PDBsum entry 3d93

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protein ligands links
Lyase PDB id
Protein chain
257 a.a. *
CO2 ×2
Waters ×352
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Apo human carbonic anhydrase ii bound with substrate carbon
Structure: Carbonic anhydrase ii. Chain: a. Synonym: carbonic anhydrase 2, carbonate dehydratase ii, ca carbonic anhydrasE C, cac. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: hca2. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.10Å     R-factor:   0.104     R-free:   0.139
Authors: J.F.Domsic,B.S.Avvaru,R.Mckenna
Key ref:
J.F.Domsic et al. (2008). Entrapment of carbon dioxide in the active site of carbonic anhydrase II. J Biol Chem, 283, 30766-30771. PubMed id: 18768466 DOI: 10.1074/jbc.M805353200
26-May-08     Release date:   02-Sep-08    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00918  (CAH2_HUMAN) -  Carbonic anhydrase 2
260 a.a.
257 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular space   11 terms 
  Biological process     angiotensin-mediated signaling pathway   22 terms 
  Biochemical function     protein binding     5 terms  


DOI no: 10.1074/jbc.M805353200 J Biol Chem 283:30766-30771 (2008)
PubMed id: 18768466  
Entrapment of carbon dioxide in the active site of carbonic anhydrase II.
J.F.Domsic, B.S.Avvaru, C.U.Kim, S.M.Gruner, M.Agbandje-McKenna, D.N.Silverman, R.McKenna.
The visualization at near atomic resolution of transient substrates in the active site of enzymes is fundamental to fully understanding their mechanism of action. Here we show the application of using CO(2)-pressurized, cryo-cooled crystals to capture the first step of CO(2) hydration catalyzed by the zinc-metalloenzyme human carbonic anhydrase II, the binding of substrate CO(2), for both the holo and the apo (without zinc) enzyme to 1.1A resolution. Until now, the feasibility of such a study was thought to be technically too challenging because of the low solubility of CO(2) and the fast turnover to bicarbonate by the enzyme (Liang, J. Y., and Lipscomb, W. N. (1990) Proc. Natl. Acad. Sci. U. S. A. 87, 3675-3679). These structures provide insight into the long hypothesized binding of CO(2) in a hydrophobic pocket at the active site and demonstrate that the zinc does not play a critical role in the binding or orientation of CO(2). This method may also have a much broader implication for the study of other enzymes for which CO(2) is a substrate or product and for the capturing of transient substrates and revealing hydrophobic pockets in proteins.
  Selected figure(s)  
Figure 1.
hCAII structure. a, overall view, showing the hydrophilic (magenta stick representation) and hydrophobic (green surface representation) sides of the active site. The active site zinc is shown in purple with the waters of the proton wire shown as small, red spheres. b and c, a close-up stereo view of the active site showing the position of bound CO[2] in holo- (b) and apohCAII (c). Electron density of the active site amino acids and W[I] (σ-weighted 2F[o] - F[c] Fourier map contoured at 2.25 σ) and CO[2] (σ-weighted F[o] - F[c] Fourier map contoured at 2.25 σ). The figure was created using PyMOL.
Figure 6.
Proposed catalytic mechanism of hCAII. A schematic representation of three discrete stages of the catalytic cycle is shown. a, unbound. Note the presence of deep water (W[DW]). b, CO[2] bound. Note the displacement of W[DW] and the hydrogen bond between the substrate and backbone amide of Thr-199. c, the formation of bicarbonate. The figure was created using ChemDraw 11.0 (available from CambridgeSoft).
  The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2008, 283, 30766-30771) copyright 2008.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21169696 U.Englich, I.A.Kriksunov, R.A.Cerione, M.J.Cook, R.Gillilan, S.M.Gruner, Q.Huang, C.U.Kim, W.Miller, S.Nielsen, D.Schuller, S.Smith, and D.M.Szebenyi (2011).
Microcrystallography, high-pressure cryocooling and BioSAXS at MacCHESS.
