5Y2R

2.5 atm CO2-pressurized human carbonic anhydrase II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.131 
  • R-Value Work: 0.114 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Active-site solvent replenishment observed during human carbonic anhydrase II catalysis.

Kim, J.K.Lomelino, C.L.Avvaru, B.S.Mahon, B.P.McKenna, R.Park, S.Kim, C.U.

(2018) IUCrJ 5: 93-102

  • DOI: 10.1107/S2052252517017626
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human carbonic anhydrase II (hCA II) is a zinc metalloenzyme that catalyzes the reversible hydration/dehydration of CO <sub>2 </sub>/HCO <sub>3 </sub> <sup>- </sup>. Although hCA II has been extensively studied to investigate the proton-transfer proc ...

    Human carbonic anhydrase II (hCA II) is a zinc metalloenzyme that catalyzes the reversible hydration/dehydration of CO 2 /HCO 3 - . Although hCA II has been extensively studied to investigate the proton-transfer process that occurs in the active site, its underlying mechanism is still not fully understood. Here, ultrahigh-resolution crystallographic structures of hCA II cryocooled under CO 2 pressures of 7.0 and 2.5 atm are presented. The structures reveal new intermediate solvent states of hCA II that provide crystallographic snapshots during the restoration of the proton-transfer water network in the active site. Specifically, a new intermediate water (W I ') is observed next to the previously observed intermediate water W I , and they are both stabilized by the five water molecules at the entrance to the active site (the entrance conduit). Based on these structures, a water network-restructuring mechanism is proposed, which takes place at the active site after the nucleophilic attack of OH - on CO 2 . This mechanism explains how the zinc-bound water (W Zn ) and W1 are replenished, which are directly responsible for the reconnection of the His64-mediated proton-transfer water network. This study provides the first 'physical' glimpse of how a water reservoir flows into the hCA II active site during its catalytic activity.


