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

    Title Crystal structure of NTF-2 like protein of unknown function (YP_166335.1) from SILICIBACTER POMEROYI DSS-3 at 1.69 A resolution. To be published
    Site JCSG
    PDB Id 3fka Target Id 391417
    Molecular Characteristics
    Source Silicibacter pomeroyi dss-3
    Alias Ids TPS20241,YP_166335.1, 3.10.450.50, 336152 Molecular Weight 13458.53 Da.
    Residues 119 Isoelectric Point 4.71
    Sequence mttsehiaaltalvetyvmamtrgdrpaleriffgkasevghyegellwnsrdafiamcedaadaetdp fwaissvsvqgdiamlhvendwagmrfddfltvllhegswrivskvyrir
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 1.69 Rfree 0.200
    Matthews' coefficent 2.62 Rfactor 0.179
    Waters 520 Solvent Content 53.06

    Ligand Information


    Google Scholar output for 3fka
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org

    Protein Summary

    Structural highlights: 3fka structure belongs to the NTF2_like Conserved Domain Superfamily. Crystal packing suggests that the tetramer is significant oligomerization state in solution. Although the function of this protein (YP_166335) is not known, the positioning of a conserved Tyr, Asp, and Lys residues at the putative active site, suggests they are important for function.


    Pfam update: NO PfamA hits. On PfamB, YP_166335 belongs in a clan of various types of enzyme:
    ID Lumazine_bd_2
    AC PF12893
    DE Putative lumazine-binding
    AU Coggill P
    SE JCSG_target_391417
    GA 22.10 22.10;
    TC 22.10 22.10;
    NC 22.00 22.00;
    BM hmmbuild --amino -o /dev/null HMM SEED
    SM hmmsearch -Z 9421015 -E 1000 --cpu 4 HMM pfamseq
    TP Family
    CL CL0051
    This is a family of uncharacterised proteins. However, the family belongs to the NTF2-like superfamily of various enzymes, and some of the members of the family are putative dehydrogenases.


    PSI-BLAST update: YP_841829, annotated as a putative 3-hydroxy-isobutyrate dehydrogenase, shows 28% seq. id. with YP_166335.


    SPO1084 gene translates into a 13.5 kilodalton, 119 amino acid long YP_166335 protein belonging to 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. 3fka structure has been refined to a resolution of 1.69 Angstroms, and belongs to the NTF2_like Conserved Domain Superfamily. This family includes members that perform a variety of diverse functions including delta-5-3-ketosteroid isomerases, scytalone dehydratases, ring hydroxylating dioxygenases, and nuclear transport factor 2 activity. Shown to the right is a ribbon representation of the 3fka structure. Analysis of the strumonomer.bmpcture using the  fastSCOP Evolutionary classification server indicates that 3fka belongs to the d.17.4 SCOP NTF-2 like superfamily.  The monomer contains a six -stranded  mixed beta sheet with one side of the beta sheet is surrounded by three alpha-helices. This target belongs to a previously uncharacterized Pfam group.


    Computational analysis of the quatenary structure using the EBI PISA web server suggests that a tetramer comprising four 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. Even though a tetramer, based on the crystal structure reported here,  is believed to be a significant oligomerization state, more analysis is needed to see if the tetramer could further multimerize into tetradecameric assembly as does the association domain of Ca2+/calmodulin-dependent kinase II (CaMKII, PDB code 1hkx) or if the proposed tetramer can dissociate into dimers.



    Individual subunits in the asymmetric unit are color-coded. Two pairs of subunits in the tetramer related by a translation (green,blue; and red,yellow) form a 12-strand beta-sheet.  Different pairs of subunits related by two-fold symmetry (yellow,blue and red,green) form a network of short-range, primarily hydrophobic interactions, between sidechains on one side of the beta-sheet on each monomer. 

