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The Open Protein Structure Annotation Network
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3nra

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

    Title Crystal structure of an aspartate aminotransferase (YP_354942.1) from Rhodobacter sphaeroides 2.4.1 at 2.15 A resolution. To be published
    Site JCSG
    PDB Id 3nra Target Id 403422
    Molecular Characteristics
    Source Rhodobacter sphaeroides 2.4.1
    Alias Ids TPS30657,YP_354942.1, 3.40.640.10, 332507 Molecular Weight 43542.97 Da.
    Residues 406 Isoelectric Point 5.89
    Sequence msieakfkklgtdnapgqevrqsaaglealirgapiegrpvdfshgdvdaheptpgafdlfsagvqsgg vqayteyrgdlgirdllaprlaaftgapvdardgliitpgtqgalflavaatvargdkvaivqpdyfan rklveffegemvpvqldyvsadetragldltgleeafkagarvflfsnpnnpagvvysaeeigqiaala arygatviadqlysrlryagasythlraeaavdaenvvtimgpskteslsgyrlgvafgsraiiarmek lqaivslraagysqavlrgwfdeapgwmedriarhqairdellhvlrgcegvfartpqagsylfprlpk lavapaefvkilrlqagvvvtpgtefsphtadsvrlnfsqdheaavaaarrivtlveryra
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.15 Rfree 0.200
    Matthews' coefficent 2.40 Rfactor 0.153
    Waters 622 Solvent Content 48.76

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3nra
    1. Assessment of ligand_binding residue predictions in CASP9
    T Schmidt, J Haas, TG Cassarino - Structure, Function, and , 2011 - Wiley Online Library
     
    2. Blind prediction of quaternary structures of homo-oligomeric proteins from amino acid sequences based on templates
    M Morita, M Kakuta, K Shimizu, S Nakamura - 2012 - hoajonline.com
     
    3. PURIFICATION OF LYSINE DECARBOXYLASE: A MODEL SYSTEM FOR PLP ENZYME INHIBITOR DEVELOPMENT AND STUDY
    LC Zohner - 2011 - digitalcommons.unl.edu
     

    Protein Summary

    This is a member of our aminotran_1_2 family (PF00155). Residue R380 is expected to be catalytic. There are already 450 structures for this family, so is of little interest to us.

     

    This target is a 406-residue protein encoded by the gene RSP_3437 (JCSG target accession code MJ14530B, GenBank accession code YP_354942.1) from Rhodobacter sphaeroides, a photosynthetic purple bacterium.  It is currently annotated as an aspartate aminotransferase (AspAT) belonging to Pfam PF00155, which is a protein family consisting of aminotransferases class I and II.  AspAT catalyzes the conversion of aspartate and alpha-ketoglutarate to oxaloacetate and glutamate:

    Oxaloacetate + glutamate ⇌ aspartate + α-ketoglutarate

    In humans, AspAT levels are often measured in diagnostic blood tests as an indicator of liver health.

    The structure of RSP_3437 was solved by the Se-MAD method to a resolution of 2.15 Angstroms and reveals an alpha/beta fold that has been observed for other aspartate aminotransferases (Figure 1).  The fold can be classified as belonging to the PLP-dependent transferase superfamily in the SCOP classification scheme.  Like other members of this protein familiy, RSP_3437 contains a lysine (residue 252) that is covalently attached to a pyridoxal-5'-phosphate (PLP) via a Schiff-base linkage at the active site.
     

    Figure 1.  Structure of a monomer of RSP_3437 (a) gradiently colored from the N- (blue) to the C-terminus (red) and (b) colored according to secondary structure (beta-strands (red), helix (blue), loops (yellow)).  Lysine-252, which is covalently attached to a pyridoxal-5'-phosphate (PLP) via a Schiff-base linkage, is shown in stick representation and labeled.

    MJ14530B-gradient.png    MJ14530B-ss.png

     

    Crystal packing and PISA analyses suggest that the functional oligomeric state of RSP_3437 is a dimer, consistent with other members of this protein family (Figure 2).

    Figure 2.  Oligomeric state of RSP_3437 is a dimer.  Subunits A and B are in orange and blue, respectively.

    MJ14530B-dimer.png

     

    A DALI structural neighbor search reveals almost all of the top matches to be aspartate aminotransferases (Table 1), with their structures being very similar (Figure 3).

    Table 1.  Top structural neighbors of RSP_3437 as assessed by DALI.

    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 1j32 45.3 2.0 367 388 22 ASPARTATE AMINOTRANSFERASE
    2 1gde 45.2 2.3 372 388 20 ASPARTATE AMINOTRANSFERASE [Ref]
    3 1gd9 45.1 2.3 372 388 20 ASPARTATE AMINOTRANSFERASE [Ref]
    4 1dju 44.6 2.2 370 375 20 AROMATIC AMINOTRANSFERASE [Ref]
    5 2o0r 44.2 2.3 365 385 22 RV0858C (N-SUCCINYLDIAMINOPIMELATE [Ref]
    6 5bj4 44.1 2.1 359 366 22 PROTEIN (ASPARTATE AMINOTRANSFERASE) [Ref]
    7 1bkg 44.1 2.1 359 382 22 ASPARTATE AMINOTRANSFERASE [Ref]
    8 5bj3 43.9 2.0 357 363 22 PROTEIN (ASPARTATE AMINOTRANSFERASE) [Ref]
    9 1gck 43.9 2.1 359 382 22 ASPARTATE AMINOTRANSFERASE [Ref]
    10 1bjw 43.8 2.3 361 382 22 ASPARTATE AMINOTRANSFERASE

     

    Figure 3.  Superposition of RSP_3437 (yellow) with top structural neighbors 1j32 (blue), 1gde (red), and 1dju (green).

    MJ14530B-superpose.png

    Ligand Summary

    Reviews

    References

     

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