PDBsum entry 1moo

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Lyase PDB id
Protein chain
256 a.a. *
4MZ ×2
Waters ×308
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Site specific mutant (h64a) of human carbonic anhydrase ii at high resolution
Structure: Carbonic anhydrase ii. Chain: a. Synonym: carbonate dehydratase ii, ca-ii, carbonic anhydrasE C. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.05Å     R-factor:   0.157     R-free:   0.177
Authors: D.M.Duda,L.Govindasamy,M.Agbandje-Mckenna,C.K.Tu, D.N.Silverman,R.Mckenna
Key ref:
D.Duda et al. (2003). The refined atomic structure of carbonic anhydrase II at 1.05 A resolution: implications of chemical rescue of proton transfer. Acta Crystallogr D Biol Crystallogr, 59, 93. PubMed id: 12499545
09-Sep-02     Release date:   18-Sep-02    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00918  (CAH2_HUMAN) -  Carbonic anhydrase 2
260 a.a.
256 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.  - Carbonate dehydratase.
[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   21 terms 
  Biochemical function     protein binding     5 terms  


    Added reference    
Acta Crystallogr D Biol Crystallogr 59:93 (2003)
PubMed id: 12499545  
The refined atomic structure of carbonic anhydrase II at 1.05 A resolution: implications of chemical rescue of proton transfer.
D.Duda, L.Govindasamy, M.Agbandje-McKenna, C.Tu, D.N.Silverman, R.McKenna.
Using synchrotron radiation and a CCD detector, X-ray data have been collected at 100 K for the His64Ala mutant of human carbonic anhydrase II complexed with 4-methylimidazole (4-MI) to a maximal 1.05 A resolution, allowing full anisotropic least-squares refinement. The refined model has a conventional R factor of 15.7% for all reflections. The C(alpha) coordinates of the model presented here have an r.m.s. deviation of 0.10 A relative to the previously determined structure at 1.6 A resolution. Several amino-acid residues (six of the 255 observed) have been identified with multiple rotamer side-chain conformations. C, N and O atoms can be differentiated with selective electron-density map contouring. The estimated standard deviations for all main-chain non-H atom bond lengths and angles are 0.013 and 0.030 A, respectively, based on unrestrained full-matrix least-squares refinement. This structure gives detailed information about the tetrahedrally arranged zinc ion coordinated by three histidine N atoms (His94 N(epsilon 2), His96 N(epsilon2) and His119 N(delta1)) and a water/hydroxide, the multiple binding sites of the proton chemical rescue molecule 4-MI and the solvent networks linking the zinc-bound water/hydroxide and 4-MI molecules. This structure presents the highest resolution structure of a carbonic anhydrase isozyme so far determined and adds to the understanding of proton-transfer processes.

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
  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.  
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.  
19036170 F.Bootorabi, J.Jänis, J.Valjakka, S.Isoniemi, P.Vainiotalo, D.Vullo, C.T.Supuran, A.Waheed, W.S.Sly, O.Niemelä, and S.Parkkila (2008).
Modification of carbonic anhydrase II with acetaldehyde, the first metabolite of ethanol, leads to decreased enzyme activity.
  BMC Biochem, 9, 32.  
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
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.  
  16511248 M.Budayova-Spano, S.Z.Fisher, M.T.Dauvergne, M.Agbandje-McKenna, D.N.Silverman, D.A.Myles, and R.McKenna (2006).
Production and X-ray crystallographic analysis of fully deuterated human carbonic anhydrase II.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 6-9.
PDB code: 2ax2
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.  
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.