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3g0k

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

    Title Crystal structure of protein of unknown function with a cystatin-like fold (YP_498150.1) from Novosphingobium aromaticivorans DSM 12444 at 1.30 A resolution. To be published
    Site JCSG
    PDB Id 3g0k Target Id 391045
    Molecular Characteristics
    Source Novosphingobium aromaticivorans dsm 12444
    Alias Ids TPS24299,SARO_25NOV03_CONTIG28_REVISED_GENE1520, 3.10.450.50, 325173 Molecular Weight 14343.34 Da.
    Residues 129 Isoelectric Point 4.93
    Sequence vartaeeqanhdlviemynkvliamdssavdryiapgyvqhsslaepsvealkgfldrvraespdarqt ihrsfvdgdhviththverwpgdaglavvdifrveggmivehwdviqdvpanpvnpnsmf
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.30 Rfree 0.143
    Matthews' coefficent 2.36 Rfactor 0.120
    Waters 183 Solvent Content 47.82

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3g0k
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     

    Protein Summary

    Gene Saro_2880 from Novosphingobium aromaticivorans dsm 12444 (GenBank: YP_498150) has been annotated as belonging to the SnoaL-like polyketide cyclase protein family (Pfam PF07366) (formerly DUF1486). YP_498150 is also annotated as a putative membrane protein (UniProtKB: Q2G4A7). This may be true, but there is no evidence to support it as of yet.

    Novosphingobium aromaticivorans DSM 12444 encodes two paralogs (Saro_2881 and Saro_0708) of target 3g0k, where the sequence of 3g0k is the shortest and lacks a predicted signal peptide cleavage site. The paralogous protein, Saro_2881, contains a predicted signal peptide cleavage site (LipoP server) and is a non-lipoprotein (LipPred server). Predictions made by LipoP and LipPred servers for Saro_0708 were unclear.

    The structure of 3g0k was solved by seleno-methionine MAD to a resolution of 1.3 Angstroms and reveals the target to be homodimeric (also supported by static light scattering analysis), with each monomer adopting a cystatin-like fold belonging to the NTF2-like superfamily (CDD cd00531; SCOP 54427) (Figures 1a,b).

    Figure 1. (a) Monomeric structure of 3g0k adopts a cystatin-like fold. (color-ramped from N-terminus (blue) to C-terminus (red). (b) Structure of 3g0k homodimer. Monomers are shown in blue and orange and calcium ion as a green sphere.

     

    1(a)                                                                                            1(b)

    MG8051B-monomer.pngMG8051B-dimer.png

    Sequence and structural comparisons using FFAS and fastSCOP yield strongest similarities to hydroxylases and cyclases, including PDB Ids 2GEY (AclR protein, a putative hydroxylase), 2GEX (SnoaL2, a putative hydroxylase, Beinker et al.), 2F98 (Aklanonic acid methyl ester cyclase, Kallio et al.), and 1SJW (SnoaL polyketide cyclase, Sultana et al.) (Figure 2).

     

    Figure 2. Superposition of 3g0k monomer (yellow) and structural homologs 2GEY (cyan), 2GEX (magenta), 2F98 (green), and 1SJW (orange).

     

    MG8051B-structural-homologs.png

    When the sequence of 3g0k is aligned with its closest sequence homologs and the results are mapped onto the structure (via ConSurf), an area of high sequence conservation is observed, suggesting that this region may be the putative active site. Among the highly-conserved residues in this region are Asp-99, His-111, and Asp-113. (Figures 3a-b).

     

    Figure 3. (a) 3g0k monomer colored according to the level of sequence conservation among homologous sequences. D99, H111, and D113 are highly conserved residues which may partly constitute the active site. (b) Space-filling model of 3g0k showing a solvent-accessible cleft at the bottom of which may be the putative active site. Coloring scheme is shown in the key below.

     

    ConSurf_legend.png 

    3(a)

    MG8051B_ConSurf.png

     

    3(b)

    MG8051B_ConSurf_cpk.png

     

    The aforementioned three residues of D99, H111, and D113 are very similar / identical to and superimpose well onto some of the putative active site residues in the hydroxylases (2GEY & 2GEX) and cyclases (2F98 & 1SJW) from the FFAS and fastSCOP results, further supporting the notion that this area is indeed the active site (Figure 4, Table 1). Moreover, the fact that two of these three residues in 3g0k are identical to their counterparts in the hydroxylases and the third residue is very similar (Asp vs. Glu) suggest that the function of 3g0k may more closely resemble that of hydroxylases than of cyclases.

     

    Figure 4. Superposition of 3g0k (yellow) with the putative hydroxylase 2GEY (cyan) shows that the highly conserved residues of D99, H111, and D113 in 3g0k correspond well to several of the putative catalytic site residues (E105, H117, and D119) in 2GEY.

     

    MG8051B-2gey-label.png

     

    Table 1. Putative active site residues of 3g0k (yellow) compared with corresponding residues in homologous structures 2GEY, 2GEX, 2F98, and 1SJW.

     

    Protein (putative) active site
    3g0k D99 H111 D113
    2GEY E105 H117 D119
    2GEX E106 H119 D121
    2F98 H107 H119 D121
    1SJW H107 H119 D121

     

     

     

     

     

    A calcium ion is found bound at the dimer interface along the crystallographic 2-fold symmetry axis. It is octahedrally coordinated by the oxygen atoms of symmetry-related glutamates, alanines, and waters (Figure 5). The significance of this bound metal cation is unclear.

     

    Figure 5. The coordination environment of the calcium ion in 3g0k. Monomers A and B are colored cyan and yellow, respectively. Calcium is represented as a green sphere, and waters as red spheres.

     

    MG8051B-calcium-label.png

     

     

    References:

    Crystal structures of SnoaL2 and AclR: two putative hydroxylases in the biosynthesis of aromatic polyketide antibiotics.  Beinker P, Lohkamp B, Peltonen T, Niemi J, Mäntsälä P, Schneider G. J Mol Biol. 2006 Jun 9;359(3):728-40.

    Crystal structure of the polyketide cyclase AknH with bound substrate and product analogue: implications for catalytic mechanism and product stereoselectivity. Kallio P, Sultana A, Niemi J, Mäntsälä P, Schneider G. J Mol Biol. 2006 Mar 17;357(1):210-20.

    Structure of the polyketide cyclase SnoaL reveals a novel mechanism for enzymatic aldol condensation.  Sultana A, Kallio P, Jansson A, Wang JS, Niemi J, Mäntsälä P, Schneider G.  EMBO J. 2004 May 5;23(9):1911-21.f annotation by Piotr Kozbial.

    Ligand Summary

    Reviews

    References

     

    No references found.

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