    Organizational Affiliation

    Department Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Campus E8.1, 66123, Saarbrücken, Germany.,Department of Chemistry, University of Florence, I-50019 Sesto Fiorentino (FI), Italy.,Department of Chemistry and Industrial Chemistry, University of Pisa, I-56126 Pisa, Italy.,Department of Pharmacology, Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Biochemistry and Molecular Biology, College of Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA.,Department of Chemistry, University of Texas, Edinburgh, TX, USA.,Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Moscow, Russian Federation.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.,Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil.,Tumor Microenvironment and Resistance to Treatment Lab, Institut de Recherche en Cancrologie de Montpellier, 34090 Montpellier, France; Institut du Cancer Montpellier, 34090 Montpellier, France; Universit Montpellier, 34298 Montpellier, France.,Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110 067, India.,Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany; Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany.,Biological Science Imaging Resource, Department of Biological Sciences, The Florida State University, 89 Chieftan Way, Rm 119, Tallahassee, FL 32306, USA.,Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA; Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.,Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA.,Department of Physics, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea.,Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA; Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL 60637, USA.,Institute of Integrative Biology, University of Liverpool, Liverpool, U.K.,Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.,Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.,School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211800, China.,Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA; Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA; Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL 60637, USA.,Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China; Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.,Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA; Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA. Electronic address: roger.b.sutton@ttuhsc.edu.,Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.,Université de Lorraine, INRA, IAM, Nancy, France.,Institute of Medical Virology, Justus Liebig University, Giessen, Germany. Electronic address: john.ziebuhr@viro.med.uni-giessen.de.,Department of Chemistry, University of California, Davis, CA, USA jbames@ucdavis.edu jwhell@ucdavis.edu.,Faculty of Biotechnology, University of Wrocław, Wrocław, Poland.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Dept. Pharmacokinetics, Toxicology and Targeting, Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands.,Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany.,Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China. Electronic address: wuzhl@cib.ac.cn.,Department of Biochemistry and Molecular Biology, College of Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA. Electronic address: mckenna@ufl.edu.,Centre of Excellence in Biocrystallography, Department of Chemical and Pharmaceutical Sciences, University of Trieste, via L. Giorgeri 1, 34127 Trieste, Italy.,Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.,Faculty of Biotechnology, University of Wrocław, Wrocław, Poland teresa.olczak@uwr.edu.pl.,Lille University, UMR8576, CNRS, 59000, Lille, France.,Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA; Natural Products Library Initiative at The Scripps Research Institute, The Scripps Research Institute, Jupiter, FL 33458, USA. Electronic address: shenb@scripps.edu.,Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA; Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA.,Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; john.rubinstein@utoronto.ca kay@pound.med.utoronto.ca.,Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany; Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany. Electronic address: wibke.diederich@staff.uni-marburg.de.,Centre of Excellence in Biocrystallography, Department of Chemical and Pharmaceutical Sciences, University of Trieste, via L. Giorgeri 1, 34127 Trieste, Italy. Electronic address: sgeremia@units.it.,Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Campus E8.1, 66123, Saarbrücken, Germany.,The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia; EMBL Australia, Monash University, Clayton, Victoria 3800, Australia.,Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.,Department of Molecular Genetics and Microbiology and Powell Gene Therapy Center, College of Medicine, University of Florida, Gainesville, FL 32610, USA.,School of Dentistry, Institute of Clinical Sciences, University of Liverpool, Liverpool, U.K.,Molecular Biology and Biochemistry, University of California Irvine, McGaugh Hall, Irvine, CA 92697-3900, USA.,Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China. Electronic address: wangg@cib.ac.cn.,Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21205, USA.,Institute of Medical Virology, Justus Liebig University, Giessen, Germany.,Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany.,Department of Pharmacy, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany.,Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China; University of Chinese Academy of Sciences, Beijing, 100049, China.,Department of Pharmacology, University of California, Davis, CA, USA.,Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom.,Department Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany.,Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI, 53705, USA; Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, 53705, USA.,Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil. Electronic address: marcos.fontes@unesp.br.,Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil.,Department of Biochemistry and Molecular Biology, and Department of Cancer Biology, University of Kansas Medical Center, 3901 Rainbow Blvd Mail Stop #3030, Kansas City, KS 66160, USA.,Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, P.O. Box 12233, Research Triangle Park, NC 27709-2233, USA.,School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea.,School of Biological Sciences, University of Essex, Colchester, U.K.,Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstrasse 7, 38106, Braunschweig, Germany.,Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil; Departamento de Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil.,Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, 53705, USA.,Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany; The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia; EMBL Australia, Monash University, Clayton, Victoria 3800, Australia. Electronic address: Max.Cryle@monash.edu.,Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA.,Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA.,Université de Lorraine, CNRS, CRM2, Nancy, France.,Department of Chemistry, University of California, Davis, CA, USA.,Department of Pharmacology, University of California, Davis, CA, USA jbames@ucdavis.edu jwhell@ucdavis.edu.,Departamento de Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil.,Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.,Department of Chemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; john.rubinstein@utoronto.ca kay@pound.med.utoronto.ca.,Lille University, UMR8576, CNRS, 59000, Lille, France. isabelle.landrieu@univ-lille1.fr.,Moscow Institute of Physics and Technology, Institutsky per., Dolgoprudnyi, Russian Federation.,BioSciences at Rice and Department of Chemistry, Rice University, Houston, TX 77251, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase 2
A
260Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens)
Go to Gene View: CA2
Go to UniProtKB:  P00918
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-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
CO2
Query on CO2

Download SDF File 
Download CCD File 
A
CARBON DIOXIDE
C O2
CURLTUGMZLYLDI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.131 
  • R-Value Work: 0.114 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.279α = 90.00
b = 41.406β = 104.16
c = 72.109γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-07-27 
  • Released Date: 2018-02-14 
  • Deposition Author(s): Kim, C.U., Park, S.Y.

Funding OrganizationLocationGrant Number
National Research Foundation of KoreaKorea, Republic Of2014R1A2A1A11051254
National Research Foundation of KoreaKorea, Republic Of2016R1A5A1013277
National Research Foundation of KoreaKorea, Republic Of2016R1D1A1A09918187

Revision History 

  • Version 1.0: 2018-02-14
    Type: Initial release