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PDBsum entry 3uyn

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protein metals links
Lyase PDB id
3uyn
Jmol
Contents
Protein chain
259 a.a.
Metals
_ZN
Waters ×53
PDB id:
3uyn
Name: Lyase
Title: Hca 3
Structure: Carbonic anhydrase 3. Chain: a. Synonym: carbonate dehydratase iii, carbonic anhydrase iii, engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: ca3. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.60Å     R-factor:   0.206     R-free:   0.201
Authors: Z.Fisher,R.Mckenna
Key ref:
I.Elder et al. (2007). Structural and kinetic analysis of proton shuttle residues in the active site of human carbonic anhydrase III. Proteins, 68, 337-343. PubMed id: 17427958 DOI: 10.1002/prot.21403
Date:
06-Dec-11     Release date:   01-Feb-12    
Supersedes: 2hfy
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P07451  (CAH3_HUMAN) -  Carbonic anhydrase 3
Seq:
Struc:
260 a.a.
259 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.4.2.1.1  - Carbonate dehydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: H2CO3 = CO2 + H2O
H(2)CO(3)
= CO(2)
+ H(2)O
      Cofactor: Zinc
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     small molecule metabolic process   5 terms 
  Biochemical function     lyase activity     5 terms  

 

 
    Added reference    
 
 
DOI no: 10.1002/prot.21403 Proteins 68:337-343 (2007)
PubMed id: 17427958  
 
 
Structural and kinetic analysis of proton shuttle residues in the active site of human carbonic anhydrase III.
I.Elder, Z.Fisher, P.J.Laipis, C.Tu, R.McKenna, D.N.Silverman.
 
  ABSTRACT  
 
We report the X-ray crystal structures and rate constants for proton transfer in site-specific mutants of human carbonic anhydrase III (HCA III) that place a histidine residue in the active-site cavity: K64H, R67H, and K64H-R67N HCA III. Prior evidence from the exchange of 18O between CO2 and water measured by mass spectrometry shows each mutant to have enhanced proton transfer in catalysis compared with wild-type HCA III. However, His64 in K64H and K64H-R67N HCA III have at most a capacity for proton transfer that is only 13% that of His64 in HCA II. This reduced rate in mutants of HCA III is associated with a constrained side-chain conformation of His64, which is oriented outward, away from the active-site zinc in the crystal structures. This conformation appears stabilized by a prominent pi stacking interaction of the imidazole ring of His64 with the indole ring of Trp5 in mutants of HCA III. This single orientation of His64 in K64H HCA III predominates also in a double mutant K64H-R67N HCA III, indicating that the positive charge of Arg67 does not influence the observed conformation of His64 in the crystal structure. Hence, the structures and catalytic activity of these mutants of HCA III containing His64 account only in small part for the lower activity of this isozyme compared with HCA II. His67 in R67H HCA III was also shown to be a proton shuttle residue, having a capacity for proton transfer that was approximately four times that of His64 in K64H HCA III. This is most likely due to its proximity and orientation inward towards the zinc-bound solvent. These results emphasize the significance of side chain orientation and range of available conformational states as characteristics of an efficient proton shuttle in carbonic anhydrase.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Active site comparison of wild type HCA II[4] and III.[3] Superposition of wild type HCA II (yellow) and HCA III (orange) active sites. The zinc atom is shown as a black sphere and the active site residues are in ball-and-stick as labeled. Residues that are invariant between the two isozymes are labeled in black. Residues that differ between HCA II and III are labeled in blue and orange, respectively.
Figure 2.
Figure 2. Active site comparison of HCA III K64H, R67H, and K64H/R67N. Superposition of HCA III K64H (orange), R67H (yellow), and K64H-R67N (cyan) active sites. The zinc atom is shown as a black sphere and active site residues are in ball-and-stick as labeled. Residues that are invariant between HCA III mutants are labeled in black. Residues differing between K64H, R67H, K64H-R67N are labeled in orange, blue, and cyan, respectively.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2007, 68, 337-343) copyright 2007.  
  Figures were selected by an automated process.  

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.  
18599462 N.Shah, D.A.Kuntz, and D.R.Rose (2008).
Golgi alpha-mannosidase II cleaves two sugars sequentially in the same catalytic site.
  Proc Natl Acad Sci U S A, 105, 9570-9575.
PDB codes: 3cv5 3czn 3czs
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