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3qz4

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

    Title Crystal structure of an Endo-1,4-beta-xylanase D (BT_3675) from Bacteroides thetaiotaomicron VPI-5482 at 1.74 A resolution. To be published
    Site JCSG
    PDB Id 3qz4 Target Id 396215
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS25889,NP_812586.1, _0029.002555_, 332847 Molecular Weight 34874.65 Da.
    Residues 310 Isoelectric Point 7.20
    Sequence qnkksgnpilpgfhadpevlyshqtkryyiyptsdgfpgwggsyfkvfssknlktwkeetvilemgknv swangnawapcieekkidgkykyffyysanpttnkgkqigvavadsptgpftdlgkpiitssptgrgqq idvdvftdpvsgksylywgngymagaelnddmlsikeettvvltpkggtlqtyayreapyviyrkgiyy ffwsvddtgspnyhvvygtaqsplgpievakepivliqnpkeeiygpahnsilqvpgkdkwyivyhrin knhlndgpgwhrevcidrmefnpdgtikqviptp
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.74 Rfree 0.2020
    Matthews' coefficent 2.32 Rfactor 0.1594
    Waters 689 Solvent Content 47.09

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3qz4
    1. Crystal Structure of a Key Enzyme in the Agarolytic Pathway,[alpha]-Neoagarobiose Hydrolase from Saccharophagus degradans 2-40
    SC Ha, S Lee, J Lee, HT Kim, HJ Ko, KH Kim - Biochemical and , 2011 - Elsevier
     

    Protein Summary

         

     

     

     

    The 5 blade beta-propeller with 2 MOLs/ASU has a 25% SEQID with another by JCSG deposited Endo-1,4-beta-xylanasestructure, with the code 3kst.  

     

     

     

    Since the catalytic triad in this and in 3kst target is conserved, the only novelty of this target is in its bound ligands. The dimeric interface of both propellers, usually carying the substrate in GH43 hydrolase family, here shows a HEPES molecule right in the entry channel on the top of the five-fold cavity. 9.5A away down into the propeller tunnel, instead of bound Ca+2, there is a Cl-1 anion in the same 7-fold coordination with 6 water molecules and HIS residue. From Cl-1 anion, 8.8A further down the propeller axis, towards the other exit of the tunnel, second ion is coordinated, a Mg+2. It  is surrounded by waters and connected to the carboxyl group of 166V.

    The entire tunnel is filled with waters divided into 3 groups, surrounding each of these ligands and extending into the outer volume of the propeller axis. PROFUNC results unambiguously assign the  

     

     

     

    ENDO-1,4-BETA-XYLANASE sequence motif for that target. The largest cleft of the monomer accomodates the EPE ligand, which otherwise a hydrolysed sugar would substitute. PISA server doesn't predict a dimerization for that target, so the dimeric arrangement in our crystals must be purely crystallographic.

    Overlap of the active side with 3kst, conforms the ASP39, acting as general base, GLU218 as general acid and ASP163 regulating the pKa of the acid and proper orienting of the acid relative to the substrate, as described in Structures 3c7g,f,h,o,e, published in J.Biochem 2009,Vol.418, p39-47 by E. Vandermarliere. That publication summarizes the chemistry of the sugar hydrolysis by GH43 family of arabinoxylan arabinofuranohydrolase in Bacillus Subtilis.

      

     

    There is a striking similarity of the additional bound ion in the central tunnel of the propeller with that in our structure, namely it has an unusual 7-fold coordination with 5 waters in one plane and one water and HIS279 perpendicular to it.

    The whole cluster is located within a hydrogen bond distance from from the general acid. 

     

     

    All the 5 planar waters around the Cl-1 anion, have bonds with sidechains or carboxyl groups from each of the 5 blades. It is as if these waters stabilize the whole propeller or 'gating' the channel activity depending on that anion. In  

     

     

     

    PX9010E target I assigned a Cl ion, which takes place of their Na ion, based on the polarity of the connecting HIS residue. That anion assignment is also based upon inspection of the anomalous signal at absorption peak, which is negligible. The second Mg+2 ion assignment was also based on the geometry and anomalous peak height. This ion overlaps with FMT ligand in 3c7g structure.

     

     

    A recent study FEBS J. 277, 2010 p.4562-4574, confirms a Ca ion instead of the Cl in GH43 from Bacillus Subtilis. Through biochemical studies it was shown that the enzyme activity strongly depends on the presence of that ion. Also structural stability of the whole beta-propeller is influenced by that ion. The 279H involved in the coordination of that ion seems to have essential function in substrate recognition and stabilization.

    2 studies (Nat. Str. Biol. 9, 2002, p. 665 and J.Biochem. 137, 2005, p.587) assigned however also a Cl ion for that potential Ca, which corresponds with our result.

     

     

    Since this propeller is not featured as the typical "closed velcro", where C and N-term are strongly hydrogen bonded to each other to stabilize the overall propeller fold, it is possible, that

    the bond or charge transfer between the HIS and the Cl ion offers that stability. The location of that ion is in the center of gravity of the propeller and the pentameric pattern of the hydrogen bonds of the waters is rotated exactly by 36deg relative to the 5 blades, i.e. the waters sit in a plane perpendicular to the central 5-fold axis right in between each blade.

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (3)

    FileSizeDateAttached by 
     ACTIVE-SIDE.jpg
    Bound Hepes molecule in the acidic active side
    505.43 kB23:44, 24 Sep 2010cbtrameActions
     chimera-side.jpg
    2 5-blade beta-propellers in ASU aligned in the direction of the 5-fold axis
    196.76 kB23:44, 24 Sep 2010cbtrameActions
     DALI-side-conserv.jpg
    Sequence conservation of PX90101E with GH43 family of xylanases
    452.09 kB23:44, 24 Sep 2010cbtrameActions
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