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The Open Protein Structure Annotation Network
PDB Keyword
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3jtw

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

    Title Crystal structure of Putative dihydrofolate reductase (YP_805003.1) from PEDIOCOCCUS PENTOSACEUS ATCC 25745 at 1.90 A resolution. To be published
    Site JCSG
    PDB Id 3jtw Target Id 394309
    Molecular Characteristics
    Source Pediococcus pentosaceus atcc 25745
    Alias Ids TPS26624,YP_805003.1, _0023.002889_, 326780 Molecular Weight 20473.47 Da.
    Residues 177 Isoelectric Point 5.47
    Sequence markvilfiamsidnyiaddqgavdwleknvhgtesddsyekmyskidtvimgrttyeqvtqklspeky vyadrqtyivtshlgedtdkikywkqspvelvkriqkekgkdvwivggaklidplvqanlidtyilttv piflgsgirlfdrleeqvpvrlidvyqknelvysiyqrg
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.90 Rfree 0.225
    Matthews' coefficent 2.28 Rfactor 0.182
    Waters 210 Solvent Content 46.02

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3jtw
    1. Characterisation of an oxidoreductase from the Arylamine N_acetyltransferase operon in Mycobacterium smegmatis
    D Evangelopoulos, N Cronin, T Daviter, E Sim - FEBS , 2011 - Wiley Online Library
     

    Protein Summary

    Pfam update: This sequence matches RibD_C (PF01872). It is not the first structure for this family.


    394309 from Pediococcus pentosaceus atcc 25745 encodes a protein which belongs to Pfam; PF01872; RibD_C; thought to be involved in riboflavin biosynthesis. 

     

    There are two protomors (A and B chains) found in the asu. Their biological dimers ( AA' and BB' chains) are formed by their own symmetry mates.

     asu2.png

    Figure 1. Two protomors in asu.

     

    AA_BBdimer2.png

     Figure 2. Two biological dimers of AA' and BB'. A and B chains are shown as green, A' and B' are shown as cyan.

    The PDB hits of structural homologs by DALI are

     No:  Chain   Z    rmsd lali nres  %id PDB  Description
    1: 1cz3-A 19.5 2.3 156 164 24 PDB MOLECULE: DIHYDROFOLATE REDUCTASE; 2: 1d1g-B 19.4 2.2 155 165 23 PDB MOLECULE: DIHYDROFOLATE REDUCTASE; 3: 1d1g-A 19.4 2.2 155 165 23 PDB MOLECULE: DIHYDROFOLATE REDUCTASE; 4: 2gd9-B 18.9 1.9 151 171 26 PDB MOLECULE: HYPOTHETICAL PROTEIN YYAP; 5: 1cz3-B 18.8 2.3 156 168 24 PDB MOLECULE: DIHYDROFOLATE REDUCTASE; 6: 2gd9-A 17.8 2.2 151 177 27 PDB MOLECULE: HYPOTHETICAL PROTEIN YYAP; 7: 3dl5-B 17.2 2.2 153 510 14 PDB MOLECULE: DIHYDROFOLATE REDUCTASE, DHFR; 8: 2oip-B 17.1 2.2 153 516 14 PDB MOLECULE: CHAIN A, CRYSTAL STRUCTURE OF DHFR; 9: 3dl5-A 17.1 2.2 152 509 14 PDB MOLECULE: DIHYDROFOLATE REDUCTASE, DHFR; 10: 3dl5-D 17.1 2.2 153 509 14 PDB MOLECULE: DIHYDROFOLATE REDUCTASE, DHFR; 11: 3dl6-A 17.1 2.4 153 507 14 PDB MOLECULE: DIHYDROFOLATE REDUCTASE, DHFR; 12: 3dl5-C 17.1 2.2 153 510 15 PDB MOLECULE: DIHYDROFOLATE REDUCTASE, DHFR; 13: 3dl5-E 17.1 2.2 152 510 14 PDB MOLECULE: DIHYDROFOLATE REDUCTASE, DHFR; 14: 1qzf-A 17.0 2.3 154 519 14 PDB MOLECULE: BIFUNCTIONAL DIHYDROFOLATE REDUCTASE-THYMIDYLATE 15: 1sej-D 17.0 2.2 152 519 14 PDB MOLECULE: BIFUNCTIONAL DIHYDROFOLATE REDUCTASE-THYMIDYLATE

     

     

    Superposition of the 394309 with 1cz3,1d1g and 2gd9 shows that their active site resides are conserved. Interestingly, there is a SO4 bound in the 394309, while 2gd9 contains a PO4, and 1d1g contains a PO4 (of the NDP) in the same position. In addition, an UNL is found In the MTX binding site of 1d1g,

     

     SO4andUNL.png

    Figure 3. Superposition of 394309 (green) with 1d1g (cyan) in the putative active site. 394309 contains SO4 and UNL (red), while 1d1g contains MTX and NDP (yellow) in the active site.

     

    References

    The crystal structure of dihydrofolate reductase from Thermotoga maritima: molecular features of thermostability.
    Authors: Dams, T.,   Auerbach, G.,   Bader, G.,   Jacob, U.,   Ploom, T.,   Huber, R.,   Jaenicke, R.

    Ligand Summary

    Reviews

    References

     

    No references found.

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