PDBsum entry 1g0e

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Lyase PDB id
Jmol PyMol
Protein chain
258 a.a. *
Waters ×318
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Site-specific mutant (his64 replaced with ala) of human carbonic anhydrase ii complexed with 4-methylimidazole
Structure: Carbonic anhydrase ii. Chain: a. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Tissue: blood. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.60Å     R-factor:   0.179     R-free:   0.200
Authors: D.Duda,R.Mckenna
Key ref:
D.Duda et al. (2001). Structural and kinetic analysis of the chemical rescue of the proton transfer function of carbonic anhydrase II. Biochemistry, 40, 1741-1748. PubMed id: 11327835 DOI: 10.1021/bi002295z
06-Oct-00     Release date:   18-Oct-00    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00918  (CAH2_HUMAN) -  Carbonic anhydrase 2
260 a.a.
258 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Carbonic anhydrase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: H2CO3 = CO2 + H2O
= CO(2)
+ H(2)O
      Cofactor: Zn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 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     6 terms  


    Added reference    
DOI no: 10.1021/bi002295z Biochemistry 40:1741-1748 (2001)
PubMed id: 11327835  
Structural and kinetic analysis of the chemical rescue of the proton transfer function of carbonic anhydrase II.
D.Duda, C.Tu, M.Qian, P.Laipis, M.Agbandje-McKenna, D.N.Silverman, R.McKenna.
Histidine 64 in human carbonic anhydrase II (HCA II) functions in the catalytic pathway of CO(2) hydration as a shuttle to transfer protons between the zinc-bound water and bulk water. Catalysis of the exchange of (18)O between CO(2) and water, measured by mass spectrometry, is dependent on this proton transfer and was decreased more than 10-fold for H64A HCA II compared with wild-type HCA II. The loss of catalytic activity of H64A HCA II could be rescued by 4-methylimidazole (4-MI), an exogenous proton donor, in a saturable process with a maximum activity of 40% of wild-type HCA II. The crystal structure of the rescued complex at 1.6 A resolution shows 4-MI bound in the active-site cavity of H64A HCA II, through pi stacking interactions with Trp 5 and H-bonding interactions with water molecules. In this location, 4-MI is about 12 A from the zinc and approximates the observed "out" position of His 64 in the structure of the wild-type enzyme. 4-MI appears to compensate for the absence of His 64 and rescues the catalytic activity of the H64A HCA II mutant. This result strongly suggests that the out conformation of His 64 is effective in the transfer of protons between the zinc-bound solvent molecule and solution.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21282642 H.M.Becker, M.Klier, C.Schüler, R.McKenna, and J.W.Deitmer (2011).
Intramolecular proton shuttle supports not only catalytic but also noncatalytic function of carbonic anhydrase II.
  Proc Natl Acad Sci U S A, 108, 3071-3076.  
21369613 K.Dave, A.Scozzafava, D.Vullo, C.T.Supuran, and M.A.Ilies (2011).
Pyridinium derivatives of histamine are potent activators of cytosolic carbonic anhydrase isoforms I, II and VII.
  Org Biomol Chem, 9, 2790-2800.  
21036610 K.Dave, M.A.Ilies, A.Scozzafava, C.Temperini, D.Vullo, and C.T.Supuran (2011).
An inhibitor-like binding mode of a carbonic anhydrase activator within the active site of isoform II.
  Bioorg Med Chem Lett, 21, 2764-2768.  
19765680 C.M.Maupin, and G.A.Voth (2010).
Proton transport in carbonic anhydrase: Insights from molecular simulation.
  Biochim Biophys Acta, 1804, 332-341.  
19634894 C.M.Maupin, J.Zheng, C.Tu, R.McKenna, D.N.Silverman, and G.A.Voth (2009).
Effect of active-site mutation at Asn67 on the proton transfer mechanism of human carbonic anhydrase II.
  Biochemistry, 48, 7996-8005.  
19438233 C.M.Maupin, R.McKenna, D.N.Silverman, and G.A.Voth (2009).
Elucidation of the proton transport mechanism in human carbonic anhydrase II.
  J Am Chem Soc, 131, 7598-7608.  
18671353 C.M.Maupin, M.G.Saunders, I.F.Thorpe, R.McKenna, D.N.Silverman, and G.A.Voth (2008).
Origins of enhanced proton transport in the Y7F mutant of human carbonic anhydrase II.
  J Am Chem Soc, 130, 11399-11408.  
18589895 J.Seravalli, and S.W.Ragsdale (2008).
13C NMR characterization of an exchange reaction between CO and CO2 catalyzed by carbon monoxide dehydrogenase.
  Biochemistry, 47, 6770-6781.  
