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The Open Protein Structure Annotation Network
PDB Keyword
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2huh

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

    Title Crystal structure of putative DNA Mismatch Repair Protein (NP_811092.1) from Bacteroides Thetaiotaomicron VPI-5482 at 1.54 A resolution. To be Published
    Site JCSG
    PDB Id 2huh Target Id 359113
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS1418,NP_811092.1, 90145 Molecular Weight 39987.69 Da.
    Residues 354 Isoelectric Point 5.66
    Sequence mkigdkvrflsevgggivtgfkgkdfvlvedadgfdipmpirecvvieaddynikrkpaatapkqeepa kpakpempviqrqpevrggdtlnvflayvpedakammttpfeaylvndsnyylyytylsaegkawnnrs hglvepntkllleeftkdvlnemervavqliafkdgkpaaikpavsvelridtvkfyklhtfsasdffe epaliydivkddvpakqvyvsaeeiqsallqkkfvdkpksqpimkpnhgqsgkngiievdlhidslldd thgmsnseilnyqldkfrevieankekreqkvvfihgkgdgvlrkaiidelkrkhsnyryqdasfqeyg fgatmvtik
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.54 Rfree 0.192
    Matthews' coefficent 2.30 Rfactor 0.166
    Waters 163 Solvent Content 46.70

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2huh
    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
     

    Protein Summary

    The protein product of the BT_2179 (NP_811092) gene from Bacteroides thetaiotaomicron VPI-5482 is a three domain protein, with a central domain (91-252) belonging to the DUF2027 group (PF09640) and a C-terminal (276-354) SMR domain homologous to a domain in mismatch repair ATPases (PF01713; COG1193; MutS family). BT_2179 is annotated as 'putative DNA mismatch repair protein'.

    The 2huh structural model covers the central part of the B. thetaiotaomicron protein (residues 81 - 227), as cleaved in limited proteolysis. Proteins from the DUF2027 family are  present in other Bacteroides species, as well as in Porphyromonas gingivalis and several soil and marine microbes, but not in human or eukaryotic genomes. The only common feature of  bacteria that contain DUF2027 homologs seems to be their ability to glide over surfaces (gliding motility). Multiple homologs of the B. thetaiotaomicron BT_2179 (including the central DUF2027) are also present in the mouse gut microbiome. SCOP classifies 2huh in the all beta class, C2 domain-like fold, Smr-associated domain-like (super)family. A structural similarity search using DALI returns mostly generic Greek-key beta barrels, with highest score [Z=6] to the complement C3 beta chain protein 3g6j). Analysis of the crystallographic packing of 2huh using the PQS server {Henrick, 1998 #73} indicates that its biologically relevant form is a dimer.


    The 2huh protein structure has a novel variant of a two sheet beta barrel greek key fold, most similar to that present in proteins with the prealbumin-like fold, in particular to transthyretin (TTR), carrier of the thyroid hormone thyroxine, but also known to bind numerous other small molecules such as  natural products (resveratrol), drugs (diflunisal, flufenamic acid) and  PCB toxins. Since TTRs bind promiscuously to many aromatic compounds, there is speculation that TTR's "true function" is to generally sweep up toxic and foreign compounds in the blood stream. True transthyretins are found only in vertebrates, but homologous proteins with unknown functions are found also in invertebrates, fungi and bacteria. Transthyretins are thought to have evolved from a 5-hydroxyisourate hydrolase (HIUase, EC: 3.2.5.17), a widely distributed enzyme of purine metabolism [Ref]. HIUase structure 2h1x is similar to 2huh (FATCAT P-val=2e-4; 3.1A RMSD over 100 residues; no twists) (DALI Z=6; RMSD 3A; lali 91 residues; 10% id.). However, B. thetaiotaomicron  BT_2179  protein has minimal (~5% seq id) sequence similarity to both transthyretins and HIUases and its function remains unknown. 


    The structure of the SMR domain from human NEDD4-interacting protein 2, was solved by RIKEN (2d9i). The SMR domain is present in the C-terminal of B. thetaiotaomicron  BT_2179, which is not covered by our model.

    Ligand Summary



    References

    Reviews

    References

     

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