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3d1c

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

    Title Crystal structure of a Baeyer-Villiger Flavin-containing monooxygenase from Staphylococcus aureus MRSA strain MU50. Proteins 2014
    Site JCSG
    PDB Id 3d1c Target Id 382610
    Molecular Characteristics
    Source Staphylococcus aureus subsp. aureus mu50
    Alias Ids TPS1767,NP_373108.1, BIG_357, 283046 Molecular Weight 41164.87 Da.
    Residues 368 Isoelectric Point 5.24
    Sequence mqhhkvaiigagaagigmaitlkdfgitdviilekgtvghsfkhwpkstrtitpsftsngfgmpdmnai smdtspaftfneehisgetyaeylqvvanhyelnifentvvtnisaddayytiatttetyhadyifvat gdynfpkkpfkygihyseiedfdnfnkgqyvviggnesgfdaayqlakngsdialytsttglndpdadp svrlspytrqrlgnvikqgariemnvhytvkdidfnngqyhisfdsgqsvhtphepilatgfdatknpi vqqlfvttnqdikltthdestrypnifmigatvendnaklcyiykfrarfavlahlltqreglpakqev ienyqknqmylddysccevsctc
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.40 Rfree 0.225
    Matthews' coefficent 3.12 Rfactor 0.181
    Waters 115 Solvent Content 60.57

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3d1c
    1. A Flavoprotein Monooxygenase that Catalyses a BaeyerVilliger Reaction and Thioether Oxidation Using NADH as the Nicotinamide Cofactor
    CN Jensen, J Cartwright, J Ward, S Hart - , 2012 - Wiley Online Library
     
    2. Distributed structure determination at the JCSG
    H van den Bedem, G Wolf, Q Xu - Section D: Biological , 2011 - scripts.iucr.org
     

    Protein Summary

    NP_373108.1 is a likely  flavin-containing monooxygenase  (FMO), it is structurally similar to FMO from S. pombe (RMSD 2.36 for 264 aligned Ca, PDB code 2gvc/1vqw/2gv8). The solved structure contains a FAD. It also contains an unidentified ligand at the same place of methimazole in SmFMO. The active site residues,  though somewhat similar to SmFMO, are not completely conserved, suggesting possible differences in substrate specificity. O2*,O3*,O4* positions of FAD in this enzyme also differs from SmFMO.

    NP_373108.1 functions as a monomer. It may also bind NADPH or NADH (NP_373108.1 contains a Pyridine nucleotide-disulphide oxidoreductase (PF07992: Pyr_redox_2) domain from Pfam, which according to Pfam is a small NADH binding domain within a larger FAD binding domain. 

    Top hits from Dali server are:

     

