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The Open Protein Structure Annotation Network
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2ig6

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

    Title Crystal structure of NimC/NimA family protein (NP_349178.1) from Clostridium Acetobutylicum at 1.80 A resolution. To be published
    Site JCSG
    PDB Id 2ig6 Target Id 367116
    Molecular Characteristics
    Source Clostridium acetobutylicum atcc 824
    Alias Ids TPS1501,NP_349178.1, 2.30.110.10, 90928 Molecular Weight 14905.40 Da.
    Residues 131 Isoelectric Point 7.63
    Sequence mkraleflkecgvfylatnegdqprvrpfgavfeyegklyivsnntkkcfkqmiqnpkveisgmnkkgq wirltgevanddrrevkelaleavpslknmysvddgifavlyftkgegticsfkgenetfsl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.80 Rfree 0.198
    Matthews' coefficent 2.53 Rfactor 0.168
    Waters 284 Solvent Content 50.97

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2ig6
    1. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
     
    2. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     
    3. The structure of a Xanthomonas general stress protein involved in citrus canker reveals its flavin-binding property
    E Hilario, Y Li, D Niks, L Fan - Acta Crystallographica Section D: , 2012 - scripts.iucr.org
     

    Protein Summary

    CA_C2569 gene from C. acetobutylicum encodes the NP_349178 protein that together with its homologs are present in bacteria and archaea and belong to COG5015, and to PF1243 group (Pyridoxamine 5`-phosphate oxidase; EC:1.4.3.5).

    2ig6 structure belongs to SCOP all beta class, FMN binding split barrel superfamily, family PNP-oxidase like [50476]. DALI top hits are with COG3871 protein 2i02 (Z-score 15.2; RMSD 2.6; 13% sequence identity for 127 superimposed residues), the PA4388 protein 2arz (Z-score 13.6, RMSD 2.6; 11% sequence identity for 124 superimposed residues), and the LIN2891 protein 3db0 (Z=12.5).
     

    The 2ig6 structure shows a dimer protein bound to a flavin mononucleotide (FMN) molecule. The highly conserved Arg27, Lys47, Gln52, and Tyr100 interacts with FMN both directly, via UNL (unknown ligand that looks simlar to 'pyridoxal 5'-phosphate'), and via an extended network of water molecules. The other, not conserved, FMN binding residues are: Val13, Arg27, Pro28, Phe29, Gly30, Val42, Ser43, Cys49, Trp70, and Arg72 (Arg72 is from the opposite chain). In some PLP-dependent enzymes a lysine residue from the opposite chain (probably corresponding to Lys123 in 2ig6, that has a disordered side chain) forms a covalent Schiff base with the PLP cofactor (PubMed:12686108, 14983000, 16225687). The other clusters of conserved residues are: (a) small cleft formed by Asn45,  Phe50, and  Phe107; (b) Lys38, Tyr40, Tyr111; (c) Met64, Trp70, (d) Thr18, Gln52 (Gln52 binds FMN via water), Asn56, Pro57,


     

    Ligand Summary



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