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    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of putative phosphosugar isomerase (YP_167080.1) from SILICIBACTER POMEROYI DSS-3 at 1.75 A resolution. To be published
    Site JCSG
    PDB Id 3fj1 Target Id 391424
    Molecular Characteristics
    Source Silicibacter pomeroyi dss-3
    Alias Ids TPS20245,YP_167080.1,, 336107 Molecular Weight 36076.87 Da.
    Residues 343 Isoelectric Point 5.48
    Sequence mtqhitrmrreideipeavqrlldhgaqdvarvaavlrlrdpsfvatvargssdhvctylsyaaelllg lpvaslgpsvasvydarlrldralclavsqsgkspdivamtrnagrdgalcvaltndaasplagvsaht idihagpelsvaatktfvtsavaglmlladwaeddglraalgnlpetlaaasridwpemrvaigarpsl ftlgrgtslavsneaalkfketcqlhaesyssaevlhgpvsiveegfpvlgfaagdaaeaplaeiadqi aakgatvfattgrvtrarvlehvrsghaltdplslivsfysmveafasergidpdaprhlnkvtetv
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 1.75 Rfree 0.195
    Matthews' coefficent 2.02 Rfactor 0.162
    Waters 1224 Solvent Content 39.19

    Ligand Information


    Google Scholar output for 3fj1

    Protein Summary

    Putative phosphosugar isomerase. Homolog of glutamine-fructose-6-phosphate transaminases (isomerizing).


    Target ID 391424 is a 36.1 kilodalton, 343 amino acid long protein encoded by Silicibacter pomeroyi dss-3, an α- proteobacterium in the roseobacter clade. The roseobacter clade is one of about 10 major taxa of marine bacteria that dominate bacterioplankton communities in coastal and open oceans.This target has been refined to a resolution of 1.75 Angstroms, and belongs to the double SIS-domain SCOP family. SIS-like proteins consist of a three layered alpha-beta-alpha motif with a beta sheet of the strand order  21345. In double-domain SIS proteins, duplicated SIS domains are related by a pseudo-dyad axis of symmetry. Several members of this family contain members that function as L-glutamine:D-fuctose-6-phosphate amidotransferase and glucosamine-6-phosphate deaminase.This target belongs to the SIS (SugarISomerase) Pfam group. The SIS (Sugar ISomerase) domain is a phosphosugar-binding domain PUBMED:10203754 found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars possibly by binding to the end-product of the pathway.


    Ribbon representation of the crystal structure of the 343 amino-acid long structure of Target ID 391424. The representation is color-coded with the N-termius in blue and the C-terminus in red.


    Both analytical size exclusion chromatography and crystal packing analysis using the EBI PISA web server suggests that a dimer comprising two subunits of the asymmetric unit in the crystal structure is a significant oligomerization state in solution. Two views of the proposed tetramer are shown as ribbons representations below.


    Ribbon representation of the dimer of target ID 391424 with the individual monomers colored in yellow and blue.

    A search of the PDB using the EBI SSM and Profunc servers shows that the following proteins show structural similarity to target ID 391424

      RMS Overlap (Angstroms) Sequence Identity PDB ID PDB Description
     1  1.92  28.3%  2V4M  The isomerase domain of human glutamine-fructose-6- phosphate transaminase 1 (gfpt1) in complex with fructose 6-phosphate
     2  2.04  21.8%  2DEC  Crystal structure of the ph0510 protein from pyrococcus horikoshii ot3
      2.18  22.2%    2CB0 Crystal structure of glucosamine 6-phosphate deaminase from pyrococcus furiosus
     4  2.05  22.2%  2EF5   Crystal structure of the ph0510 protein from pyrococcus horikoshii ot3 in complex with phosphate ion
     5  1.85  31.0%  1MOR   Isomerase domain of glucosamine 6-phosphate synthase complexed with glucose 6-phosphate
     6  2.06  22.2%  2DF8   Crystal structure of the ph0510 protein from pyrococcus horikoshii ot3 in complex with beta-d-fructopyranose-1- phosphate
     7  1.95  31.0%  1MOQ Isomerase domain of glucosamine 6-phosphate synthase complexed with glucosamine 6-phosphate
     8  2.25  21.4%  3C3J   Crystal structure of tagatose-6-phosphate ketose/aldose isomerase from escherichia coli
     9  2.46  21.3%  1J5X Crystal structure of glucosamine-6-phosphate deaminase (tm0813) from thermotoga maritima at 1.8 a resolution
     10  2.13  27.4%  2POC   The crystal structure of isomerase domain of glucosamine-6- phosphate synthase from candida albicans




    Shown above is a representation of an SSM positioning of the structures of target ID 391424 and PDB ID 24VM, the isomerase subunit of human glutamine-fructose-6-phosphate transaminase.







    Shown below is a multiple amino acid sequence alignment for target ID 291424 (PDB ID 3FJ1) and related structures identified from the SSM search. Conserved residues (target ID 391424 numbering) include Glu 11, Ile 12, Pro 16, Gly 51, Ser 53, Ser 98, Ser 100, Gly 101, Ser 129, Glu 146, Val 149, Thr 151, Gly 211, Gly 213, Glu 221, Leu 224, Lys 225, Lys 227, Glu 228, His 231, Gly 232, Val 256, Ala 323, Gly 327, Asp 331, Pro 333, Arg 334, Leu 336, Lys 338.




    Negatively charged chloride ions were in the crystal structure of 3fj1 at a similar relative position for the negatively-charged fructose-6-phosphate substrate bound to the human protein. Shown below is an alignment for the active site residues on PDB ID 3fj1(green sticks) and PDB ID 2v4m (the human glutamine-fuctose-6-phosphate transaminase isomerase domain from  (blue sticks). The active site on both proteins consists of residues from a dyad-related subunit in the dimer. Two active site sidechains, Glu 228 and Lys 225 (3fj1 numbering) are believed to be important for catalysis and are conserved. A significant difference between the active site environment on 3fj1 versus 2v4m and related structures is the substitution of Arg 50 for a conserved Cys residue and suggests. (A Lys 594 sidechain in 2v4m is located in the vicinity of the Arg 50 sidechain on 3fji.







    Glutamine-fructose 6-phosphate transaminase EC









    Ligand Summary




    No references found.

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