The Open Protein Structure Annotation Network
PDB Keyword


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

    Title Crystal structure of Putative polyketide cyclase. (NP_743055.1) from PSEUDOMONAS PUTIDA KT2440 at 1.24 A resolution. To be published
    Site JCSG
    PDB Id 3f7x Target Id 391191
    Molecular Characteristics
    Source Pseudomonas putida kt2440
    Alias Ids TPS20203,NP_743055.1, 3.10.450.50, 87443 Molecular Weight 14725.83 Da.
    Residues 132 Isoelectric Point 4.88
    Sequence mtatelvnayyaafnagdmpaflallsedvihdinqgerqmgkarfaafmekmnrcyrerladivvmqn adgsraaaeftvhgqyladdeglptangqtyvlpagaffyihcgkiarvtnyynlndwveqva
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.24 Rfree 0.150
    Matthews' coefficent 1.87 Rfactor 0.120
    Waters 202 Solvent Content 34.24

    Ligand Information



    Protein Summary

    Gene PP0894 from Pseudomonas putida kt2440 encodes the NP_743055 amino acid sequence. Pseudomonas putida kt2440 is a gram-negative bacterium that has been investigated for its bioremediation capabilities.  NP_743055 structure (3f7x) has been refined to a resolution of 1.3 Angstroms. The target 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. NP_743055 belongs to the SnoaL-like polyketide cyclase Pfam family (PF07366). This Pfam family is represented by two structures in the Protein Data Bank, PDB ID 1tuh, a soil derived mobile gene cassette,  and PDB ID 1sjw, a bacterial polyketide cyclase. Analysis of PP0894 genomic neighborhood with STRING indicates a possible functional link (score 0.97) with its neighbor PP0896, a carbon-nitrogen hydrolase family protein.


    monomer_ribbons.pngShown to the left is a ribbon representation of a single subunit of 3f7x. The N-terminal end of the protein is in blue and the C-terminal end is in red. An un-identified ligand, represented by the red sticks, is observed in the crystals structure, and is bound to the putative active site of the protein. Analysis of the structure using the  fastSCOP Evolutionary classification server indicates that 3f7x belongs to the d1nwwa SCOP ID (protein:limonene-1,2-epoxide hydrolase, family: limonene-1,2-epoxide hydrolase, superfamily:NTF2-like, fold: cystatin-like, class: alpha and beta proteins (a+b). The monomer contains a four stranded twisted anti-parallel beta sheet. One side of the beta sheet is surrounded by three alpha-helices.


    dimer.pngThe EBI PISA server suggests that a probable oligomerization state of 3f7x is a dimer. A two-fold axis of symmetry relates each monomer within the dimer. A ribbon representation of the dimer is shown to the right with the individual monomers in green and blue.  The monomer-monomer interface is formed by oneside of the anti-parallel twisted that is opposite the side facing the alpha helices. Intermolecular sidechain interactions stabilizing the dimer include salt-bridges, hydrogen bonds and non-polar interactions. However, the structure suggests that structural elements from the symmetry-related dimer do not contribute to the individual active sites on each monomer.

    An NCBI BLAST search using the amino acid sequence of 3f7x shows that the top-scoring amino acid sequence homologs (i.e. those with sequence identities > 30%) are annotated as hypothetical proteins.In order to gain some insights into the possible function of  3f7x, the structure reported here was used for an NCBI VAST search. This search shows a several related structures are found in the Protein Data Bank. The results of this VAST seach are shown below:



