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3eqx

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

    Title Crystal structure of the Fic (Filamentation induced by cAMP) family protein SO4266 (gi|24375750) from Shewanella oneidensis MR-1 at 1.6 A resolution. Proteins 75 264-271 2009
    Site JCSG
    PDB Id 3eqx Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1682,NP_719793.1, BIG_271, PF02661, 104192
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 2
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.36 Rfactor 0.168
    Waters
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    Solvent Content 47.95

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3eqx
    1. Fido, a novel AMPylation domain common to fic, doc, and AvrB
    LN Kinch, ML Yarbrough, K Orth, NV Grishin - PLoS One, 2009 - dx.plos.org
     
    2. Kinetic and structural insights into the mechanism of AMPylation by VopS Fic domain
    P Luong, LN Kinch, CA Brautigam, NV Grishin - Journal of Biological , 2010 - ASBMB
     
    3. Structural basis of Fic-mediated adenylylation
    J Xiao, CA Worby, S Mattoo, B Sankaran - Nature structural & , 2010 - nature.com
     
    4. AMPylation: something old is new again
    AR Woolery, P Luong, CA Broberg - Frontiers in Microbiology, 2010 - ncbi.nlm.nih.gov
     
    5. Fic domain_catalyzed adenylylation: Insight provided by the structural analysis of the type IV secretion system effector BepA
    DV Palanivelu, A Goepfert, M Meury, P Guye - Protein , 2011 - Wiley Online Library
     
    6. Crystal structure of the Fic (Filamentation induced by cAMP) family protein SO4266 (gi| 24375750) from Shewanella oneidensis MR_1 at 1.6 resolution
    D Das, S Krishna, D McMullan - Proteins: Structure, , 2009 - Wiley Online Library
     
    7. Adenylylation control by intra-or intermolecular active-site obstruction in Fic proteins
    P Engel, A Goepfert, FV Stanger, A Harms, A Schmidt - Nature, 2012 - nature.com
     
    8. Comparative analysis of Histophilus somni IbpA with other FIC enzymes reveals differences in substrate and nucleotide specificities
    S Mattoo, E Durrant, MJ Chen, J Xiao, CS Lazar - Journal of Biological , 2011 - ASBMB
     
    9. Comparative Analysis of Histophilus somni Immunoglobulin-binding Protein A (IbpA) with Other Fic Domain-containing Enzymes Reveals Differences in Substrate and
    S Mattoo, E Durrant, MJ Chen, J Xiao, CS Lazar - Journal of Biological , 2011 - ASBMB
     

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    Protein Summary

    Gene SO_4266 from Shewanella oneidensis encodes the NP_719793 protein that belongs to the Fic domain Pfam PF02661, which is the Fic protein family consisting of the Fic (filamentation induced by cAMP) protein and its relatives. As of May 2008, there were 647 unique protein sequences classified in this family, with 2 of them being human proteins. Fic proteins are distributed in all kingdoms of life and vary in size from ~200-500 amino acids. It is possible to segregate the Fic proteins into 18 protein clusters using a sequence identity cut-off of 30%.

    NP_719793 protein structure correspond to two identical PDB IDs: 3eqx and 2qc0. There is extremely limited functional characterization of Fic proteins and the details of their molecular and cellular roles remains unknown. However, some progress has been made in the structural investigation of Fic proteins and several other unpublished structures are available with PDB accession ids of 2g03 (Dali Z-scr=12; 194 residues, 2.2A resolution), 2f6s (Dali Zscr=12; 201 residues, 2.5A) and 3cuc (Dali Zscr=20; 262 residues, 2.7A). The first two structures belong to the same sequence cluster of 16 members and display ~60% sequence identity. All the Fic crystal structures have been determined by the PSI-2 Structural Genomics centers.

     BepA, which is a Type IV secretion system (T4S) substrate in bacteria, contains the Fic domain. Amongst humans, the HYPE protein (Huntingtin Interacting Protein E, Uniprot  Q9BVA6_HUMAN ), a protein of unknown function that may interact with Huntingtin in the Huntington disease pathway, has the Fic domain. 

    Interestingly, both the HYPE and this protein (along with the 3cuc) belong to the same and largest sequence cluster in this protein family (466 out of 647 proteins) and have ~32% sequence identity in the Fic domain.

    Members of this Pfam are characteized by the presence of the Fic motif HPFXXGNG motif. In this protein, this motif  includes  residues 198-205 in a loop in which the His198 faces the purine-like ligand density as if in a base stacking interaction. The Phe200 faces inwards. This has been tentatively modeled in the structure as a peptide and some modeling experiments suggest that this could be a mimic of a folate derivative. Folate derivate COE: Furo(2,3D) Pyrimidine antifolate can be fit approximately fit into this density. There is additional electron density in Chain A in a (surface exposed hydrophobic) cleft surrounded by amino acids Thr248, Leu244, Tyr241, L145, Tyr155, Leu245, and near the former electron density. The first density assumes a U-shape conformation around second density. 

    There are many hits in PSI-BLAST with Fic proteins and hypothetical proteins. There are no structures available of proteins that are close in sequence to this target. No reliable clues about identity of the ligands from the crystal structures of the DALI hits. Most of the top DALI hits indicate nucleotide binding capacity.

    FATCAT structure comparison (and also profile-profile alignments) indicate that the 2 domains of the protein are distant homologs of the structures 2G03.pdb (putative cell filamentation protein) and 1SFX.pdb (putative HTH transcription regulator). However, the combination of these domains in this protein appears novel.

    References [Ref]:

    More information about this protein can be found at:

    Paper published in Proteins: Structure, Function & Bioinformatics.

    1: Res Microbiol. 1991 Feb-Apr;142(2-3):269-77. Functional analysis of the fic gene involved in regulation of cell division.
    Komano T, Utsumi R, Kawamukai M.

    Ligand Summary


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