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The Open Protein Structure Annotation Network
PDB Keyword
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3ke3

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

    Title Crystal structure of Putative serine-pyruvate aminotransferase (YP_263484.1) from PSYCHROBACTER ARCTICUM 273-4 at 2.20 A resolution. To be published
    Site JCSG
    PDB Id 3ke3 Target Id 391141
    Molecular Characteristics
    Source Psychrobacter arcticus 273-4
    Alias Ids TPS18332,YP_263484.1, 3.40.640.10, 85587 Molecular Weight 41418.96 Da.
    Residues 378 Isoelectric Point 4.89
    Sequence mtalrqdidpnglleysvvytdralnhmskafqevmndllsnlktvynaeaaviipgsgtygmeavarq ltidedcliirngwfsyrwtqilekgkfaksstvltaertedteapkpfapvdietavakikedksaiv yaphvetssgiilseeyikalseavhsvggllvidciasgcvwldmkelgidvlisapqkgwsstpcag lvmlsaaaikkvestesncfsldlkqwltimrayengghayhatmptdslrqfrdaileakeigfdilr daqwelgnrvrkvltdkgiesvaaegfeapgvvvsyterddmhkgsafaeaglqiaagvplkvgepdnf ktfrlglfgldkltdidgtverfekaldevlak
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.20 Rfree 0.210
    Matthews' coefficent 2.18 Rfactor 0.167
    Waters 170 Solvent Content 43.46

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3ke3

    Protein Summary

    Target 391141 (JCSG target ID 391141, JCSG target accession code MG3368B, GenBank accession code YP_263484.1, gene name agxT) is a 378-residue long protein from Psychrobacter arcticus 273-4, a bacterium that is commonly found in cold environments and associated with food spoilage.

    agxT belongs to Pfam PF00266 (aminotransferase class-V) and is annotated as a serine-pyruvate aminotransferase, an enzyme that catalyzes the following reaction in serine metabolism:

    L-serine + pyruvate <=> 3-hydroxypyruvate + L-alanine

     

    The structure of agxT, solved by Se-Met MAD to a resolution of 2.2 Angstroms, adopts an alpha-beta structure that belongs to the PLP-dependent transferases superfamily in the SCOP classification scheme.  The protein was co-crystallized with 1 mM pyridoxal-5'-phosphate (PLP), and indeed the structure shows that Lys-198 is covalently attached via a Schiff-base linkage to PLP to form 2-lysine(3-hydroxy-2-methyl-5-phophonooxymethylpyridin-4-ylmethane) (LLP) at the putative active site (Figures 1ab).

    Figure 1.  Structure of a monomer of agxT (a) gradiently colored from the N- (blue) to the C-terminus (red) and (b) colored by secondary structural elements (helices in blue, beta strands in red, loops in yellow).  The covalently modified Lys-198 is represented as yellow sticks in both panels.

    (a)                                                                                    (b)

    MG3368B-gradient.png   MG3368B-ss.png

     

    Crystal packing, static light scattering (SLS), and PISA analyses all suggest that agxT is stable as a dimer in solution (Figure 2).

    Figure 2.  Quaternary structure of agxT (monomer A in green, monomer B in purple, LLP in yellow sticks).

    MG3368B-dimer.png

     

    Both sequence and structural analysis by FFAS and DALI, respectively, yield top matches that are also aminotransferases.  Results from the DALI search are listed in Table 1.

    Table 1.  Top structural neighbors of agxT as assessed by Dali.

    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 2bkw 39.7 2.0 337 381 23 ALANINE-GLYOXYLATE AMINOTRANSFERASE 1
    2 2huu 37.7 1.9 326 385 20 ALANINE GLYOXYLATE AMINOTRANSFERASE
    3 2hui 37.7 1.9 326 385 20 ALANINE GLYOXYLATE AMINOTRANSFERASE
    4 2huf 37.7 1.9 326 385 20 ALANINE GLYOXYLATE AMINOTRANSFERASE
    5 2dr1 37.4 2.0 325 381 20 386AA LONG HYPOTHETICAL SERINE AMINOTRANSFERASE
    6 2ch2 37.3 1.9 324 387 19 3-HYDROXYKYNURENINE TRANSAMINASE
    7 1j04 37.3 1.9 326 387 23 ALANINE--GLYOXYLATE AMINOTRANSFERASE
    8 1vjo 37.2 1.9 324 377 22 ALANINE--GLYOXYLATE AMINOTRANSFERASE
    9 1h0c 37.2 2.0 325 385 23 ALANINE--GLYOXYLATE AMINOTRANSFERASE
    10 2yri 37.1 1.9 319 352 24 AMINOTRANSFERASE, CLASS V

     

    A superposition of agxT with several of these structural neighbors reveals very similar overall folds and the same dimeric architecture.  All of these aminotransferases contain the PLP cofactor attached to a lysine as well (Figures 3ab).

    Figure 3.  (a) Superposition of the monomers of agxT (yellow) with structural neighbors 2bkw (cyan), 2huu (magenta), 2dr1 (green), 2ch2 (salmon), and 1j04 (gray) reveals similar overall topologies and presence of LLP at the active site (circled in red) (b) Superposition of dimers of agxT (yellow), 2huu (magenta), and 2dr1 (green) shows identical dimeric arrangement.

    (a)                                                                                           (b)

    MG3368B-superpose-monomer-label.png   MG3368B-superpose-dimer.png

     

    A superposition of the putative active sites of agxT and 2dr1 shows that many of the corresponding residues surrounding the LLP residue in both structures are identical, further supporting the assignment of agxT as a serine aminotransferase (Figure 4).

    Figure 4.  Superposition of the putative active sites of agxT (yellow) and 2dr1 (green).

    MG3368B-superpose-active-site.png

     

    A ConSurf analysis of the residue conservation among agxT and its top ten PSI-Blast matches reveals that many of the residues surrounding and including the LLP residue are highly conserved, further supporting the notion that this site is indeed the active site of the protein (Figure 5).  Further biochemical investigation is needed to confirm this.

    Figure 5.  Residue conservation mapped onto the surface of agxT dimer, showing that the residues surrounding the LLP are highly conserved (putative active sites circled in red).

    MG3368B-consurf-label.png

    consurf_legend.png

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    Ligand Summary

    Reviews

    References

     

    No references found.

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