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The Open Protein Structure Annotation Network
PDB Keyword
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4rgl

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

    Title Crystal structure of a Fic family protein (Dde_2494) from Desulfovibrio desulfuricans G20 at 2.70 A resolution. To be published
    Site JCSG
    PDB Id 4rgl Target Id 374857
    Molecular Characteristics
    Source Desulfovibrio desulfuricans g20
    Alias Ids TPS6795,YP_388986.1, PF02661, BIG_271, 531343 Molecular Weight 38773.84 Da.
    Residues 342 Isoelectric Point 5.30
    Sequence mikpsnyqppytitpaivnlvaeigeiigrytvlaeqnltprlrrenrirtiqaslaienntltleqvt avidgkrvlghpreiqevrnafatyeamedwdasvegdllaahellmrglvdetgryrsggvgifrgeq lvhmappadrvpklmadlldwlentnehplvascifhyefefihpfadgngrmgrlwqtlilrnwkpll aylpvetvirdrqedyyrvlavadsqadatpfvefmlgalrdavreavstdhvgdqvtdqvaaliraig ggelssndlmqalglshrptfrnnylnpamedewiertqpdsprsptqryrltgkgqrwlqhhade
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.70 Rfree 0.2627
    Matthews' coefficent 2.52 Rfactor 0.2274
    Waters 20 Solvent Content 51.18

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Target ID 374857 belongs to the Fic (PF374857 Pfam Family). Several structres for this family have been determined. The Fic/DOCfamily of proteins is designated as the  the filamentation induced by cAMP) protein and the Doc (Death on curing) protein. Several publications on this family of proteins are found in the literature. For example, target id shows 53.6% sequence identity with a homolog from Vibro cholerae [Ref]. (there are several more citations which are not listed here).  Other citations include in the literature on this class of protein include [Ref] and [Ref]   In addition a sequence search of the PDB shows that JCSG has previously determined structures from this Pfam Family including PDB ID 3EQX[Ref] and PDB ID 3CUC.

    PJ02661R_ribbons.bmp

    The structure was solved and refined at only a modest resolution of 2.7 Angstroms. The structure consists of two domains, a larger N-terminal domain (residues 1-259)  and a smaller C-terminal domain (residues 263-342). Unfortunately electron density is disorded for the linker region connecting the two domains. The positioning of the C-terminal domain relative to the N-terminal domain was determined by the proximity of the break on the  N-terminal domain at   259 with the starting residue 263  on the C-terminal domain residue 259. A search of SCOP reverals that the N-terminal domain can be classified as a member of the Fic-like fold consisting of one central helix surrounded by seven other helices.  An unknown ligand was modeled into the putative active side of the structure based on the structure of the ATP-complex of a related structure. [Ref]

    A DALI search reveals similarity of the structure of target id to the following structures shown in the table below. The DALI search only show hits with the large N-terminal domain. Thus, the C-terminal domain of terget id 374857 is most like to show a different positioning of the C-terminal domain than others. (Need to run a FATCAT search to see if twists in the domains can accomodate an overlap of both domains). The hit highlighted in bold is a JCSG structure.

     

    PDB ID Z-Score rmsd (Ang) length of alignment number of residues in related structure % sequence identity Description
    3zcn 26.2 3.1 260 369 20 Fic protein from SHEWANELLA ONEIDENSIS in complex with ATP[Ref]
    3zec 26.0 3.0 259 371 20 Fic protein from SHEWANELLA ONEIDENSIS (E73G mutant) in complex with AMPPNP [Ref]
    3cuc 25.3 2.2 226 268 21 CRYSTAL STRUCTURE OF A FIC DOMAIN CONTAINING SIGNALING PROTEIN (BT_2513) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 2.71 A RESOLUTION (JCSG Structure)
    3eqx 24.1 3.0 258 364 20 CRYSTAL STRUCTURE OF A FIC FAMILY PROTEIN (SO_4266) FROM SHEWANELLA ONEIDENSIS AT 1.6 A RESOLUTION (JCSG structure) [Ref]
    3n3v 14.6 2.9 188 296 14 Crystal Structure of IbpAFic2-H3717A in complex with adenylylated Cdc42[Ref]
    3se5 14.2 2.3 150 155 18 Fic protein from NEISSERIA MENINGITIDIS mutant delta8 in complex with AMPPNP [Ref]
    2f6s 13.4 3.0 156 180 15 Structure of cell filamentation protein (fic) from Helicobacter pylori (MCSG structure)
    2g03 13.4 2.8 155 177 17 Structure of a putative cell filamentation protein from Neisseria meningitidi (MCSG structure)
    3zlm 13.3 2.6 153 177 17 Fic protein from Neisseria meningitidis mutant E186G in complex with AMPPNP [Ref]

     

     

    Show below is a superpositioning of the structures of target id 374857 (green) with that the DALI hit PDB ID 3eqx (magenta), a JCSG structure that was reporting on in the literature [Ref]. The C-terminal domain of PDB ID 3eqx is also a winged helix domain.

    3eqx_comparison.png

     

    This comparison shows that although that altough the individual N and C-terminal domains show similar structure the positioning of the two domains is different, and two different positionings of the C-terminal domain could have functional relevance.  The C-terminal domain of target id 374857 alone  has structural similarity with the following DALI hits. The hits highlighted in bold font are JCSG structures.

    PDB ID DALI Z-score rmsd (Ang) length of alignment number of residues in target % sequence identity Description
    4k2e 9.2 1.8 65 95 17 HlyU from Vibrio cholerae N16961
    3pqk 9.0 2.3 64 101 25 Crystal Structure of the transcriptional repressor BigR from Xylella fastidiosa [Ref]
    3vod 9.0 2.8 67 136 15 Crystal Structure of mutant MarR C80S from E.coli[Ref]
    1okr 8.9 1.9 63 120 13 THREE-DIMENSIONAL STRUCTURE OF S.AUREUS METHICILLIN-RESISTANCE REGULATING TRANSCRIPTIONAL REPRESSOR MECI.[Ref]
    3bdd 8.8 1.8 61 133 15 Crystal structure of putative multiple antibiotic-resistance repressor (MarR) (ZP_00875883.1) from Streptococcus suis 89/1591 at 2.20 A resolution JCSG STRUCTURE)
    2qww 8.7 1.7 64 144   Crystal structure of multiple antibiotic-resistance repressor (MarR) (YP_013417.1) from Listeria monocytogenes 4b F2365 at 2.07 A resolution
    3pqj 8.7 1.9 65 98 26 Crystal Structure of the transcriptional repressor BigR from Xylella fastidiosa [Ref]
    2nnn 8.6 3.2 67 133 13 Crystal structure of probable transcriptional regulator from Pseudomonas aeruginosa (MCSG structure)

     

    A fastSCOP search indicated that the C-terminal domain of targetid  374837 can most likely be classidied as a member of the the SCOP fold of DNA/RNA binding proteins that contain a 3-helical bundle core. Several of the DALI hits are DNA and RNA binding proteins and this is evidence that target id 374387 is also a DNA or RNA binding protein.

    A flexible FATCAT search of the PDB reveals that if one twist is applied, both the N and C-terminal domains of the the recently-reported structure Fic protein from SHEWANELLA ONEIDENSIS in complex with ATP [Ref]. In this suoerpositioning, 304 residues of both proteins show an rmsd of 2.74 Angstroms. Shown below is a ribbons representation of the alignment with the structure of target id 374857 (green) with that of the homolog from Shewanella oneidensis.

     

    3zcn_superposition.png

     

     

     

     

     

    Ligand Summary

    Reviews

    References

     

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