  J Synchrotron Radiat, 18, 70-73.  
20445238 A.H.Robbins, J.F.Domsic, M.Agbandje-McKenna, and R.McKenna (2010).
Structure of a monoclinic polymorph of human carbonic anhydrase II with a doubled a axis.
  Acta Crystallogr D Biol Crystallogr, 66, 628-634.
PDB code: 3ks1
20000378 B.S.Avvaru, C.U.Kim, K.H.Sippel, S.M.Gruner, M.Agbandje-McKenna, D.N.Silverman, and R.McKenna (2010).
A short, strong hydrogen bond in the active site of human carbonic anhydrase II.
  Biochemistry, 49, 249-251.
PDB code: 3ks3
20445237 C.A.Behnke, I.Le Trong, J.W.Godden, E.A.Merritt, D.C.Teller, J.Bajorath, and R.E.Stenkamp (2010).
Atomic resolution studies of carbonic anhydrase II.
  Acta Crystallogr D Biol Crystallogr, 66, 616-627.
PDB codes: 1lug 3k34
20922253 F.Pacchiano, M.Aggarwal, B.S.Avvaru, A.H.Robbins, A.Scozzafava, R.McKenna, and C.T.Supuran (2010).
Selective hydrophobic pocket binding observed within the carbonic anhydrase II active site accommodate different 4-substituted-ureido-benzenesulfonamides and correlate to inhibitor potency.
  Chem Commun (Camb), 46, 8371-8373.
PDB codes: 3mzc 3n0n 3n2p 3n3j 3n4b
19679198 J.F.Domsic, and R.McKenna (2010).
Sequestration of carbon dioxide by the hydrophobic pocket of the carbonic anhydrases.
  Biochim Biophys Acta, 1804, 326-331.  
20629007 J.Schulze Wischeler, A.Innocenti, D.Vullo, A.Agrawal, S.M.Cohen, A.Heine, C.T.Supuran, and G.Klebe (2010).
Bidentate Zinc chelators for alpha-carbonic anhydrases that produce a trigonal bipyramidal coordination geometry.
  ChemMedChem, 5, 1609-1615.
PDB code: 3m1k
19679199 R.L.Mikulski, and D.N.Silverman (2010).
Proton transfer in catalysis and the role of proton shuttles in carbonic anhydrase.
  Biochim Biophys Acta, 1804, 422-426.  
20025241 S.Z.Fisher, A.Y.Kovalevsky, J.F.Domsic, M.Mustyakimov, R.McKenna, D.N.Silverman, and P.A.Langan (2010).
Neutron structure of human carbonic anhydrase II: implications for proton transfer.
  Biochemistry, 49, 415-421.
PDB code: 3kkx
19583303 B.S.Avvaru, S.A.Busby, M.J.Chalmers, P.R.Griffin, B.Venkatakrishnan, M.Agbandje-McKenna, D.N.Silverman, and R.McKenna (2009).
Apo-human carbonic anhydrase II revisited: implications of the loss of a metal in protein structure, stability, and solvent network.
  Biochemistry, 48, 7365-7372.
PDB code: 3gz0
19520834 B.Sjöblom, M.Polentarutti, and K.Djinovic-Carugo (2009).
Structural study of X-ray induced activation of carbonic anhydrase.
  Proc Natl Acad Sci U S A, 106, 10609-10613.
PDB codes: 2vva 2vvb
  19851004 K.H.Sippel, A.H.Robbins, J.Domsic, C.Genis, M.Agbandje-McKenna, and R.McKenna (2009).
High-resolution structure of human carbonic anhydrase II complexed with acetazolamide reveals insights into inhibitor drug design.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 992-995.
PDB code: 3hs4
  19407386 S.Z.Fisher, A.Y.Kovalevsky, J.F.Domsic, M.Mustyakimov, D.N.Silverman, R.McKenna, and P.Langan (2009).
Preliminary joint neutron and X-ray crystallographic study of human carbonic anhydrase II.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 495-498.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.