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PDBsum entry 1ym3

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protein metals links
Lyase PDB id
1ym3
Jmol
Contents
Protein chain
193 a.a. *
Metals
_MG
_ZN
Waters ×130
* Residue conservation analysis
PDB id:
1ym3
Name: Lyase
Title: Crystal structure of carbonic anhydrase rv3588c from mycobac tuberculosis
Structure: Carbonic anhydrase (carbonate dehydratase) (carbo dehydratase). Chain: a. Engineered: yes
Source: Mycobacterium tuberculosis. Organism_taxid: 83332. Strain: h37rv. Gene: rv3588c. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
1.75Å     R-factor:   0.181     R-free:   0.229
Authors: A.S.Covarrubias,A.M.Larsson,M.Hogbom,J.Lindberg,T.Bergfors, C.Bjorkelid,S.L.Mowbray,T.Unge,T.A.Jones,Structural Proteom Europe (Spine)
Key ref:
A.Suarez Covarrubias et al. (2005). Structure and function of carbonic anhydrases from Mycobacterium tuberculosis. J Biol Chem, 280, 18782-18789. PubMed id: 15753099 DOI: 10.1074/jbc.M414348200
Date:
20-Jan-05     Release date:   08-Mar-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam  
P9WPJ8  (MTCA2_MYCTO) -  Carbonic anhydrase 2
Seq:
Struc:
207 a.a.
193 a.a.
Protein chain
Pfam  
P9WPJ9  (MTCA2_MYCTU) -  Carbonic anhydrase 2
Seq:
Struc:
207 a.a.
193 a.a.
Key:    Secondary structure  CATH domain

 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     lyase activity     4 terms  

 

 
    Added reference    
 
 
DOI no: 10.1074/jbc.M414348200 J Biol Chem 280:18782-18789 (2005)
PubMed id: 15753099  
 
 
Structure and function of carbonic anhydrases from Mycobacterium tuberculosis.
A.Suarez Covarrubias, A.M.Larsson, M.Högbom, J.Lindberg, T.Bergfors, C.Björkelid, S.L.Mowbray, T.Unge, T.A.Jones.
 
  ABSTRACT  
 
Carbonic anhydrases catalyze the reversible hydration of carbon dioxide to form bicarbonate. This activity is universally required for fatty acid biosynthesis as well as for the production of a number of small molecules, pH homeostasis, and other functions. At least three different carbonic anhydrase families are known to exist, of which the alpha-class found in humans has been studied in most detail. In the present work, we describe the structures of two of the three beta-class carbonic anhydrases that have been identified in Mycobacterium tuberculosis, i.e. Rv1284 and Rv3588c. Both structures were solved by molecular replacement and then refined to resolutions of 2.0 and 1.75 A, respectively. The active site of Rv1284 is small and almost completely shielded from solvent, whereas that of Rv3588c is larger and quite open to solution. Differences in coordination of the active site metal are also observed. In Rv3588c, an aspartic acid side chain displaces a water molecule and coordinates directly to the zinc ion, thereby closing the zinc coordination sphere and breaking the salt link to a nearby arginine that is a feature of Rv1284. The two carbonic anhydrases thus exhibit both of the metal coordination geometries that have previously been observed for structures in this family. Activity studies demonstrate that Rv3588c is a completely functional carbonic anhydrase. The apparent lack of activity of Rv1284 in the present assay system is likely exacerbated by the observed depletion of zinc in the preparation.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. Overall structures. Ribbon diagrams illustrate the structures of Rv1284 (A) and Rv3588c (B). The two subunits of each protein are shown in differing shades of gray, and the active site metals are seen as black spheres. The N and C terminus of one subunit of each CA is labeled.
Figure 2.
FIG. 2. Active sites. Residues involved in metal chelation in Rv1284 (A) and Rv3588c (B) are shown with ball-and-stick models, with the hydrogen bonds mentioned in the text indicated by black dotted lines. In C, the two structures are superimposed, with Rv1284 shown in darker gray.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 18782-18789) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
22012399 M.J.Smeulders, T.R.Barends, A.Pol, A.Scherer, M.H.Zandvoort, A.Udvarhelyi, A.F.Khadem, A.Menzel, J.Hermans, R.L.Shoeman, H.J.Wessels, L.P.van den Heuvel, L.Russ, I.Schlichting, M.S.Jetten, and H.J.Op den Camp (2011).
Evolution of a new enzyme for carbon disulphide conversion by an acidothermophilic archaeon.
  Nature, 478, 412-416.
PDB codes: 3ten 3teo
19221587 K.Chen, and L.Kurgan (2009).
Investigation of atomic level patterns in protein--small ligand interactions.
  PLoS ONE, 4, e4473.  
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
19365544 S.Elleuche, and S.Pöggeler (2009).
Beta-carbonic anhydrases play a role in fruiting body development and ascospore germination in the filamentous fungus Sordaria macrospora.
  PLoS ONE, 4, e5177.  
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
18167490 C.T.Supuran (2008).
Carbonic anhydrases: novel therapeutic applications for inhibitors and activators.
  Nat Rev Drug Discov, 7, 168-181.  
18161740 K.D'Ambrosio, B.Masereel, A.Thiry, A.Scozzafava, C.T.Supuran, and G.De Simone (2008).
Carbonic anhydrase inhibitors: binding of indanesulfonamides to the human isoform II.
  ChemMedChem, 3, 473-477.
PDB codes: 2qo8 2qoa
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.  
16980506 A.Grover, and R.Sharma (2006).
Identification and characterization of a major Zn(II) resistance determinant of Mycobacterium smegmatis.
  J Bacteriol, 188, 7026-7032.  
16691555 D.Kurian, K.Phadwal, and P.Mäenpää (2006).
Proteomic characterization of acid stress response in Synechocystis sp. PCC 6803.
  Proteomics, 6, 3614-3624.  
16698543 M.J.Bennett, M.R.Sawaya, and D.Eisenberg (2006).
Deposition diseases and 3D domain swapping.
  Structure, 14, 811-824.  
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.