6HKE

MatC (Rpa3494) from Rhodopseudomonas palustris with bound malate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history

Literature

A New Mechanism for High-Affinity Uptake of C4-Dicarboxylates in Bacteria Revealed by the Structure of Rhodopseudomonas palustris MatC (RPA3494), a Periplasmic Binding Protein of the Tripartite Tricarboxylate Transporter (TTT) Family.

Rosa, L.T.Dix, S.R.Rafferty, J.B.Kelly, D.J.

(2019) J. Mol. Biol. 431: 351-367

  • DOI: 10.1016/j.jmb.2018.11.016

  • PubMed Abstract: 
  • C4-dicarboxylates play a central role in cellular physiology as key metabolic intermediates. Under aerobic conditions, they participate in the citric acid cycle, while in anaerobic bacteria, they are important in energy-conserving fermentation and re ...

    C4-dicarboxylates play a central role in cellular physiology as key metabolic intermediates. Under aerobic conditions, they participate in the citric acid cycle, while in anaerobic bacteria, they are important in energy-conserving fermentation and respiration processes. Ten different families of secondary transporters have been described to participate in C4-dicarboxylate movement across biological membranes, but only one of these utilizes an extracytoplasmic solute binding protein to achieve high-affinity uptake. Here, we identify the MatBAC system from the photosynthetic bacterium Rhodopseudomonas palustris as the first member of the tripartite tricarboxylate transport family to be involved in C4-dicarboxylate transport. Tryptophan fluorescence spectroscopy showed that MatC, the periplasmic binding protein from this system, binds to l- and d-malate with K d values of 27 and 21 nM, respectively, the highest reported affinity to date for these C4-dicarboxylates, and to succinate (K d = 110 nM) and fumarate (K d = 400 nM). The 2.1-Å crystal structure of MatC with bound malate shows a high level of substrate coordination, with participation of two water molecules that bridge hydrogen bonds between the ligand proximal carboxylic group and the main chain of two conserved loops in the protein structure. The substrate coordination in MatC correlates with the binding data and explains the protein's selectivity for different substrates and respective binding affinities. Our results reveal a new function in C4-dicarboxylate transport by members of the poorly characterized tripartite tricarboxylate transport family, which are widely distributed in bacterial genomes but for which details of structure-function relationships and transport mechanisms have been lacking.