18335973 V.M.Krishnamurthy, G.K.Kaufman, A.R.Urbach, I.Gitlin, K.L.Gudiksen, D.B.Weibel, and G.M.Whitesides (2008).
Carbonic anhydrase as a model for biophysical and physical-organic studies of proteins and protein-ligand binding.
  Chem Rev, 108, 946.  
17319695 C.M.Maupin, and G.A.Voth (2007).
Preferred orientations of His64 in human carbonic anhydrase II.
  Biochemistry, 46, 2938-2947.  
17071654 D.Bhatt, S.Z.Fisher, C.Tu, R.McKenna, and D.N.Silverman (2007).
Location of binding sites in small molecule rescue of human carbonic anhydrase II.
  Biophys J, 92, 562-570.
PDB codes: 2fnk 2fnm 2fnn
17202139 H.Shimahara, T.Yoshida, Y.Shibata, M.Shimizu, Y.Kyogoku, F.Sakiyama, T.Nakazawa, S.Tate, S.Y.Ohki, T.Kato, H.Moriyama, K.Kishida, Y.Tano, T.Ohkubo, and Y.Kobayashi (2007).
Tautomerism of histidine 64 associated with proton transfer in catalysis of carbonic anhydrase.
  J Biol Chem, 282, 9646-9656.  
17427958 I.Elder, Z.Fisher, P.J.Laipis, C.Tu, R.McKenna, and D.N.Silverman (2007).
Structural and kinetic analysis of proton shuttle residues in the active site of human carbonic anhydrase III.
  Proteins, 68, 337-343.
PDB codes: 2hfw 3uyn 3uyq
17429993 J.M.Swanson, C.M.Maupin, H.Chen, M.K.Petersen, J.Xu, Y.Wu, and G.A.Voth (2007).
Proton solvation and transport in aqueous and biomolecular systems: insights from computer simulations.
  J Phys Chem B, 111, 4300-4314.  
16557501 A.Roy, and S.Taraphder (2006).
Proton transfer pathways in the mutant His-64-Ala of human carbonic anhydrase II.
  Biopolymers, 82, 623-630.  
17165785 D.Riccardi, P.König, X.Prat-Resina, H.Yu, M.Elstner, T.Frauenheim, and Q.Cui (2006).
"Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis.
  J Am Chem Soc, 128, 16302-16311.  
16106378 D.Bhatt, C.Tu, S.Z.Fisher, J.A.Hernandez Prada, R.McKenna, and D.N.Silverman (2005).
Proton transfer in a Thr200His mutant of human carbonic anhydrase II.
  Proteins, 61, 239-245.
PDB codes: 1yo0 1yo1 1yo2
15784624 P.Venkataraman, R.A.Lamb, and L.H.Pinto (2005).
Chemical rescue of histidine selectivity filter mutants of the M2 ion channel of influenza A virus.
  J Biol Chem, 280, 21463-21472.  
14512428 T.K.Kim, P.Lee, and R.F.Colman (2003).
Critical role of Lys212 and Tyr140 in porcine NADP-dependent isocitrate dehydrogenase.
  J Biol Chem, 278, 49323-49331.  
12171926 C.Tu, M.Qian, H.An, N.R.Wadhwa, D.Duda, C.Yoshioka, Y.Pathak, R.McKenna, P.J.Laipis, and D.N.Silverman (2002).
Kinetic analysis of multiple proton shuttles in the active site of human carbonic anhydrase.
  J Biol Chem, 277, 38870-38876.
PDB code: 1lzv
11863462 H.An, C.Tu, D.Duda, I.Montanez-Clemente, K.Math, P.J.Laipis, R.McKenna, and D.N.Silverman (2002).
Chemical rescue in catalysis by human carbonic anhydrases II and III.
  Biochemistry, 41, 3235-3242.  
12009884 M.Ferraroni, S.Tilli, F.Briganti, W.R.Chegwidden, C.T.Supuran, K.E.Wiebauer, R.E.Tashian, and A.Scozzafava (2002).
Crystal structure of a zinc-activated variant of human carbonic anhydrase I, CA I Michigan 1: evidence for a second zinc binding site involving arginine coordination.
  Biochemistry, 41, 6237-6244.
PDB codes: 1j9w 1jv0
11493685 D.A.Whittington, A.Waheed, B.Ulmasov, G.N.Shah, J.H.Grubb, W.S.Sly, and D.W.Christianson (2001).
Crystal structure of the dimeric extracellular domain of human carbonic anhydrase XII, a bitopic membrane protein overexpressed in certain cancer tumor cells.
  Proc Natl Acad Sci U S A, 98, 9545-9550.
PDB codes: 1jcz 1jd0
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 codes are shown on the right.