6DQO

Crystal structure of SsuE FMN reductase Y118A mutant in FMN bound form.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.705 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Not as easy as pi : An insertional residue does not explain the pi-helix gain-of-function in two-component FMN reductases.

McFarlane, J.S.Hagen, R.A.Chilton, A.S.Forbes, D.L.Lamb, A.L.Ellis, H.R.

(2019) Protein Sci. 28: 123-134

  • DOI: 10.1002/pro.3504
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The π-helix located at the tetramer interface of two-component FMN-dependent reductases contributes to the structural divergence from canonical FMN-bound reductases within the NADPH:FMN reductase family. The π-helix in the SsuE FMN-dependent reductas ...

    The π-helix located at the tetramer interface of two-component FMN-dependent reductases contributes to the structural divergence from canonical FMN-bound reductases within the NADPH:FMN reductase family. The π-helix in the SsuE FMN-dependent reductase of the alkanesulfonate monooxygenase system has been proposed to be generated by the insertion of a Tyr residue in the conserved α4-helix. Variants of Tyr118 were generated, and their X-ray crystal structures determined, to evaluate how these alterations affect the structural integrity of the π-helix. The structure of the Y118A SsuE π-helix was converted to an α-helix, similar to the FMN-bound members of the NADPH:FMN reductase family. Although the π-helix was altered, the FMN binding region remained unchanged. Conversely, deletion of Tyr118 disrupted the secondary structural properties of the π-helix, generating a random coil region in the middle of helix 4. Both the Y118A and Δ118 SsuE SsuE variants crystallize as a dimer. The MsuE FMN reductase involved in the desulfonation of methanesulfonates is structurally similar to SsuE, but the π-helix contains a His insertional residue. Exchanging the π-helix insertional residue of each enzyme did not result in equivalent kinetic properties. Structure-based sequence analysis further demonstrated the presence of a similar Tyr residue in an FMN-bound reductase in the NADPH:FMN reductase family that is not sufficient to generate a π-helix. Results from the structural and functional studies of the FMN-dependent reductases suggest that the insertional residue alone is not solely responsible for generating the π-helix, and additional structural adaptions occur to provide the altered gain of function.