    A search of the Pfam data base shows that YP_166335 sequence has not been assigned to any specific Pfam group; thus, structural comparisons in particular most likely offers valuable information. A structural comparison was performed using the Profunc server, and the following results are obtained:

    Hit   Q-score   Z-score   No. 
     1  0.706 7.9 9 1.68  19.3%   3blzA  Crystal structure of a ntf2-like protein of unknown function (yp_001049020.1) from shewanella baltica os155 at 1.75 a resolution
     2  0.511 5.9 9 1.99  10.9%   2rgqA  Crystal structure of domain of unknown function with a cystatin-like fold (zp_00111510.1) from nostoc punctiforme pcc 73102 at 1.80 a resolution
     3  0.504 5.8 8 2.19  13.4%   2f86B  The association domain of c. Elegans camkii
     4  0.496 5.0 8 2.32  16.0%   2ux0A  Structure of the oligomerisation domain of calcium- calmodulin dependent protein kinase ii gamma
     5  0.488 5.5 8 2.26  11.8%   1hkxA  Crystal structure of calcium/calmodulin-dependent protein kinase
     6  0.488 4.3 8 2.27  19.3%   1gy5A  D92n,d94n double point mutant of human nuclear transport factor 2 (ntf2)
     7  0.484 4.2 6 2.05  19.3%   3cnxA  Crystal structure of ntf2-like protein of unknown function (np_825848.1) from streptomyces avermitilis at 2.10 a resolution
     8  0.483 4.2 8 2.36  19.3%   1jb2A  Crystal structure of ntf2 m84e mutant
     9  0.477 4.2 8 2.29  19.3%   1askA  Nuclear transport factor 2 (ntf2) h66a mutant
     10  0.476 4.7 8 2.28  15.1%   3b7cA  Crystal structure of ntf-2 like protein of unknown function (np_715767.1) from shewanella oneidensis at 1.70 a resolution



    Shown below is is a superpositioning of the crystal structure (alpha-carbon trace) of the monomer  of 3fka (green) with related structures from the  Profunc search including PDB ID  3blz (yellow), PDB ID 2rgq (red), and PDB ID 2f86 (blue). Many of these related structures have been determined by JCSG and include PDB ID 3blz, 2rgq, and 3b7c.




    Structure based amino acid sequence alignement for 3fka (labeled xactive_site_conserved2.bmpxxx( versus the sequences from related structures listed by their PDB ID codes. Alignments were determined using the 3D-TCoffee server and the ESPript server. Based on analysis, Asp 25, Ala 83, and Trp 109 in 3fka are conserved across the six structurally-related proteins analyzed. The positions of these three highlighted residues are shown in the Figure to the right. and these sidechains are highlighted in magenta. The putative active site on each monomer of 3fka is indicated  in the ribbon representation by the sidechains coloured in green and the red spheres. The red spheres correspond with atoms of an unknown ligand. These conserved residues are relatively distant from the active site are are not likely to be involved either the binding of potential substrates or in a catalytic role. These three residues are at the surface of the protein, and the possible significance of this result requires further investigation.











    Shown above is the structure surrounding the proposed active site on 3fka. A 2fo-fc omit electron density map contoured a 1 standard deviation above the background level of the map is shown in the blue mesh. The putative substrates and or ligands bound to the proposed active site are not known; therefore, these ligands are represented as oxygen atoms (red spheres). These atoms of the unknown ligands were omitted from the model for calculation of the electron density map. The Lys 114 sidechain is in dual conformations.



    Structural Comparison using the NCBI VAST server for structurally-related targets in the PDB with the largest degree of amino acid sequence identity.

