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The Open Protein Structure Annotation Network
PDB Keyword
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3if2

    Title Crystal structure of Putative amino-acid aminotransferase (YP_265399.1) from Psychrobacter arcticum 273-4 at 2.50 A resolution. To be published
    Site JCSG
    PDB Id 3if2 Target Id 391142
    Molecular Characteristics
    Source Psychrobacter arcticus 273-4
    Alias Ids TPS18334,YP_265399.1, 3.40.640.10, 91482 Molecular Weight 49025.04 Da.
    Residues 443 Isoelectric Point 4.93
    Sequence mkfskfgqkftqptgisqlmddlgdalksdqpvnmlgggnpakidavnelfletykalgndndtgkans saiismanysnpqgdsafidalvgffnrhydwnltsenialtngsqnaffylfnlfggafvnehsqdke sksvdksillpltpeyigysdvhvegqhfaavlphidevthdgeegffkyrvdfealenlpalkegrig aiccsrptnptgnvltdeemahlaeiakrydipliidnaygmpfpniiysdahlnwdnntilcfslski glpgmrtgiivadakvieavsamnavvnlaptrfgaaiatplvandrikqlsdneikpfyqkqatlavk llkqalgdyplmihkpegaiflwlwfkdlpistldlyerlkakgtlivpseyffpgvdvsdyqhaheci rmsiaadeqtlidgikvigevvrelydnk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.50 Rfree 0.221
    Matthews' coefficent 2.96 Rfactor 0.178
    Waters 203 Solvent Content 58.45

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3if2
    1. Alat za prianjanje proteina: modul za utvr_ivanje interakcija
    D _oli_ - 2010 - bib.irb.hr
     

    Protein Summary

    The protein YP_265399.1 is annotated as putative valine--pyruvate aminotransferase. YP_265399.1 belongs to PFAM PF00155 Aminotran_1_2 which consists of aminotransferases. These proteins share certain mechanistic features with other pyridoxal-phosphate dependent enzymes, such as the covalent binding of the pyridoxal-phosphate group to a lysine residue. PLP is bound in both the chains in this structure,

     

    The monomeric structure is shown below with the ligand PLP bound to it.

    MG11417F_mon.png

    The protein forms a stable dimer as shown below.

    MG11417F.png

     

     

    There are several structurally similar proteins as found by a DALI search.

    DALI Structural Homologs
    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 3g7q 52.1 1.5 383 388 46 VALINE-PYRUVATE AMINOTRANSFERASE
    2 1gck 39.8 2.5 372 382 22 ASPARTATE AMINOTRANSFERASE
    3 1bkg 39.7 2.5 372 382 22 ASPARTATE AMINOTRANSFERASE
    4 1gc3 39.6 2.4 372 382 22 ASPARTATE AMINOTRANSFERASE
    5 1x0m 39.5 2.4 385 403 22 AMINOTRANSFERASE II HOMOLOGUE
    6 1wst 39.5 2.6 387 403 23 MULTIPLE SUBSTRATE AMINOTRANSFERASE
    7 1gc4 39.5 2.4 371 382 21 ASPARTATE AMINOTRANSFERASE
    8 5bj4 39.4 2.5 359 366 22 PROTEIN (ASPARTATE AMINOTRANSFERASE)
    9 1b5p 39.3 2.6 372 382 22 PROTEIN (ASPARTATE AMINOTRANSFERASE)
    10 1bjw 39.2 2.6 372 382 21 ASPARTATE AMINOTRANSFERASE

     

    Some of these proteins have ligands bound in the same location as this protein. An overall superposition and a zoomed-in view of the active site are shown below.

    all.pngall_ligand.png

     

    YP_265399.1 (green), 1b5p (cyan), 1bjw (lightmagenta), 1bkg (yellow), 1gc3 (salmon), 1gc4 (lightgrey), 1gck (slate), 1wst (orange), 1x0m (lime), 3g7q (deepteal), 5bj4 (hotpink)
     

     

    Literature references
    1. Nakai T, Okada K, Akutsu S, Miyahara I, Kawaguchi S, Kato R, Kuramitsu S, Hirotsu K; , Biochemistry 1999;38:2413-2424.: Structure of Thermus thermophilus HB8 aspartate aminotransferase and its complex with maleate. PUBMED:10029535

    2. Ko TP, Wu SP, Yang WZ, Tsai H, Yuan HS; , Acta Crystallogr D Biol Crystallogr 1999;55:1474-1477.: Crystallization and preliminary crystallographic analysis of the Escherichia coli tyrosine aminotransferase. PUBMED:10417420

     

    Ligand Summary

    Reviews

    References

     

    No references found.

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