    Organizational Affiliation

    Department of Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, 1 rue Laurent Fries, 67404, Illkirch CEDEX, France.,PRESTO, JST, Nagoya 464-8601, Japan.,ERATO Itami Molecular Nanocarbon Project, JST, Nagoya 464-8601, Japan.,Department of Chemistry, University of York, Heslington, York, YO10 5DD, United Kingdom.,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110 029, India.,The Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama, 36849.,Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Physics, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan, and RIKEN Center for Computational Science, Kobe 650-0047, Japan.,Vollum Institute, Oregon Health & Science University, Portland, United States.,Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India.,Laboratoire d'Innovation Moléculaire et Applications, Université de Strasbourg|, Université de Haute-Alsace|, CNRS|, LIMA (UMR 7042), Equipe de Synthèse Organique et Molécules Bioactives (SYBIO), ECPM, 25 rue Becquerel, 67000, Strasbourg, France.,School of Cellular & Molecular Medicine , University of Bristol , Bristol BS8 1TD , U.K.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China. shi-lab@tsinghua.edu.cn.,Division for Structural Biochemistry, OE8830, Hannover Medical School, Hannover, Germany.,Laboratory of Molecular Physiology, NHLBI, National Institutes of Health, Bethesda, United States.,Graduate School of Science, Osaka Prefecture University, Osaka 599-8531, Japan.,Center for Drug Discovery, Northeastern University, Boston, MA 02115, USA.,Cell Adhesion Laboratory, Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, United States.,Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Uji-shi, Japan.,School of Pharmacy , University of Waterloo , Waterloo , Ontario , Canada N2L 3G1.,Center for Inflammation Research, University of Texas Southwestern Medical Center, Dallas, TX, USA. Zhijian.Chen@UTSouthwestern.edu.,Institute of Biotechnology, Vilnius University, Vilnius, Lithuania. Electronic address: siksnys@ibt.lt.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.,Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115, USA. Electronic address: c.mattos@northeastern.edu.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China. shi-lab@tsinghua.edu.cn.,Centre for Structural Systems Biology (CSSB), German Electron Synchrotron (DESY), Hamburg, Germany.,National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence on Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China.,Department of Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, Salerno, Italy.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, 430072, Wuhan, China.,Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK.,Cambridge Institute for Medical Research and Department of Haematology, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, England.,Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110 029, India tpsingh.aiims@gmail.com.,Department of Biology , University of Waterloo , Waterloo , Ontario , Canada N2L 3G1.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China.,Department of Chemistry, College of Science , University of Hail , Saudi Arabia.,Shanghai Institute of Precision Medicine, 200125, Shanghai, China. huangchh@shsmu.edu.cn.,Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA. Zhijian.Chen@UTSouthwestern.edu.,Key laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China. leim@shsmu.edu.cn.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA. Zhijian.Chen@UTSouthwestern.edu.,Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan.,Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan.,The Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, 66045.,Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK. Electronic address: d.wigley@imperial.ac.uk.,Faculty of Natural Sciences, Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, England.,Institute for Biophysical Chemistry, OE4350, Hannover Medical School, Hannover, Germany.,Instituto de Física de Líquidos y Sistemas Biológicos, CONICET, UNLP, Calle 59 No. 789, La Plata, Argentina.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA. Xiaochen.Bai@UTSouthwestern.edu.,Department of Chemistry and Biochemistry , Laurentian University , Sudbury , Ontario , Canada P3E 2C6.,Department of Stem Cell Biology and Medicine/Cancer Stem Cell Research, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan.,Institute of Biotechnology, Vilnius University, Vilnius, Lithuania.,Department of Physiology, Faculty of Medicine, Saitama Medical University, Saitama 350-0495, Japan.,Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115, USA.,Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA. Xiaochen.Bai@UTSouthwestern.edu.,Department of Chemistry , University of Waterloo , Waterloo , Ontario , Canada N2L 3G1.,MRC Laboratory of Molecular Biology, Cambridge, UK. mg@mrc-lmb.cam.ac.uk.,Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China. huangchh@shsmu.edu.cn.,Applied Biotechnology Group, Biomedical Science School, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670, Villaviciosa de Odón, Spain; Grupo de Investigación en Desarrollo Agroindustrial Sostenible, Universidad de la Costa, CUC, Calle 58 # 55 - 66, Barranquilla, Colombia. Electronic address: jesus.fernandez2@universidadeuropea.es.,Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA. Xuewu.Zhang@UTSouthwestern.edu.,Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China.,Department of Physiology and Advanced Research Center for Medical Science, Toho University School of Medicine, Tokyo 143-8540, Japan.,Center for Advanced Medical Innovation, Kyushu University, Fukuoka 812-8582, Japan.,Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.,Shanghai Institute of Precision Medicine, 200125, Shanghai, China.,MRC Laboratory of Molecular Biology, Cambridge, UK.,Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukui-shi, Japan.,Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, China.,Shanghai Institute of Precision Medicine, 200125, Shanghai, China. leim@shsmu.edu.cn.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan.,Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, Wood Lane, London W12 0BZ, England.,Department of Applied Chemistry, Waseda University, Tokyo 169-8555, Japan.,Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, Stuttgart, Germany.,Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China. leim@shsmu.edu.cn.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA. Xuewu.Zhang@UTSouthwestern.edu.,Applied Biotechnology Group, Biomedical Science School, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670, Villaviciosa de Odón, Spain.,Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,MRC Laboratory of Molecular Biology, Cambridge, UK. scheres@mrc-lmb.cam.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FMN reductase (NADPH)
A
191Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: ssuE (ycbP)
EC: 1.5.1.38
Find proteins for P80644 (Escherichia coli (strain K12))
Go to UniProtKB:  P80644
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download SDF File 
Download CCD File 
A
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.705 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.184 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 80.911α = 90.00
b = 110.847β = 90.00
c = 41.727γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
AutoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (United States)United StatesMCB-1244320
National Science Foundation (United States)United StatesCHE-1403293

Revision History 

  • Version 1.0: 2019-01-09
    Type: Initial release