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3imk

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

    Title Crystal structure of Putative molybdenum carrier protein (YP_461806.1) from SYNTROPHUS ACIDITROPHICUS SB at 1.45 A resolution. To be published
    Site JCSG
    PDB Id 3imk Target Id 392645
    Molecular Characteristics
    Source Syntrophus aciditrophicus sb
    Alias Ids TPS26565,YP_461806.1, 325671 Molecular Weight 17242.67 Da.
    Residues 157 Isoelectric Point 5.63
    Sequence mdekpaitkiisggqtgadraaldfaikhhipyggwvpkgrlaeggrvpetyqlqemptsdyskrtekn vldsdgtliishgilkggsalteffaeqykkpclhidldrisiedaatlinswtvshhiqvlniagpra gkdpeiyqatmdllevfla
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.45 Rfree 0.177
    Matthews' coefficent 2.27 Rfactor 0.152
    Waters 211 Solvent Content 45.88

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3imk

    Protein Summary

     

    Gene YP_461806.1 encodes a protein with 157 amino acids from Syntrophus aciditrophicus (strain SB), which is a syntrophic benzoate-degrading bacterium. The protein belongs to alpha and beta proteins containing central beta strands and flanking alpha helices around. It has been annotated as a putative molybdenum carrier protein in the new Pfam family - MoCo_carrier (PF12694) - which is part of the DprA clan (CL0349). This is the first structure for the new family.

    The protein contains one monomer in the asymmetric unit, which is also a biological unit.  

     

    all.png

    Fig 1. YP_461806.1 structure. This is also a biomolecule of YP_461806.1

    GOL-1 is located near the putative active site. In this region, R65/G87/S88 aligns to R98/G117/T118 of the 1ydh.    (The PGGxGTxxE motif of LDC proteins.) The D19/P38 aligns to M(se)54/P73 of 1ydh. (M54/P73 are invariant residues of Molybdenum cofactor (MOco) carrier protein.)

     

     GOL_active.png

     Fig 2.  Superposition of YP_461806.1 (green) to 1ydh (orange color) near the putative active site.

     Glycerol is bound in this region. The funtionally important residues are shown as stick model.

     From top, clockwise, Pro38-Asp19-Ser88-Gly87-Arg65 of YP_461806.1 are shown green sticks.

     Pro73-Mse54-Thr118-Gly117-Arg98 of 1ydh are shown as orange sticks.

     

     

     

     

    Dali hits (top 20) are shown as below. 

        No:  Chain   Z    rmsd lali nres  %id PDB  Description
       1:  1rcu-A  9.7  1.8  105   170   13 PDB  MOLECULE: CONSERVED HYPOTHETICAL PROTEIN VT76;                       
       2:  2iz7-A  9.4  2.2  107   162   15 PDB  MOLECULE: MOCO CARRIER PROTEIN;                                      
       3:  1ydh-A  8.5  3.0  115   184   10 PDB  MOLECULE: AT5G11950;                                                 
       4:  1weh-A  8.4  2.6  107   171   13 PDB  MOLECULE: CONSERVED HYPOTHETICAL PROTEIN TT1887;                     
       5:  2a33-A  7.9  2.5  106   175   15 PDB  MOLECULE: HYPOTHETICAL PROTEIN;                                      
       6:  2nx2-A  7.9  2.6  106   178   17 PDB  MOLECULE: HYPOTHETICAL PROTEIN YPSA;                                 
       7:  1wek-A  7.2  2.6  104   208   13 PDB  MOLECULE: HYPOTHETICAL PROTEIN TT1465;                               
       8:  3dnf-B  6.6  3.0   93   282   13 PDB  MOLECULE: 4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE                   
       9:  1t35-E  6.6  2.9  107   184   20 PDB  MOLECULE: HYPOTHETICAL PROTEIN YVDD, PUTATIVE LYSINE                 
      10:  3bq9-A  6.2  3.2  118   446   19 PDB  MOLECULE: PREDICTED ROSSMANN FOLD NUCLEOTIDE-BINDING                 
      11:  2ffh-A  6.0  2.8   99   407   11 PDB  MOLECULE: PROTEIN (FFH);                                             
      12:  1o1x-A  5.8  3.3  105   145   13 PDB  MOLECULE: RIBOSE-5-PHOSPHATE ISOMERASE RPIB;                         
      13:  1usl-C  5.8  3.1  105   158    8 PDB  MOLECULE: RIBOSE 5-PHOSPHATE ISOMERASE B;                            
      14:  2npn-A  5.7  3.3   91   238   11 PDB  MOLECULE: PUTATIVE COBALAMIN SYNTHESIS RELATED PROTEIN;              
      15:  2j37-W  5.5  2.8   96   479    5 PDB  MOLECULE: SRP RNA;                                                   
      16:  1nn4-A  5.3  3.2  104   159    9 PDB  MOLECULE: RIBOSE 5-PHOSPHATE ISOMERASE B;                            
      17:  1yco-A  5.3  3.5  104   276    7 PDB  MOLECULE: BRANCHED-CHAIN PHOSPHOTRANSACYLASE;                        
      18:  3gh1-A  5.3  3.3  119   448   19 PDB  MOLECULE: PREDICTED NUCLEOTIDE-BINDING PROTEIN;                      
      19:  2vaw-A  5.1  4.3  115   315    9 PDB  MOLECULE: CELL DIVISION PROTEIN FTSZ;                                
      20:  1cbf    5.1  3.3   92   240    7 PDB  MOLECULE: COBALT-PRECORRIN-4 TRANSMETHYLASE;                         

     

    super_2iz7_1rcu.png

    Fig 2. Suerposition of YP_461806.1 with homologs- 1rcu (light pink) and 2iz7 (light blue). The central four beta- strands are superimposed very well between all three structures. However, both 1rcu and 2iz7 contain extra strands and helices.

     

    References

    Function and Structure of the Molybdenum Cofactor Carrier Protein from Chlamydomonas Reinhardtii.
    Fischer, K.,   Llamas, A.,   Tejada-Jimenez, M.,   Schrader, N.,   Kuper, J.,   Ataya, F.S.,   Galvan, A.,   Mendel, R.R.,   Fernandez, E.,   Schwarz, G.
    (2006) J.Biol.Chem. 281: 30186

    PubMed: 16873364 View PubMed Abstract at NCBI


     

    Ligand Summary

    Reviews

    References

     

    No references found.

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