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PDBsum entry 2a5v

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
2a5v
Jmol
Contents
Protein chains
210 a.a. *
Ligands
SCN ×4
Metals
_ZN ×11
Waters ×311
* Residue conservation analysis
PDB id:
2a5v
Name: Lyase
Title: Crystal structure of m. Tuberculosis beta carbonic anhydrase tetrameric form
Structure: Carbonic anhydrase (carbonate dehydratase) (carbo dehydratase). Chain: a, b, c, d. Engineered: yes
Source: Mycobacterium tuberculosis. Organism_taxid: 83332. Strain: h37rv. Gene: rv3588c. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.20Å     R-factor:   0.165     R-free:   0.214
Authors: A.S.Covarrubias,T.Bergfors,T.A.Jones,M.Hogbom
Key ref:
A.S.Covarrubias et al. (2006). Structural mechanics of the pH-dependent activity of beta-carbonic anhydrase from Mycobacterium tuberculosis. J Biol Chem, 281, 4993-4999. PubMed id: 16321983 DOI: 10.1074/jbc.M510756200
Date:
01-Jul-05     Release date:   20-Sep-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam  
P9WPJ9  (MTCA2_MYCTU) -  Carbonic anhydrase 2
Seq:
Struc:
207 a.a.
210 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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: Zn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     protein binding     5 terms  

 

 
    Added reference    
 
 
DOI no: 10.1074/jbc.M510756200 J Biol Chem 281:4993-4999 (2006)
PubMed id: 16321983  
 
 
Structural mechanics of the pH-dependent activity of beta-carbonic anhydrase from Mycobacterium tuberculosis.
A.S.Covarrubias, T.Bergfors, T.A.Jones, M.Högbom.
 
  ABSTRACT  
 
Carbonic anhydrases catalyze the reversible hydration of carbon dioxide to form bicarbonate, a reaction required for many functions, including carbon assimilation and pH homeostasis. Carbonic anhydrases are divided into at least three classes and are believed to share a zinc-hydroxide mechanism for carbon dioxide hydration. beta-carbonic anhydrases are broadly spread among the domains of life, and existing structures from different organisms show two distinct active site setups, one with three protein coordinations to the zinc (accessible) and the other with four (blocked). The latter is believed to be inconsistent with the zinc-hydroxide mechanism. The Mycobacterium tuberculosis Rv3588c gene, shown to be required for in vivo growth of the pathogen, encodes a beta-carbonic anhydrase with a steep pH dependence of its activity, being active at pH 8.4 but not at pH 7.5. We have recently solved the structure of this protein, which was a dimeric protein with a blocked active site. Here we present the structure of the thiocyanate complexed protein in a different crystal form. The protein now forms distinct tetramers and shows large structural changes, including a carboxylate shift yielding the accessible active site. This structure demonstrated for the first time that a beta-carbonic anhydrase can switch between the two states. A pH-dependent dimer to tetramer equilibrium was also demonstrated by dynamic light scattering measurements. The data presented here, therefore, suggest a carboxylate shift on/off switch for the enzyme, which may, in turn, be controlled by a dimer-to-tetramer equilibrium.
 
  Selected figure(s)  
 
Figure 3.
Stereo images of the active site structures. A, the accessible thiocyanate-bound active site of Rv3588c. Bubbles indicate the salt link between Asp-53 and Arg-55. B, comparison of the accessible (dark gray) and blocked (light gray) sites. Note in particular the shift of Asp-53 and the drastic changes of Ser-54 and Val-56.
Figure 4.
Buried charged residues in the tetramer-forming interface. Chain A is in blue, chain B is in green, chain C is in gold, and chain D is in red. Tyr-126 and Asp-80 are indicated. Bubbles show hydrogen bonds and salt links.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 4993-4999) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20803169 C.T.Supuran (2011).
Carbonic anhydrase inhibition with natural products: novel chemotypes and inhibition mechanisms.
  Mol Divers, 15, 305-316.  
21298147 F.Pannetier, G.Ohanessian, and G.Frison (2011).
Comparison between α- and β-carbonic anhydrases: can Zn(His)3(H2O) and Zn(His)(Cys)2(H2O) sites lead to equivalent enzymes?
  Dalton Trans, 40, 2696-2698.  
19459702 R.S.Rowlett, C.Tu, J.Lee, A.G.Herman, D.A.Chapnick, S.H.Shah, and P.C.Gareiss (2009).
Allosteric site variants of Haemophilus influenzae beta-carbonic anhydrase.
  Biochemistry, 48, 6146-6156.
PDB codes: 3e1v 3e1w 3e24 3e28 3e2a 3e2w
19852838 Y.B.Teng, Y.L.Jiang, Y.X.He, W.W.He, F.M.Lian, Y.Chen, and C.Z.Zhou (2009).
Structural insights into the substrate tunnel of Saccharomyces cerevisiae carbonic anhydrase Nce103.
  BMC Struct Biol, 9, 67.
PDB code: 3eyx
18931408 J.Jeyakanthan, S.Rangarajan, P.Mridula, S.P.Kanaujia, Y.Shiro, S.Kuramitsu, S.Yokoyama, and K.Sekar (2008).
Observation of a calcium-binding site in the gamma-class carbonic anhydrase from Pyrococcus horikoshii.
  Acta Crystallogr D Biol Crystallogr, 64, 1012-1019.
PDB codes: 1v3w 1v67 2fko
18004750 M.C.Yang, H.H.Guan, M.Y.Liu, Y.H.Lin, J.M.Yang, W.L.Chen, C.J.Chen, and S.J.Mao (2008).
Crystal structure of a secondary vitamin D3 binding site of milk beta-lactoglobulin.
  Proteins, 71, 1197-1210.
PDB code: 2gj5
19012038 S.Morishita, I.Nishimori, T.Minakuchi, S.Onishi, H.Takeuchi, T.Sugiura, D.Vullo, A.Scozzafava, and C.T.Supuran (2008).
Cloning, polymorphism, and inhibition of beta-carbonic anhydrase of Helicobacter pylori.
  J Gastroenterol, 43, 849-857.  
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.  
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.