PDBsum entry 2nxs

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Lyase PDB id
Jmol PyMol
Protein chain
258 a.a. *
Waters ×114
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Structural and kinetic effects of hydrophobic mutations in the active site of human carbonic anhydrase ii
Structure: Carbonic anhydrase 2. Chain: a. Synonym: carbonic anhydrase ii, carbonate dehydratase ii, ca-ii, carbonic anhydrasE C. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: ca2. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
1.80Å     R-factor:   0.178     R-free:   0.200
Authors: S.Z.Fisher,R.Mckenna
Key ref: S.Z.Fisher et al. (2007). Speeding up proton transfer in a fast enzyme: kinetic and crystallographic studies on the effect of hydrophobic amino acid substitutions in the active site of human carbonic anhydrase II. Biochemistry, 46, 3803-3813. PubMed id: 17330962
19-Nov-06     Release date:   24-Apr-07    
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    
Biochemistry 46:3803-3813 (2007)
PubMed id: 17330962  
Speeding up proton transfer in a fast enzyme: kinetic and crystallographic studies on the effect of hydrophobic amino acid substitutions in the active site of human carbonic anhydrase II.
S.Z.Fisher, C.Tu, D.Bhatt, L.Govindasamy, M.Agbandje-McKenna, R.McKenna, D.N.Silverman.
Catalysis of the hydration of CO2 by human carbonic anhydrase isozyme II (HCA II) is sustained at a maximal catalytic turnover of 1 mus-1 by proton transfer between a zinc-bound solvent and bulk solution. This mechanism of proton transfer is facilitated via the side chain of His64, which is located 7.5 A from the zinc, and mediated via intervening water molecules in the active-site cavity. Three hydrophilic residues that have previously been shown to contribute to the stabilization of these intervening waters were replaced with hydrophobic residues (Y7F, N62L, and N67L) to determine their effects on proton transfer. The structures of all three mutants were determined by X-ray crystallography, with crystals equilibrated from pH 6.0 to 10.0. A range of changes were observed in the ordered solvent and the conformation of the side chain of His64. Correlating these structural variants with kinetic studies suggests that the very efficient proton transfer (approximately 7 micros-1) observed for Y7F HCA II in the dehydration direction, compared with the wild type and other mutants of this study, is due to a combination of three features. First, in this mutant, the side chain of His64 showed an appreciable inward orientation pointing toward the active-site zinc. Second, in the structure of Y7F HCA II, there is an unbranched chain of hydrogen-bonded waters linking the proton donor His64 and acceptor zinc-bound hydroxide. Finally, the difference in pKa of the donor and acceptor appears favorable for proton transfer. The data suggest roles for residues 7, 62, and 67 in fine-tuning the properties of His64 for optimal proton transfer in catalysis.

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.  
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
19765680 C.M.Maupin, and G.A.Voth (2010).
Proton transport in carbonic anhydrase: Insights from molecular simulation.
  Biochim Biophys Acta, 1804, 332-341.  
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.  
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
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.  
  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.  
18175010 A.C.O'Donoghue, T.L.Amyes, and J.P.Richard (2008).
Slow proton transfer from the hydrogen-labelled carboxylic acid side chain (Glu-165) of triosephosphate isomerase to imidazole buffer in D(2)O.
  Org Biomol Chem, 6, 391-396.  
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.  
18942852 J.Zheng, B.S.Avvaru, C.Tu, R.McKenna, and D.N.Silverman (2008).
Role of hydrophilic residues in proton transfer during catalysis by human carbonic anhydrase II.
  Biochemistry, 47, 12028-12036.
PDB codes: 3dv7 3dvb 3dvc 3dvd
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.  
18322527 Y.Xu, L.Feng, P.D.Jeffrey, Y.Shi, and F.M.Morel (2008).
Structure and metal exchange in the cadmium carbonic anhydrase of marine diatoms.
  Nature, 452, 56-61.
PDB codes: 3bob 3boc 3boe 3boh 3boj
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.