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The Open Protein Structure Annotation Network
PDB Keyword
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4jqs

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

    Title Crystal structure of a hypothetical protein (BACUNI_01602) from Bacteroides uniformis ATCC 8492 at 2.30 A resolution. To be published
    Site JCSG
    PDB Id 4jqs Target Id 418017
    Related PDB Ids 4pxy 
    Molecular Characteristics
    Source Bacteroides uniformis atcc 8492
    Alias Ids TPS76839,ZP_02070184.1, 323290 Molecular Weight 28654.94 Da.
    Residues 249 Isoelectric Point 5.71
    Sequence qvpegypanyakaprfkaliyytqhaeeahvqfaeqattffkklnygdgfvldittdfskypyeklkey nviimlntspntkaerdafeqymengggwvgfhaaayndknthwpwfvkflgggvfycnnwppqpvlve vdneehpvtknlpasfvapasewyqwtpsprqnkdvevllslspknyplgikdvvnfgdfpivwsnkny rmiylnmghgdeefidgtqnlllvnafrwvvskdksgnpflk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 3
    Resolution (Å) 2.30 Rfree 0.2061
    Matthews' coefficent 2.28 Rfactor 0.1623
    Waters 258 Solvent Content 46.00

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Pfam Annotation: I found it overlapped immediately with the ThuA family PF06283. This family is in Glutaminase_I (CL0014). There are structures for this family but the funciton is still unknown, 1qtb 4e5v. The alignment produced had all the key conserved residues as seen in the HMM-logo for the ThuA family so is likely to have a similar function. Solution of the structure should prove very interesting

     

    Target id 418017 is a member of the Trehalose utilization (Thu A, Pfam 06283) family. A DELTA-BLAST seach of the PDB shows two other structures, PDB ID 1T0B ( a MCSG structre) and PDB ID 4E5V  (a JCSG Structure)show sequence similarity to target id 418017. Shown below is a ribbons representation of a monomer of target id 418017. The structure of target id 418017 was determined in two different space groups. The most significant structural difference between the to crystal forms is a zinc is bound to the structure in one of the crystal forms but not the other.

    monomer.png

     

    fastSCOP predicts target id 418017 belongs to the the Class I glutamine-amidotransferase SCOP Superfamily,
    EBI-PISA indicates that a hexamer is a siginificant oligomerization state. Show below is a ribbons representation of the hexamer with the individual subunits in different colors. Proteins within this family show a flavodoxin-like SCOP fold. Within the Class I glutanine-amidotransferase SCOP Superfamily, target id will most likely be classified into the ThuA-like family. Another structural genomics target PDB ID 1T0B (mentioned above) has already been classified into this SCOP family.

    hexamer.png

    Two crystal forms of target id 418017. For both crystal forms, EBI-PISA predicts that similar trimers (shown below) are significant oligomerization states.

    trimer.png

     

     

     

    A DALI structural similarity search shows that there are numerous other structures in the PDB that show structural similarity to target id 418017. Shown below are the top-scoring hits.

    PDB ID DALI Z-score rmsd (Ang) length of alignment number of residues in hit %sequence id Description
    4e5v 19.5 2.4 206 280 17 Crystal structure of a Putative thua-like protein (PARMER_02418) from Parabacteroides merdae ATCC 43184 at 1.75 A resolution (JCSG)
    1t0b 17.6 2.3 205 279 18 Structure of ThuA-like protein from Bacillus stearothermophilus (MCSG)
    3osz 16.0 2.8 191 245 13 Crystal Structure of the complex of proteinase K with an antimicrobial nonapeptide, at 2.26 A resolution
    2gk3 15.8 2.7 189 248 17 Cytoplasmic Protein STM3548 from Salmonella typhimurium [Ref]
    3rht 15.6 2.7 191 252 15 Crystal structure of type 1 glutamine amidotransferase (GATase1)-like protein from Planctomyces limnophilus
    4ads 15.0 2.9 189 217 10 Crystal structure of plasmodial PLP synthase complex [Ref]
    1i7s 14.6 2.8 176 192 10  ANTHRANILATE SYNTHASE FROM SERRATIA MARCESCENS IN COMPLEX WITH ITS END PRODUCT INHIBITOR L-TRYPTOPHAN [Ref]
    3tts 14.5 3.2 190 675 15 Crystal structure of beta-galactosidase from Bacillus circulans sp. alkalophilus [Ref]
    2abw 14.5 3.0 188 216 10 Glutaminase subunit of the plasmodial PLP synthase (Vitamin B6 biosynthesis) [Ref]
    1i1q 14.4 2.7 171 186 9 STRUCTURE OF THE COOPERATIVE ALLOSTERIC ANTHRANILATE SYNTHASE FROM SALMONELLA TYPHIMURIUM [Ref]

     

     

    Shown below is a MES binding site on target id 418017. The 2fo-fc electron density shown in pink is countoured at 1 sigma. The positioing of two key acidic residues, Asp 104 and Glu 107 suggests that target id 418017 is a glucosidase with the MES mimcing a six-membered sugar ring. The proximity of the sidechain of Lys 100 to the acid pair suggests it plays a role in the catalysis.mes_site.bmp

    A substructure search of the PDB on the putative active site surrounding the MES shows that PDB ID  3myv, a SusD homolog and a JCSG target shares a similar positioning of two acidic sidechains and a basic residue. This could provide some evidence that PDB id 3myv and target id 418017 perform similar functions and/or share similar substrates.

    3myv_overlap.bmp

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

    Ligand Summary

    Zinc and MES

    Reviews

    References

     

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