5MBZ

Crystal Structure of Ser202Phe mutant of Human Prolidase with Mn ions and GlyPro ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for prolidase deficiency disease mechanisms.

Wilk, P.Uehlein, M.Piwowarczyk, R.Dobbek, H.Mueller, U.Weiss, M.S.

(2018) FEBS J. 285: 3422-3441

  • DOI: 10.1111/febs.14620
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Prolidase is a metallopeptidase that cleaves iminodipeptides containing a proline (Pro) or hydroxyproline (Hyp) residue at their C-terminal end. The disease prolidase deficiency (PD) is a rare recessive human disorder characterized by reduced prolida ...

    Prolidase is a metallopeptidase that cleaves iminodipeptides containing a proline (Pro) or hydroxyproline (Hyp) residue at their C-terminal end. The disease prolidase deficiency (PD) is a rare recessive human disorder characterized by reduced prolidase activity. PD manifests itself by a wide range of severe clinical symptoms, most commonly as skin ulceration, recurrent infections of the respiratory tract, and mental retardation. Several mutations in the PEPD gene have been identified that are responsible for the loss or the reduction of prolidase activity. In contrast, the structural basis of enzyme inactivation has so far remained elusive. In this study, we present high resolution crystal structures of a number of human prolidase (HsProl) variants, in which single amino acids are either substituted by others or deleted. The observed implications of the mutations on the three-dimensional structure of HsProl are reported and discussed and related to their enzymatic activity. The resulting structures may be divided into four groups depending on the presumed effect of the corresponding mutations on the reaction mechanism. The four possible inactivation mechanisms, which could be elucidated, are disruption of the catalytic Mn 2 (OH - )-center, introduction of chain disorder along with the displacement of important active site residues, rigidification of the active site, and flexibilization of the active site.


    Organizational Affiliation

    Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Division of Hematology, Department of Medicine, The Ohio State University, Columbus, Ohio. rosa.lapalombella@osumc.edu john.byrd@osumc.edu.,Novartis Institutes for Biomedical Research, Cambridge, MA, 02139, USA. Michael.Acker@novartis.com.,The RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sato-gun, Hyogo, 678-5248, Japan.,Plexxikon Inc., Berkeley, California.,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK.,Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden.,Department of Hematology, Hôpital Necker, Assistance Publique Hôpitaux de Paris, University Paris Descartes, 75006 Paris, France.,INSERM U1163 and CNRS 8254, Imagine Institute, Université Sorbonne Paris Cité, Paris, France.,Northern Institute for Cancer Research, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden.,Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.,Departments of Biochemistry and Biophysics and Neurochemistry, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden.,Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA.,Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.,INSERM U944, Institute of Hematology, St. Louis Hospital, 75010 Paris, France.,Department of Picobiology/Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo, 678-1297, Japan.,Department of Food Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea.,Promega Corporation, 2800 Woods Hollow Road, Madison, WI 53711, USA.,Xtal BioStructures Inc., Natick, MA 01760, USA.,Queensland Brain Institute, The University of Queensland, St. Lucia, QLD 4072, Australia.,Sheffield Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK.,Department of Pharmacology, Monash University, Clayton, VIC 3800, Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3083, Australia. Electronic address: M.Maher@latrobe.edu.au.,Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands. b.j.c.janssen@uu.nl.,Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea.,Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Germany.,Northern Institute for Cancer Research, Medical School , Newcastle University , Paul O'Gorman Building, Framlington Place , Newcastle upon Tyne NE2 4HH , U.K.,Laboratoire des biomolécules, LBM, Département de chimie , École normale supérieure, PSL University, Sorbonne Université, CNRS , 75005 Paris , France.,Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.,INSERM U1163 and CNRS 8254, Imagine Institute, Université Paris Saclay, 91190 Paris, France.,Novartis Institutes for BioMedical Research , Cambridge , Massachusetts 02139 , United States.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA.,Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands.,Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA.,School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.,4Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA.,Beijing Advanced Innovation Center for Structural Biology, Beijing, 100084 China.,Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio.,Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA. fwagner@broadinstitute.org kimberly_stegmaier@dfci.harvard.edu.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. Stephen_Blacklow@hms.harvard.edu.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.,Helmholtz-Zentrum Berlin, Macromolecular Crystallography (HZB-MX), Germany.,College of Veterinary Medicine, The Ohio State University, Columbus, Ohio.,Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK g.l.challis@warwick.ac.uk.,State Key Laboratory of Membrane Biology, Beijing, 100084 China.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.,Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Okayama, 700-8530, Japan.,Center for Biostatistics, The Ohio State University, Columbus, Ohio.,Division of Hematology, Department of Medicine, The Ohio State University, Columbus, Ohio.,3Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, 100084 China.,Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.,5Present Address: Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA. fwagner@broadinstitute.org kimberly_stegmaier@dfci.harvard.edu.,Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; l.rash@uq.edu.au glenn.king@imb.uq.edu.au.,Department of Pathology, St. Olavs Hospital, Trondheim, Norway.,Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Novartis Institutes for Biomedical Research, Cambridge, MA, 02139, USA.,School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD 4072, Australia.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France.,Centre for Advanced Imaging, The University of Queensland, St. Lucia, QLD 4072, Australia.,Novartis Institutes for BioMedical Research , Novartis Campus , CH-4056 Basel , Switzerland.,Cayman Chemical Co., Ann Arbor, MI 48108, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3083, Australia.,LCM, CNRS, Ecole Polytechnique , Université Paris-Saclay , 91128 Palaiseau Cedex , France.,Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA. Stephen_Blacklow@hms.harvard.edu.,Institute of Cellular and Molecular Radiobiology, Institut François Jacob, CEA, Universités Paris Diderot and Paris-Sud, Fontenay aux Roses, France.,Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea. Electronic address: jsunkim@chonnam.ac.kr.,Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Xaa-Pro dipeptidase
A, B
484Homo sapiensMutation(s): 1 
Gene Names: PEPD (PRD)
EC: 3.4.13.9
Find proteins for P12955 (Homo sapiens)
Go to Gene View: PEPD
Go to UniProtKB:  P12955
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
GLY
Query on GLY

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Download CCD File 
A, B
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
OH
Query on OH

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Download CCD File 
A, B
HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
 Ligand Interaction
PRO
Query on PRO

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Download CCD File 
A, B
PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 103.785α = 90.00
b = 106.945β = 90.00
c = 216.316γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-08-15
    Type: Data collection, Database references
  • Version 1.2: 2018-09-26
    Type: Data collection, Database references