The Open Protein Structure Annotation Network
PDB Keyword


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

    Title Crystal structure of Putative DNA binding protein (NP_810029.1) from Bacteroides thetaiotaomicron VPI-5482 at 1.50 A resolution. To be Published
    Site JCSG
    PDB Id 3htn Target Id 393032
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS20291,NP_810029.1, RER070207003073, 324991 Molecular Weight 16661.89 Da.
    Residues 148 Isoelectric Point 6.48
    Sequence aqneknmysykkignkyivsinnhteivkalnafckekgilsgsingigaigeltlrffnpktkayddk tfreqmeisnltgnissmneqvylhlhitvgrsdysalaghllsaiqngagefvvedyserisrtynpd lglniydfer
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 3
    Resolution (Å) 1.50 Rfree 0.167
    Matthews' coefficent 2.53 Rfactor 0.143
    Waters 554 Solvent Content 51.31

    Ligand Information


    Google Scholar output for 3htn
    1. Structure-based de novo prediction of zinc-binding sites in proteins of unknown function
    W Zhao, M Xu, Z Liang, B Ding, L Niu, H Liu - , 2011 - Oxford Univ Press

    Protein Summary

    Gene BT_1116 from Bacteriodes thetaiotaomicron vpi-5482 encodes the NP_810029 protein with 185 residues. It belongs to the DUF296 group (PF03479).  The search results from NCBI sequence alignment indicates that this protein carries a putative DNA binding domain. 

    Pre-SCOP classifies 3htn inside the alpha+beta class, AF0104/ALDC/Ptd012-like superfamily, AF0104 family. DALI, FFAS and SSM suggest 3htn is a structurally similar to PDB:3hwu (Z-scr=20), PDB:2dt4 (Z-scr=18), PDB:2h6l (Z-scr=18), PDB:2nmu (Z-scr=16), and PDB:2p6y (Z-scr=16).  A metal-binding is identified during structure refinement. Interestingly, these metal ion binding sites show different chelating status across the three subunits in the asymmetric unit.  Ni and Fe ions are modeled in subunit A and B, respectively. There is no metal ion in the metal binding site of subunit C.  The interface interaction indicates that the biomolecule of protein 3htn should be a trimer.



    Figure 1. Protein 3htn monomer carries mainly the β-barrel folding core with two arms. One metal binding site is identified in the structure. 




    Figure 2.  The biomolecule of 3htn should be a trimer.


    Figure 3. Protein 3htn (green) share the folding with 2DT4.


    Figure 4. Superposition of all protein structures mentioned above, highlighting conserved residues by opacity. Chain A of protein structure 3htn was used as the master structure for alignment with Mustang. Structures 3hwu, 2h6l, 2dt4, 2nmu were aligned to 3htn and the multiple, structure based alignment is displayed here. It shows several strictly conserved residues, namely Glu-113, His-131, His-133, Glu-158, Arg-170 (numbering from 3htn). Many of these residues contribute in metal ion binding, Arg-170 is located close to the metal ion (8.1Å) and may be of functional importance. Residue His-147 participates in metal ion binding and is in fact also perfectly conserved and has somehow been sorted out by the Mustang algorithm. (His-147 is equivalent to His-100 in 2nmu (chain A) in a pairwise structure alignment using TopMatch.)

    Ligand Summary




    No references found.

    Tag page

    Files (4)

    FileSizeDateAttached by 
    No description
    166.83 kB16:50, 7 Apr 2009kevinjinActions
    No description
    250.98 kB16:50, 7 Apr 2009kevinjinActions
    No description
    217.45 kB16:51, 7 Apr 2009kevinjinActions
    3htn multiple structure alignment
    39.33 kB22:30, 2 Aug 2010chrisxActions
    You must login to post a comment.
    All content on this site is licensed under a Creative Commons Attribution 3.0 License
    Powered by MindTouch