     PDB ID
    Ali. Len.
    3BLZ B 
    118 1.7 22.0 Crystal Structure Of A Ntf2-Like Protein Of Unknown Function (Yp_001049020.1) From Shewanella Baltica Os155 At 1.75 A Resolution
    2RCD B 
    106 2.6 21.7 Crystal Structure Of Uncharacterized Protein Conserved In Bacteria With A Cystatin-Like Fold (Yp_051588.1) From Erwinia Carotovora Subsp. Atroseptica Scri1043 At 2.32 A Resolution
    2OWP A 
    101 2.3 19.8 Crystal Structure Of Hypothetical Protein Bxe_b1374 (Yp_553940.1) From Burkholderia Xenovorans Lb400 At 2.00 A Resolution
    2RFR A 
    106 1.9 18.9 Crystal Structure Of Uncharacterized Protein (Yp_001166107.1) From Novosphingobium Aromaticivorans Dsm 12444 At 1.16 A Resolution
    3CNX C 
    110 2.1 18.2 Crystal Structure Of Ntf2-Like Protein Of Unknown Function (Np_825848.1) From Streptomyces Avermitilis At 2.10 A Resolution
    1OHP A 
    88 1.8 18.2 Crystal Structure Of 5-3-Ketosteroid Isomerase Mutant D38n From Pseudomonas Testosteroni Complexed With 5alpha-Estran-3,17-Dione
    3EJV A 
    109 1.9 17.4 Crystal Structure Of Protein Of Unknown Function With A Cystatin-Like Fold (Yp_498036.1) From Novosphingobium Aromaticivorans Dsm 12444 At 1.40 A Resolution
    3CU3 A 
    112 2.6 16.1 Crystal Structure Of Domain Of Unknown Function With A Cystatin-Like Fold (Zp_00107529.1) From Nostoc Punctiforme Pcc 73102 At 2.00 A Resolution
    3CU3 A 1
    108 2.4 15.7 Crystal Structure Of Domain Of Unknown Function With A Cystatin-Like Fold (Zp_00107529.1) From Nostoc Punctiforme Pcc 73102 At 2.00 A Resolution
    3EF8 A 
    111 2.1 15.3 Crystal Structure Of Putative Scyalone Dehydratase (Yp_496742.1) From Novosphingobium Aromaticivorans Dsm 12444 At 1.50 A Resolution
    2CHC A 
    111 2.0 15.3 Structure Of Rv3472(D26n), A Function Unknown Protein From Mycobacterium Tuberculosis
    1JKG A 
    109 2.5 14.7 Structural Basis For The Recognition Of A Nucleoporin Fg- Repeat By The Ntf2-Like Domain Of Tap-P15 Mrna Nuclear Export Factor
    1JN5 B 
    104 2.7 14.4 Structural Basis For The Recognition Of A Nucleoporin Fg- Repeat By The Ntf2-Like Domain Of Tap-P15 Mrna Export Factor
    3B7C A 
    104 2.2 14.4 Crystal Structure Of Ntf-2 Like Protein Of Unknown Function (Np_715767.1) From Shewanella Oneidensis At 1.70 A Resolution
    1KVD A 
    14 2.3 14.3 Killer Toxin From Halotolerant Yeast
    3DXO B 
    86 1.9 14.0 Crystal Structure Of Snoal-Like Protein With Unknown Function (17739112) From Agrobacterium Tumefaciens Str. C58 (Dupont) At 2.70 A Resolution
    3BB9 D 
    87 1.6 13.8 Crystal Structure Of Putative Ketosteroid Isomerase (Yp_750657.1) From Shewanella Frigidimarina Ncimb 400 At 1.80 A Resolution
    2GXF A 
    89 2.1 13.5 Crystal Structure Of The Hypothetical Protein Yybh From Bacillus Subtilis, Northeast Structural Genomics Target Sr506
    1OH0 B 
    96 2.1 13.5 Crystal Structure Of Ketosteroid Isomerase Complexed With Equilenin




    Shown here is a strucure based sequence alignment between 3fka (labeled MG14467A_refinetab2.pdb) and PDB ID 3blz, the top scoring related structure from the VAST search. This alignment reveals several residues to be conserved, inducing Thr 2, Ala 9, Tyr 17, Arg 23, Asp 25, Phe 33, Ala 37, Gly 41, Leu 47, Ala 72, Ile 73, Gly 80, Ala 83, Asp 90, Gly 93, Arg 95, Phe 96,Asp 98, Phe 99,  Leu 103, Glu 106, Gly 107, Trp 109, Val 112, Ser 113, Lys 114, Tyr 116. Based on this large degree of both sequence and structural homology between 3fka and PDB ID 3blz, the two proteins are likely to show functional similarities. In agreement, DALI top hit for a 3fka search is with 3blz (Z=19).




     Shown above is a superpositioning of the monomers of 3fka and its most closely related structural and sequence homolog from the NCBI BLAST search. The conserved sidechains belonging to 3fka are in green and the sidechains belonging to PDB ID 3blz are in cyan. The Unknown ligand bound to the putative active site of 3fka is denoted by red spheres. The conserved residues in close range contact to the unknown ligand are labeled (3fka numbering).  Three of the sidechains, Lys 114, Asp 98, and Tyr 17 are within close proximity and form a hydrogen bonding triad. This suggests an involvement of these three residues in potential catalytic activites of this target protein.

    Ligand Summary




    No references found.

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