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The Open Protein Structure Annotation Network
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3ce8

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

    Title Crystal structure of putative PII-like nitrogen regulatory protein (YP_001048502.1) from Shewanella baltica OS155 at 2.40 A resolution. To be published
    Site JCSG
    PDB Id 3ce8 Target Id 378293
    Molecular Characteristics
    Source Shewanella baltica os155
    Alias Ids TPS1722,YP_001048502.1, 92037 Molecular Weight 11518.67 Da.
    Residues 101 Isoelectric Point 5.18
    Sequence msteqllvliaqndikddivdtlieleflsgfslgnicgfsrehshfnikeqvegyrefckfeimhpaa qqaalltalalvckhnpcrywimpiyqngtls
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.40 Rfree 0.236
    Matthews' coefficent 2.15 Rfactor 0.196
    Waters 9 Solvent Content 42.83

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3ce8
    1. PII signal transduction proteins: nitrogen regulation and beyond
    LF Huergo, G Chandra - FEMS Microbiology , 2012 - Wiley Online Library
     

    Protein Summary

    Gene Sbal_0098 from Shewanella baltica os155 encodes the YP_001048502 amino acid sequence that belongs to the DUF3240 (PF11582). Analysis of its genome vicinity identifies the heavy metal efflux pump CzcA (Sbal_0099) with a 0.87 score.

    SCOP classifies 3ce8 in the alpha+beta class, ferredoxin-like fold, GlnB-like superfamily.

    3ce8 structure forms a trimer by lending its C-terminal strand to the neighboring molecule to form a beta sheet (see Figure 1). DALI top hits (Z=12) are with PII-like proteins PDB:1vfj, PDB:2z0g, and PDB:2nuu. There are a number of proteins with similar structures, most notably PDB:1kr4 (Z=10) and PDB:2pii (Z=11) [Ref]. A superposition of them is shown in Figure 2. Based on this, 3ce8 is annotated as putative PII-like nitrogen regulatory protein. There is an ATP binding pocket in a structurally related protein given by PDB code 2rd5 (chain D, [Ref]), a nitrogen sensing protein. The binding loops are somewhat different in 3ce8 and sequence conservation of binding residues is not evident from a structure superposition alone, since a crucial loop in 3ce8 has not been modeled. This loop starts after Arg-42 and terminates with Glu-54 and is given by the sequence EHSHFNIKEQV. The gamma phosphate group of the ATP molecule is hydrogen bonded by Gln-50 via the terminal side-chain nitrogen which corresponds to Glu-55 not modeled in 3ce8. This is still a reasonable interaction with the phosphate group since the carbonyl oxygen of Gly-48 in 2rd5 (corresponds to Ser-41 in 3ce8) interacts in the same way with the beta phosphate. Gly-99 (2rd5) is in a loop region which is much shorter in 3ce8. This residue interacts with the gamma phosphate group with its backbone nitrogen. In 3ce8 this role may be played by Asn-85, provided the loop moves a little bit closer to the ligand such that the side-chain amide nitrogen can perform the stabilization. Finally, Lys-102 in 2rd5 is substituted by Arg-88, a perfectly conservative exchange. Therefore, a possible ATP binding site can be spotted in 3ce8.

    Figure 1. Trimer of 3ce8. Each monomer lends its C-terminal strand to the neighboring molecule.



    Figure 2. Structurally similar proteins superposed on this target:  2pii (magenta), 1kr4 (orange), and 3ce8 (green).

    Ligand Summary



    References

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