       1:  3d1c-A 60.0  0.0  358   358  100 PDB  MOLECULE: FLAVIN-CONTAINING PUTATIVE MONOOXYGENASE;                  
       2:  4a9w-A 28.9  2.4  300   330   15 PDB  MOLECULE: MONOOXYGENASE;                                             
       3:  4a9w-B 28.8  2.5  302   330   15 PDB  MOLECULE: MONOOXYGENASE;                                             
       4:  3s5w-B 24.5  3.3  298   415   15 PDB  MOLECULE: L-ORNITHINE 5-MONOOXYGENASE;                               
       5:  3s5w-A 24.5  3.2  299   411   15 PDB  MOLECULE: L-ORNITHINE 5-MONOOXYGENASE;                               
       6:  3s61-A 24.5  3.5  302   414   15 PDB  MOLECULE: L-ORNITHINE 5-MONOOXYGENASE;                               
       7:  3s61-B 24.4  3.3  299   411   15 PDB  MOLECULE: L-ORNITHINE 5-MONOOXYGENASE;                               
       8:  4b69-A 24.0  3.4  305   449   13 PDB  MOLECULE: L-ORNITHINE N5 MONOOXYGENASE;                              
       9:  4b63-A 23.9  3.5  307   452   12 PDB  MOLECULE: L-ORNITHINE N5 MONOOXYGENASE;                              
      10:  4b66-A 23.8  3.5  305   449   12 PDB  MOLECULE: L-ORNITHINE N5 MONOOXYGENASE;                              
      11:  4b64-A 23.7  3.5  307   455   13 PDB  MOLECULE: L-ORNITHINE N5 MONOOXYGENASE;                              
      12:  4b68-A 23.5  3.6  306   455   12 PDB  MOLECULE: L-ORNITHINE N5 MONOOXYGENASE;                              
      13:  4b65-A 23.5  3.5  304   456   13 PDB  MOLECULE: L-ORNITHINE N5 MONOOXYGENASE;                              
      14:  2vqb-D 23.5  3.1  296   443   20 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      15:  2vqb-B 23.5  3.1  296   443   20 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      16:  2vqb-A 23.5  3.1  296   443   20 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      17:  4b67-A 23.4  3.5  305   458   13 PDB  MOLECULE: L-ORNITHINE N5 MONOOXYGENASE;                              
      18:  2xvh-C 23.4  3.1  296   446   19 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      19:  2gv8-A 23.4  2.8  293   442   21 PDB  MOLECULE: MONOOXYGENASE;                                             
      20:  2gv8-B 23.4  2.8  293   442   21 PDB  MOLECULE: MONOOXYGENASE;                                             
      21:  2vqb-C 23.4  3.1  296   443   20 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      22:  2vq7-B 23.4  3.1  296   443   19 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      23:  2vq7-A 23.4  3.1  296   443   19 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      24:  3cty-A 23.4  3.1  284   304   20 PDB  MOLECULE: THIOREDOXIN REDUCTASE;                                     
      25:  2xvh-B 23.3  3.2  299   445   19 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      26:  2xvi-C 23.3  3.2  296   446   19 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      27:  2xlp-C 23.3  3.2  298   445   19 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      28:  2xlp-B 23.3  3.1  296   445   19 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      29:  2xlt-C 23.3  3.1  296   446   19 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      30:  2vq7-D 23.3  3.1  296   443   19 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      31:  2vq7-C 23.3  3.1  296   445   19 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      32:  2xlp-D 23.2  3.2  297   446   19 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      33:  2xlt-D 23.2  3.3  298   446   19 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      34:  2xlp-A 23.2  3.2  296   446   19 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      35:  2xvh-A 23.2  3.2  297   445   19 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      36:  2xlu-C 23.2  3.1  296   445   19 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      37:  2xlt-B 23.2  3.1  296   446   19 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      38:  2xls-D 23.2  3.1  296   447   19 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      39:  2xlt-A 23.2  3.1  297   446   19 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      40:  2xlu-A 23.2  3.1  296   446   19 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      41:  2xls-B 23.2  3.1  296   447   19 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      42:  2xlu-D 23.2  3.1  296   446   19 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      43:  2xls-A 23.2  3.1  296   446   19 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      44:  2xvj-C 23.2  3.1  297   446   19 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      45:  2gvc-E 23.2  2.9  293   442   20 PDB  MOLECULE: MONOOXYGENASE;                                             
      46:  3cty-B 23.2  3.2  283   305   19 PDB  MOLECULE: THIOREDOXIN REDUCTASE;                                     
      47:  1vqw-A 23.1  2.8  292   442   21 PDB  MOLECULE: PROTEIN WITH SIMILARITY TO FLAVIN-CONTAINING               
      48:  2xls-C 23.1  3.3  298   447   19 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      49:  2xvj-B 23.1  3.3  298   445   18 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;                           
      50:  2xlu-B 23.1  3.3  298   445   19 PDB  MOLECULE: FLAVIN-CONTAINING MONOOXYGENASE;  
    

     

    Top Hits from FFAS

    1

    -104.000

    3d1c_A mol:protein length:369 Flavin-containing Putative Monooxygenase

    2

    -59.200

    4a9w_A mol:protein length:357 MONOOXYGENASE

    3

    -46.200

    3uov_A mol:protein length:545 OTEMO

    4

    -45.700

    3ucl_A mol:protein length:573 Cyclohexanone monooxygenase

    5

    -45.600

    1vqw_A mol:protein length:457 PROTEIN WITH SIMILARITY TO FLAVIN-CONTAINING

    6

    -45.100

    4aos_A mol:protein length:549 STEROID MONOOXYGENASE

    7

    -44.500

    1w4x_A mol:protein length:542 PHENYLACETONE MONOOXYGENASE

    8

    -44.000

    3s5w_A mol:protein length:463 L-ornithine 5-monooxygenase

    9

    -43.300

    4b63_A mol:protein length:501 L-ORNITHINE N5 MONOOXYGENASE

    10

    -42.900

    2vq7_A mol:protein length:461 FLAVIN-CONTAINING MONOOXYGENASE

     

    It was found, by both Dali and FFAS, to be similar to another FMO (PDB 4A9W), a Baeyer–Villiger monooxygenase, suggestive of similar function.

     

    References
    [Ref]

    [Ref]

    Ligand Summary



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