The Open Protein Structure Annotation Network
PDB Keyword


    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


    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.


    The protein forms a stable dimer as shown below.




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

    DALI Structural Homologs
    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.



    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


    Kinetic assays demonstrate valine-pyruvate aminotransferase (VPAT) activity of 3IF2

    Protein YP_265399.1 from Psychrobacter arcticus (PDB id 3IF2)was putatively annotated as a valine-pyruvate aminotransferase (PaVPAT; transaminase C; VPATs are members of the aspartate aminotransferase family. This family is characterized by a pyridoxal-5’-phosphate (PLP) dependent fold type I having a conserved catalytic lysine and conserved PLP-binding residues. A Clustal W sequence alignment of 3IF2 with functionally characterized transaminase C from E. coli and a putative VPAT from Salmonella typhimurium highlights the conserved catalytic lysine, residues associated with PLP binding, and residues expected to be involved in binding substrate (Figure 1)1,2.

    Kinetic data substantiates the annotation of PaVPATas a VPAT. Functional assays were conducted in which the activity was coupled to lactate dehydrogenase (LDH). VPAT enzymes convert L-alanine and α-ketoisovalerate (KIV; 3-Methyl-2-oxobutanoate) to pyruvate and valine through a transamination reaction. The pyruvate product is then converted to lactate by LDH with the concomitant oxidation of NADH to NAD+.  The change in NADH concentration is observed spectrophotometrically at 340 nm. Unless otherwise noted, assays were conducted at 22 °C using the following conditions: 100 mM Tris pH 8, 125 μM PLP, 50 mM L-alanine, 5 mM α-ketoisovalerate, 0.28 mM NADH and 4 U/mL LDH3,4.   L-leucine was at 50 mM when tested as a potential inhibitor against varying amounts of both substrates.

    PaVPATfollows Michaelis-Menten kinetics with respect to both L-alanine and KIV (Figure 2). The Km for L-alanine (4.4 mM) is an order of magnitude higher than for KIV (0.28 mM) (Figure 2; Table 1), indicating that PaVPATmay have a higher binding affinity for KIV than L-alanine2. These values are in line with the published parameters for the VPATs from S. typhimurium (3G7Q; alanine Km = 2.2 mM; KIV Km = 0.10 mM)5 and Brevibacterium flavum ATCC 14067 (alanine Km = 1.5 mM; KIV Km = 0.23 mM)3.

    Kinetic assays with PaVPATin the presence of L-leucine showed competitive inhibition with regard to L-alanine (higher  Km  in the presence of L-leucine) and non-competitive inhibition with respect to KIV (lower Km and Vmax in the presence of L-leucine) (Figure 2; Table 1).

    BioLEd Contributors: Sarah Bentley, David Chang, Jonny Coleman, Kanishk Jain, Autrine Loghmanian, John McGuinn, Shaun Moshasha, David Nyenhuis, Briony Strachan, Ellen Schleckman, Cameron Mura, Carol Price, Linda Columbus. Funded by NSF DUE 1044858.


    1.    Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J., Higgins, D. G. 2007. Clustal W and clustal X version 2.0. Bioinformatics. 23:2947-2948.

    2.    Segel, I.H. 1975. Behavior and Analysis of Rapid Equilibrium and Steady-State Enzyme Systems. Enzyme Kinetics. Wiley-Interscience, New York.

    3.    Ambartsumyan, A. A., Bezirdzhyan, Kh. O. 1994. Catalytic Properties of Valine Pyruvate Aminotransferases from Brevibacterium flavum. Biochemistry Moscow. 59:1027-1032.

    4.    Ambartsumyan, A. A., Bezirdzhyan, Kh. O. 1994. Isolation and preliminary Characterization of Valine: Pyruvate Aminotransferase fromBrevibacterium flavum. Biochemistry Moscow. 59:1021-1026

    5.    BioLEd TOPSAN entry http://www.topsan.org/Proteins/JCSG/3g7q?highlight=3g7q


    Table 1. Kinetic parameters for PaVPAT (3IF2)a




    Vmax (μM s-1)

           4.2 ± 0.10

            2.5 ± 0.072

    Km (mM)

           4.4 ± 0.25

            0.28 ± .015

    kcat (s-1)

           7.7 ± 0.18

            4.6 ± 0.029

    kcat/Km (M-1s-1)

    1700 ± 100

    16000 ± 860

    aStandard assay conditions: 100 mM Tris pH 8.0, 0.28 mM NADH, 125 µM PLP, 4 U/mL LDH.

    Ligand Summary




    No references found.

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