Open Protein Structure Annotation Network
PDB Keyword
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3l39

    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of Putative PhoU-like phosphate regulatory protein (BT4638) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.93 A resolution. To be published
    Site JCSG
    PDB Id 3l39 Target Id 356900
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS2485,BT4638, PF01865, 89871, 283184 Molecular Weight 25000.18 Da.
    Residues 215 Isoelectric Point 4.97
    Sequence mknsffskftpkepkffpllkqlsdvlsassvllvesmehdlpteradyykqikdmeregdrlthlifd elsttfitpfdredihdlascmddvidginssakriviynprpisesgkelsrliheeainigkamdel etfrknpkplrdyctqlhdienqaddvyelfitklfeeekdcielikikeimhelekttdaaehvgkil knlivkys
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.93 Rfree 0.202
    Matthews' coefficent 2.73 Rfactor 0.166
    Waters 187 Solvent Content 54.94

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3l39

    Protein Summary

    Pfam Update: This protein is now in family PF01865.9 PhoU_div CL0297, with other structures.

     

    Gene BT_4638 from Bacteroides thetaiotaomicron vpi-5482 translates into the NP_813549 protein that  belongs to the DUF47(PF01865). This family include prokaryotic proteins of unknown function although it is believed that this class of proteins is distantly related to the PhoU (PF01895) Pfam class. The members of the PhoU (PF01895) contain phosphate regulatory proteins. The structure was refined at a resolution of 1.93 Angstroms. Primary phasing was accomplished by molecular replacement using PDB ID 2iiu and 1xwm as molecular replacement models. Several molecular replacement models were built using intermediate templates obtained by morphing homologous models found by the FFAS onto each other.

     

    Shown below is a ribbons representation of the structure 3l39 color coded with the N-terminal end in blue and the C-terminal end in red. The structure can most likely be classified into the all-alpha class, spectrin repeat-like fold,  PhoU-like SCOP (super)family.

     

    monomer_ribbons.png

     

     

    An EBI-DALI search shows that the structure 3l39 is related to the following proteins:

    PDB ID Z-Score rmsd lali nres %seqence id Description
    2olt 22.5 2.3 199 214 19 NP_719307.1 FROM SHEWANELLA ONEIDENSIS  AT 2.00 A RESOLUTION
    2iiu 22.1 2.4 197 209 19 PUTATIVE PHOU-LIKE PHOSPHATE REGULATORY PROTEIN FROM SHENWANELLA ONEIDENSIS MR-1 AT 2.28 A RESOLUTION
    1t72 20.6 3.0 194 215 11 PHOSPHATE TRANSPORT SYSTEM PROTEIN PHOU FROM AQUIFEX AEOLICUS
    1t8b 20.3 2.6 190 208 11 REFOLDED PHOU-LIKE PROTEIN (GI2983430) FROM AQUIFEX AEOLICUS
    2i0m 19.8 2.5 188 207 11 THE PHOSPHATE TRANSPORT SYSTEM REGULATORY PROTEIN PHOU FROM STREPTOCOCCUS PNEUMONIAE
    1xwm 19.5 2.4 189 212 15 PHOU (PHOSPHATE UPTAKE REGULATOR)
    1sum 19.3 2.8 192 224 11 PHOSPHATE TRANSPORT SYSTEM PROTEIN PHOU HOMOLOG

     

     Two of these structurally-related proteins, PDB ID 2olt and PDB 1D 2iiu were determined by JCSG. The figure below shows a representation of the of the superimposed  structures of 3l39 (green), PDB ID 2olt (blue), and PDB ID 2iiu (red).

    TB5121A_homologs_overlap.png

     

     The EBI-PISA server predicts that a hexamer is a significant oligomerization state of 3l39. Shown below are two views of the predicted hexamer with each monomer in a different color

    hexamer.bmp

     

    3l39 was crystallized in the presence of ammonium phosphate, and several molecules of phosphate were observed in the crystal structure.

    phosphate.png

     

     

    The DUF47 (PF01865) family is related by remote homology to other phosphate binding families (FFAS score -15.5 for PF01895 (PhoU), FFAS score -10.6 for PF04344 (chemotaxis phosphatase CheZ)). Several DUF47 homologs are fused with MFS (major facilitator superfamily) or Nudix domains, domains involved in the transport of small solutes and phosphate hydrolysis respectively. SCO4137, a DUF47 homolog in Streptomyces coelicor is strongly predicted to be functionally associated with SCO4138 and SCO1845, genes that have been shown to be expressed in response to phosphate deprivation [Ref].

    Ligand Summary

    Reviews

    References

     

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