    Organizational Affiliation

    Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, USA. jennyh@niddk.nih.gov.,College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shanxi, China.,College of Chemistry, Fuzhou University, Fuzhou 350116, Fujian, China.,Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305; shannon-au@cuhk.edu.hk wahc@stanford.edu.,Service of Infectious Diseases, University Hospital Geneva, Geneva, Switzerland thilo.kohler@unige.ch.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States.,Pohang Accelerator Laboratory, Pohang, Gyeongbuk 37673, Republic of Korea.,Department of Genetics, Harvard Medical School, Boston, United States.,Centre for BioImaging Sciences, National University of Singapore, Singapore 117557.,Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States.,Biological Science Imaging facility (BSIR), Department of Biology, 89 Chieftan Way, Florida State University, Tallahassee, FL 32306, USA.,Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, United States.,Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan. Electronic address: titoh@ac.shoyaku.ac.jp.,Department of Biological Sciences, Virginia Tech, Derring Hall, Blacksburg, VA 24061, U.S.A. bscharf@vt.edu fschubot@vt.edu.,Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland.,NAmur MEdicine & Drug Innovation Center (NAMEDIC), NARILIS, UNamur , rue de Bruxelles 61 , B-5000 Namur , Belgium.,Institute of Chemical Biology and Drug Discovery and Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA.,Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street, Houston, TX 77005, USA.,Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany. becker@genzentrum.lmu.de.,Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812.,School of Biological Sciences, Nanyang Technological University, Singapore 637551; ygao@ntu.edu.sg yangliang@ntu.edu.sg rero@ntu.edu.sg.,Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany. beckmann@genzentrum.lmu.de.,Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland.,School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, Fife, Scotland, United Kingdom.,Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany. beatrix@genzentrum.lmu.de.,College of Veterinary Medicine, Jilin University, Changchun 130062, Jilin, China; Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, Henan, China.,School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea.,Service of Infectious Diseases, University Hospital Geneva, Geneva, Switzerland.,HIV Dynamics and Replication Program, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA.,Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA.,Biosciences Division, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025.,HIV Dynamics and Replication Program, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA hughesst@mail.nih.gov.,Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA.,Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan.,Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA.,Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM) , ULiège , Quartier Hôpital, Avenue Hippocrate, 15, B36 , B-4000 Liège , Belgium.,Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland.,CryoEM and Bioimaging Division, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025.,Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, USA.,Department of Biological Sciences, Virginia Tech, Derring Hall, Blacksburg, VA 24061, U.S.A.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551.,Department of Bioengineering, Rice University, 6100 Main St., Houston, TX 77005, USA.,Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , DK-2100 Copenhagen , Denmark.,Center for Structural Genomics of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA e-filippova@northwestern.edu wf-anderson@northwestern.edu.,School of Life Sciences, GIST, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea. Electronic address: misunjin@gist.ac.kr.,School of Life Sciences, GIST, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea.,Jacobs University, Bremen, Germany.,Rega Institute for Medical Research and Department of Microbiology and Immunology, Leuven, Belgium.,New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Republic of Korea.,Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases , ULiège , B34, Quartier Hôpital, Avenue de l'hôpital, 11 , B-4000 Liège , Belgium.,Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA.,Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA; Department of Physiology, University of California, Los Angeles, Los Angeles, CA, USA. Electronic address: tgonen@ucla.edu.,School of Life Sciences, Sun Yat-Sen University, 510275 Guangzhou, China.,Department of Biochemistry and Molecular Biology, University of Florida, 1200 Newell Drive, Gainesville, FL 32610, USA.,School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, Hong Kong.,Biozentrum, University of Basel, Basel, Switzerland.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158.,Department of Biochemistry , Brandeis University , Waltham , Massachusetts 02454 , United States.,School of Life Sciences, GIST, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea; Advanced Photonics Research Institute, GIST, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea.,Department of Biochemistry, Virginia Tech, Engel Hall, Blacksburg, VA 24061, U.S.A.,Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland.,Skaggs Institute for Chemical Biology, Scripps Research, La Jolla, California, USA.,Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany.,Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland.,Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland. Electronic address: allain@mol.biol.ethz.ch.,Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA.,School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, Hong Kong; shannon-au@cuhk.edu.hk wahc@stanford.edu.,School of Biological Sciences, Nanyang Technological University, Singapore 637551.,Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea.,Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, Henan, China.,Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.,State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China.,Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK.,Institute of Molecular Medicine, University of Texas Health Science Center at Houston, 6767 Bertner Avenue, Houston, TX 77225, USA.,Institute of Structural Biology, Nanyang Technological University, Singapore 639798.,National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York, USA.,Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA.,Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.,Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland; Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, 3800 VIC, Australia. Electronic address: fionna.loughlin@monash.edu.,Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305.,Department of Bioengineering, Rice University, 6100 Main St., Houston, TX 77005, USA. Electronic address: jsuh@rice.edu.,Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA.,GE Healthcare Life Sciences, Beijing 100176, China.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673.,Department of Immunology and Microbiology, Scripps Research, La Jolla, California, USA.,College of Veterinary Medicine, Jilin University, Changchun 130062, Jilin, China; Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, Henan, China; College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shanxi, China; College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan, China; Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, Jiangsu, China. Electronic address: zhanggaiping2003@163.com.,Department of Immunology and Microbiology, Scripps Research, La Jolla, California, USA erica@scripps.edu.,Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, Illinois, USA.,Keck Biophysics Facility, Northwestern University, Evanston, Illinois, USA.,Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK. Electronic address: d.kelly@sheffield.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Possible TctC subunit of the Tripartite Tricarboxylate Transport(TTT) Family
A, B, C
318Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)Mutation(s): 2 
Find proteins for Q6N446 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009))
Go to UniProtKB:  Q6N446
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLT
Query on MLT

Download SDF File 
Download CCD File 
A, B, C
D-MALATE
(2R)-2-HYDROXYBUTANEDIOIC ACID; 2-HYDROXY-SUCCINIC ACID
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
 Ligand Interaction
LMR
Query on LMR

Download SDF File 
Download CCD File 
A, B, C
(2S)-2-hydroxybutanedioic acid
L-Malate
C4 H6 O5
BJEPYKJPYRNKOW-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 80.800α = 90.00
b = 205.750β = 90.00
c = 47.620γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Brazilian National Council for Scientific and Technological DevelopmentBrazil248597/2013-2

Revision History 

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 2.0: 2019-01-02
    Type: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2019-01-23
    Type: Data collection, Database references