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2pnk

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

    Title Crystal structure of uncharacterized protein (NP_241359.1) from Bacillus halodurans at 2.00 A resolution. To be published
    Site JCSG
    PDB Id 2pnk Target Id 367095
    Molecular Characteristics
    Source Bacillus halodurans c-125
    Alias Ids TPS1500,NP_241359.1, 90919 Molecular Weight 49942.49 Da.
    Residues 427 Isoelectric Point 5.24
    Sequence msinsrevlaekvknavnnqpvtdmhthlfspnfgeillwdidelltyhylvaevmrwtdvsieafwam skreqadliweelfikrspvseacrgvltclqglgldpatrdlqvyreyfakktseeqvdtvlqlanvs dvvmtndpfddneriswlegkqpdsrfhaalrldpllneyeqtkhrlrdwgykvndewnegsiqevkrf ltdwiermdpvymavslpptfsfpeesnrgriirdcllpvaekhnipfammigvkkrvhpalgdagdfv gkasmdgvehllreypnnkflvtmlsrenqhelvvlarkfsnlmifgcwwfmnnpeiinemtrmrmeml gtsfipqhsdarvleqliykwhhsksiiaevlidkyddilqagwevteeeikrdvadlfsrnfwrfvgr ndhvtsvkveqqt
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 12
    Resolution (Å) 2.00 Rfree 0.178
    Matthews' coefficent 2.89 Rfactor 0.148
    Waters 3732 Solvent Content 57.50

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2pnk
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     

    Protein Summary

    Gene BH0493 (NP_241359.1) codes for an uncharacterized protein showing an weak, but statistically significant match (e-value=3.6e-5) to the amidohydrolase type 2 family (PF04909). Interestingly, FFAS shows a much stronger (scr=-81 vs. -21) match to a PFAM family of glucuronate isomerases (PF02614). Its genome context analysis suggests an associaction with the altronate oxidoreductase uxaB (NP_241358.1).

     

    SCOP classifies 2pnk in the class alpha/beta, TIM beta/alpha barrel fold, metalodependent hydrolase superfamily, uronate isomerase-like family(SUNID:75082. Its structure shows strong structural similarity (Dali Z-scr=32.1; FATCAT P-val=5e-13) to a glucuronate isomerase TM0064 from Thermotoga maritima PDB:1j5s,  [Ref]. The active site resides in 1j5s are H30 (H26 in 2pnk), H32 (H28), W366 (W325), D397 (D355), all of which are conserved in a 17% sequence identity structural superposition between 2pnk and 1j5s (over 338 equivalent residues with an rmsd of 2.6A) using the program TopMatch. There is higher sequence conservation around W366, with W366,W367,F368 (equivalent to residues 325-327 in 2pnk) being the same. In both structures the expected Zn ion is missing. However, a later determined structure  2qee (which is 100% identical to this entry, 2pnk) contains the Zn metal at the predicted site. Recently, a publication identified the active site and performed inhibition/mutation experiments [Ref]. In one of their structures, 3hk9, the substrate D-glucuronate is bound at exactly the location where in this JCSG structure a glycerol molecule is found.

    2pnk-3hk9-superpos.png

    Figure 1: Superposition of 2pnk (white) and 3hk9 (cyan). In the active site of 3hk9, the substrate D-glucuronate is bound. In the JCSG structure this location is occupied by a glycerol cryoprotectant molecule. The JCSG predicted Zn ion is present in 3hk9 and is shown as a sphere. Residues His-26, His-28, and Asp-355 are coordinating the metal ion, distances are given in units of Angstrom.

     

    2pnk-3hk9-Gol-Rel-g.png

    Figure 2: Closeup view of the glycerol cryoprotectant and the D-glucuronate ligand. The orientation of the two ligands is derived from the structure alignment. Notice that glycerol is mimicking the binding pattern of D-glucuronate.

    We therefore conclude that  BH0493  is an uronate isomerase, similar to TM0064 (PDB entry 1j5s).  After the JCSG structure of BH0493 was deposited in PDB, the same protein was also solved by NYSGXCR (PDB code PDB:2qee, PDB:2q6e, PDB:2q08 ) and again by the Raushel group from Texas AM (PDB entires PDB:3hk5, PDB:3hk7 , PDB:3hk8, PDB:3hk9, PDB:3hkA ).

    Ligand Summary



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    Files (2)

    FileSizeDateAttached by 
     2pnk-3hk9-Gol-Rel-g.png
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    77.79 kB21:25, 18 Mar 2010chrisxActions
    2pnk-3hk9-superpos.png
    2pnk superpositioned with 3hk9
    227.09 kB21:25, 18 Mar 2010chrisxActions
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