    PDB ID Alignment Length VAST Score RMSD (Angstroms) % Sequence ID Description
    2bng 120 19.8 2.1 16.7 Structure Of An M.Tuberculosis Leh-Like Epoxide Hydrolase
    1nu3 120 18.1 1.8 15.8 Limonene-1,2-Epoxide Hydrolase In Complex With Valpromide
    2a15 117 17.9 2.1 19.7 X-Ray Crystal Structure Of Rv0760 From Mycobacterium Tuberculosis At 1.68 Angstrom Resolution
    1s5a 121 17.4 2.0 20.7 Crystal Structure Of Hypothetical Protein Apc1116 From Bacillus Subtilis
    1tuh 115 17.2 1.6 19.1 Structure Of Bal32a From A Soil-Derived Mobile Gene Cassette
    3ec9 122 16.6 1.7 12.3 Crystal Structure Of Ntf2-Like Protein Of Unknown Function (Yp_440611.1) From Burkholderia Thailandensis E264 At 1.60 A Resolution
    3bb9 106 16.5 1.8 14.2 Crystal Structure Of Putative Ketosteroid Isomerase (Yp_750657.1) From Shewanella Frigidimarina Ncimb 400 At 1.80 A Resolution
    3dm8 115 15.9 1.7 13.0 Crystal Structure Of Putative Isomerase From Rhodopseudomonas Palustris
    2gey 124 15.4 2.2 16.9 Crystal Structure Of Putative Isomerase From Rhodopseudomonas Palustris
    1ohp 106 15.8 1.6 23.6 Crystal Structure Of 5-3-Ketosteroid Isomerase Mutant D38n From Pseudomonas Testosteroni Complexed With 5alpha-Estran-3,17-Dione


    Thus, this VAST search indicates that 3f7x functions as a 1,2-epoxide hydrolase or a keto-steriod isomerase. DALI corroborates this result returning as top hits for a 3f7x search: 3i0y (Z=25), 3f8h (Z=22) and 3kkg (Z=17).

    active_site.bmpShown on the right is a representation of the putative active site of 3f7x. The unidentified ligand and active the active site is shown in red. 2Fo-Fc electron density contoured at 0.75 sigma corresponding to the unidentified ligand is shown in blue. Amino acid sidechains within van der Waals contact distance are shown in green. This unidentified ligand is situated within a hydrophobic pocket on the monomer. However, the sidechain of Glu 59, is situated in close proximity to the unidentified ligand. In addition, this acidic sidechain is within hydrogen bonding distance of the sidechain of Tyr 100. The position of this Glu-Tyr sidchain pair at the putative active site suggests these two residues are involved in the catalytic mechanism for this target. The positioning of these residues at the active site of this target can be used to aid in the functional annotation. A preliminary search of the literature indicates Glu(Asp)-Tyr sidechain pairs play a role in the catalytic mechanism of certain enzymes such as bacterial keto-steroid isomerases and nucleoside 2'-deoxyribosyltransferase.


    Issues to be further investigated.

    1). Is the shape, characteristics of the unknown ligand representative of the natural substrate? How large is the binding cavity without the ligand?

    2). There is a second unknown ligand modeled. This second ligand is near a second Tyr-Asp pair?



    1. Ha, Nam-Chul; Choi, Gildon; Choi, Kwan Yong; and Oh, Byung-Ha "Structure and Enzymology of delta5-3-ketosteroid isomerase" (2001) Current Opinion in Structural Biology vol 11 pp. 674-678


    2. Short, Steven A,m Arnstrong, Shelly R., Ealick, Steven, E., and Porter, David J.T. "Active Site Amino Acids That Participate in the Catalytic Mechanism of Nucleoside-2'-Deoxyribosyltransferase" (1996) J. Biol. Chem.  Vol 271 No 9.March 1 pp. 4978-4987.


    3. Arand, M. et al. (2003) "Structure of Rhodococcus erythropolis limonene 1,2-epoxide hydrolase reveals a novel active site" The EMBO Journal. Vol 22 No 11 pp. 2583-2592.


    4. Ames BD, Korman TP, Zhang W, Smith P, Vu T, Tang Y, Tsai SC. (2008) "Crystal structure and functional analysis of tetracenomycin ARO/CYC: implications for cyclization specificity of aromatic polyketides." Proc Natl Acad Sci U S A. 2008 Apr 8;105(14):5349-54.


    Ligand Summary




    No references found.

    Tag page

    Files (3)

    FileSizeDateAttached by 
    active site with Unknown ligand
    1324.27 kB19:57, 20 Oct 2008haxelrodActions
    191.65 kB16:00, 20 Oct 2008haxelrodActions
    monomer ribbons and unknown ligand
    122.59 kB23:49, 19 Oct 2008haxelrodActions
    You must login to post a comment.
    All content on this site is licensed under a Creative Commons Attribution 3.0 License
    Powered by MindTouch