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PDBsum entry 1yo2

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protein metals links
Lyase PDB id
1yo2
Jmol PyMol
Contents
Protein chain
258 a.a. *
Metals
_ZN
Waters ×93
* Residue conservation analysis
PDB id:
1yo2
Name: Lyase
Title: Proton transfer from his200 in human carbonic anhydrase ii
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. Gene: ca2. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.80Å     R-factor:   0.168     R-free:   0.201
Authors: D.Bhatt,C.Tu,S.Z.Fisher,J.A.Hernandez Prada,R.Mckenna, D.N.Silverman
Key ref:
D.Bhatt et al. (2005). Proton transfer in a Thr200His mutant of human carbonic anhydrase II. Proteins, 61, 239-245. PubMed id: 16106378 DOI: 10.1002/prot.20615
Date:
26-Jan-05     Release date:   20-Sep-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

 Enzyme reactions 
   Enzyme class: E.C.4.2.1.1  - Carbonic anhydrase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: H2CO3 = CO2 + H2O
H(2)CO(3)
= 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: 10.1002/prot.20615 Proteins 61:239-245 (2005)
PubMed id: 16106378  
 
 
Proton transfer in a Thr200His mutant of human carbonic anhydrase II.
D.Bhatt, C.Tu, S.Z.Fisher, J.A.Hernandez Prada, R.McKenna, D.N.Silverman.
 
  ABSTRACT  
 
Human carbonic anhydrase II (HCA II) has a histidine at position 64 (His64) that donates a proton to the zinc-bound hydroxide in catalysis of the dehydration of bicarbonate. To examine the effect of the histidine location on proton shuttling, His64 was replaced with Ala and Thr200 replaced with histidine (H64A-T200H HCAII), effectively relocating the proton shuttle residue 2 A closer to the zinc-bound hydroxide compared to wild type HCA II. The crystal structure of H64A-T200H HCA II at 1.8 A resolution shows the side chain of His200 directly hydrogen-bonded with the zinc-bound solvent. Different proton transfer processes were observed at pH 6 and at pH 8 during the catalytic hydration-dehydration cycle, measured by mass spectrometry as the depletion of 18O from C18O2 by H64A-T200H HCA II. The process at pH 6.0 is attributed to proton transfer between the side chain of His200 and the zinc-bound hydroxide, in analogy with proton transfer involving His64 in wild-type HCA II. At pH 8.0 it is attributed to proton transfer between bicarbonate and the zinc-bound hydroxide, as supported by the dependence of the rate of proton transfer on bicarbonate concentration and on solvent hydrogen isotope effects. This study establishes that a histidine directly hydrogen-bonded to the zinc-bound hydroxide, can adopt the correct distance geometry to support proton transfer
 
  Selected figure(s)  
 
Figure 4.
Figure 4. The pH profile of the logarithm of k[cat]/K[m] (M^-1s^-1) for hydration of CO[2] catalyzed by H64A HCA II ( ), and H64A-T200H HCA II ( ). Experimental conditions were as described in Figure 1. For H64A-T200H HCA II the solid line is a fit to two ionizations (Equation 6) with pK[a1] = 5.8 ± 0.4 and pK[a2] = 8.0 ± 0.4. For H64A HCA II the data are fit to a single ionization with pK[a] = 6.9 ± 0.1.
Figure 5.
Figure 5. The structure of the active site of H64A-T200H HCA II crystallized at pH 9.3. His94, His96, and His 119 and the zinc-bound solvent, W262, are direct ligands of the zinc. The dotted red lines indicate plausible hydrogen-bonds. The distance from W262 to ND1 His200 is 3.1 Å, from W262 to OG1 Thr199 is 2.7 Å, fromW387 to ND1 His200 is 3.1 Å, from W387 to W363 is 2.8 Å and from W363 to ND2 Gln67 is 2.8 Å. Electron density (2F[o] - F[c]) contoured at 1.5 (blue) is shown for His200, Zn^2+, W262, W363, and W387. Superimposed on Ala64 is the in orientation of the side chain of the proton shuttle residue His64 of wild-type HCA II.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2005, 61, 239-245) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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.

 

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