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The Open Protein Structure Annotation Network
PDB Keyword
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3llx

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

    Title Crystal structure of PROTEIN OF UNKNOWN FUNCTION (YP_156143.1) from Idiomarina loihiensis L2TR at 1.50 A resolution. To be published
    Site JCSG
    PDB Id 3llx Target Id 401538
    Molecular Characteristics
    Source Idiomarina loihiensis l2tr
    Alias Ids TPS30622,YP_156143.1, BIG_836, BIG_846, 342484 Molecular Weight 40803.85 Da.
    Residues 375 Isoelectric Point 5.83
    Sequence mksapdwiahpdtpyllideaklksninylkqrveslgshlrphlktlrtleaagylldsksapatvst laeaeayakagytdllyavgiapaklkrvaalrqqginlhilldnitqaqavvdyaaefgqdfsvfiei dsddhrggikpsdsklltiaktlgehftglmthaggsyacnteqglknfakqecdavriarnnletagi hcaitsvgstptahfgedfsdisevragvyttfdlvmknigvcdfshiamsvvttvighnkeknwlltd sgwmalsrdsgtagqnrdfgygqvckidgsvldglcvnstsqehgvielsdayqledfpvghqlrimpn hacataamhpvyhvlmsdgshntwqritgw
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.50 Rfree 0.158
    Matthews' coefficent 3.13 Rfactor 0.141
    Waters 547 Solvent Content 60.72

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3llx
    1. Crystal structure of a zinc-dependent D-serine dehydratase from chicken kidney
    H Tanaka, M Senda, N Venugopalan - Journal of Biological , 2011 - ASBMB
     
    2. Turning pyridoxal-5-phosphate-dependent enzymes into thermostable binding proteins: D-serine dehydratase from baker's yeast as a case study
    M Baldassarre, A Scir, F Tanfani - Biochimie, 2011 - Elsevier
     
    3. Insights into the structural properties of d-serine dehydratase from Saccharomyces cerevisiae: An FT-IR spectroscopic and in silico approach
    M Baldassarre, A Scir, I Fiume, F Tanfani - Biochimie, 2011 - Elsevier
     
    4. D-Serine-Dehydratase from Saccaromyces cerevisiae: A Pyridoxal 5-phosphate-Dependent Enzyme for Advanced Biotech Applications
    M Staiano, M Strianese, A Varriale - Protein and Peptide , 2012 - ingentaconnect.com
     
    5. Role of zinc ion for catalytic activity in d_serine dehydratase from Saccharomyces cerevisiae
    T Ito, K Koga, H Hemmi, T Yoshimura - FEBS Journal, 2012 - Wiley Online Library
     

    Protein Summary

     

    Pfam: member of Ala_racemase_N family. K46 is expected to be active site residue.

     

    Gene IL1761 from Idiomarina loihiensis L2TR encodes the  protein YP_156143.1 (PDB 3LLX) with 375 residues and an isoelectric point of 5.83.  The NCBI blast sequence alignment indicates that this protein contains a putative conserved domain belonging to the amino acid aldolase or racemase superfamily, which is assigned to the Ala-racemase N-terminal group in Pfam (PF01168).  Pre-SCOP classifies 3llx in the alpha/beta class, PLP-binding barrel superfamily, Ala racemase-like N-terminal domain family. DALI top hits are with Ser-deaminase PDB:3gwq (Z=28), Ala-racemases PDB:2vd8 (Z=24) and PDB:1vfs (Z=23), and diaminopimelate decarboxylases PDB:2qgh and PDB:3c5q (Z=24). 

    However, both Dali search and SSM search indicates that protein can also be a structural homolog to serine racemerase, instead of alanine racemases [Ref].  In current model of protein  YP_156143.1, Lys46 is covalently linked with a pyridoxal-5'-phosphate (PLP) molecule coming from bacterial protein production. A Zn ion, from the bacteria growing media, complexes with His346, Cys348 and Tris-Buffer with hydrogen bonding distance to the PLP molecule, which indicates a possible metal-binding site for substrate binding. The tri-anion with multi-conformations may be considered as the structural homolog to D-serine and L-Serine. Such structural information may provide some insight for a unique mechanism in this putative Ser racemase, which should be metal-dependent differing from reported serine racemeases.  The interface interaction suggests that the biomolecule of 3llx is a dimer.

     

    401538_2.png

    Figure 1. 3llx structure consists of two domains.

     

     

    401538_1.png

    Figure 2.  The likely biomolecule of 3llx is a dimer.

     

    401538_4.png

     

    Figure 3. 3llx (green) is  a structurally similar to D-serine deaminase(PDB ID 3gwq, magenta), and alanine racemases(PDB ID: 1vfh yellow; 1rcq blue).  

     

    401538_3.png

    Figure 4. In the 3llx structure, Lys46 is modified to PLP coming from bacterial protein production.

    A Zn ion complexes with His346, Cys348 and Tris-buffer next to PLP.

    Ligand Summary

     LLP, Tris buffer, Zn ion

    Reviews

    References

     

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