The Open Protein Structure Annotation Network
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    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of protein with a cupin-like fold and unknown function (YP_001165807.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.91 A resolution. To be published
    Site JCSG
    PDB Id 3es1 Target Id 391033
    Molecular Characteristics
    Source Novosphingobium aromaticivorans dsm 12444
    Alias Ids TPS14629,YP_001165807.1,, 85592 Molecular Weight 18685.97 Da.
    Residues 171 Isoelectric Point 5.17
    Sequence msealsdsglppvqrvvtghdahgravfksedvtptrmipsgdasfllvwttatvpadnndetdgrqre agltldggsvirvvdmlpgkespmhrtnsidygivlegeielelddgakrtvrqggiivqrgtnhlwrn ttdkpcriafilieapaylhngqplpedkpdhk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.91 Rfree 0.205
    Matthews' coefficent 2.51 Rfactor 0.170
    Waters 188 Solvent Content 50.94

    Ligand Information



    Protein Summary

    Gene Saro_3421 from Novosphingobium Aromaticivorans DSM 12444 encodes the YP_001165807.1 protein.  The search results from NCBI sequence alignment reveals that this target belong to the CUPIN-2 superfamily (PF07883). Genome context analysis provides two 0.9 scored hits, based on neighborhood and co-ocucrrence, with the genes Saro_3422 (fumarylacetoacetate hydrolase) and with Saro_3435 (NAD-dependent epimerase/dehydratase).    


    SCOP classifies 3es1 in the all beta class, RmlC-like cupins superfamily. DALI hits are with the Mn-containing cupin 1vj2 (Zscr=13), the putative decarboxylase 1o4t (Zscr=12), 2pfw and the auxin binding protein 1lr5 (Zscr=11). Based on both SSM alignment and FFAS alignment, 3es1 is structurally similar to 1LR5 and 1FI2 . There is one 3es1 molecule in each asymmetric unit. The interface interaction suggests that the likely biomolecule of 3es1 is a dimer.




    Figure 1. 3es1 structure belongs to the CUPIN-2 superfamily and consists of β-strands mainly. 



    Figure 2. The biomolecule of 3es1 is a dimer based on interface interaction.



    Figure 3. 3es1 structure (green) is structurally similar to 1FI2 and 1LR5.



     1.    Woo, E.J.,  Dunwell, J.M.,  Goodenough, P.W.,  Marvier, A.C.,  Pickersgill, R.W.   (2000) Germin is a manganese containing homohexamer with oxalate oxidase and superoxide dismutase activities.  Nat.Struct.Biol.   7: 1036-1040   (PDB IFI2)

    2.    Woo, E.J.,  Marshall, J.,  Bauly, J.,  Chen, J.G.,  Venis, M.,  Napier, R.M.,  Pickersgill, R.W.  (2002) Crystal structure of auxin-binding protein 1 in complex with auxin.  EMBO J.  21: 2877-2885  (PDB 1LR5)






























    Ligand Summary




    No references found.

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