spacer
spacer

PDBsum entry 1ekj

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Lyase PDB id
1ekj
Jmol
Contents
Protein chains
(+ 2 more) 210 a.a. *
Ligands
ACT ×9
AZI ×4
EDO ×4
CIT
Metals
_CL ×8
_ZN ×8
_CU ×4
Waters ×811
* Residue conservation analysis
PDB id:
1ekj
Name: Lyase
Title: The x-ray crystallographic structure of beta carbonic anhydrase from the c3 dicot pisum sativum
Structure: Beta-carbonic anhydrase. Chain: a, b, c, d, e, f, g, h. Ec: 4.2.1.1
Source: Pisum sativum. Pea. Organism_taxid: 3888. Organ: leaf. Cellular_location: nuclear encoded
Biol. unit: Octamer (from PDB file)
Resolution:
1.93Å     R-factor:   0.229     R-free:   0.250
Authors: M.S.Kimber,E.F.Pai
Key ref:
M.S.Kimber and E.F.Pai (2000). The active site architecture of Pisum sativum beta-carbonic anhydrase is a mirror image of that of alpha-carbonic anhydrases. EMBO J, 19, 1407-1418. PubMed id: 10747009 DOI: 10.1093/emboj/19.7.1407
Date:
08-Mar-00     Release date:   07-Jun-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P17067  (CAHC_PEA) -  Carbonic anhydrase, chloroplastic
Seq:
Struc:
328 a.a.
210 a.a.
Key:    PfamA domain  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)
Bound ligand (Het Group name = ACT)
matches with 75.00% similarity
+ 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     carbon utilization   1 term 
  Biochemical function     carbonate dehydratase activity     2 terms  

 

 
    Added reference    
 
 
DOI no: 10.1093/emboj/19.7.1407 EMBO J 19:1407-1418 (2000)
PubMed id: 10747009  
 
 
The active site architecture of Pisum sativum beta-carbonic anhydrase is a mirror image of that of alpha-carbonic anhydrases.
M.S.Kimber, E.F.Pai.
 
  ABSTRACT  
 
We have determined the structure of the beta-carbonic anhydrase from the dicotyledonous plant Pisum sativum at 1.93 A resolution, using a combination of multiple anomalous scattering off the active site zinc ion and non-crystallographic symmetry averaging. The mol- ecule assembles as an octamer with a novel dimer of dimers of dimers arrangement. Two distinct patterns of conservation of active site residues are observed, implying two potentially mechanistically distinct classes of beta-carbonic anhydrases. The active site is located at the interface between two monomers, with Cys160, His220 and Cys223 binding the catalytic zinc ion and residues Asp162 (oriented by Arg164), Gly224, Gln151, Val184, Phe179 and Tyr205 interacting with the substrate analogue, acetic acid. The substrate binding groups have a one to one correspondence with the functional groups in the alpha-carbonic anhydrase active site, with the corresponding residues being closely superimposable by a mirror plane. Therefore, despite differing folds, alpha- and beta-carbonic anhydrase have converged upon a very similar active site design and are likely to share a common mechanism.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 Ligand binding in various of the active sites of -CA. (A) Stereo picture of the active site of molecule D showing [A]-weighted electron density for the acetate ion. The map is contoured at 1.5 (blue) and 8 (orange). (B) Stereo picture of the active site of molecule G showing [A]-weighted electron density for the acetic acid molecule. The map is contoured at 1.5 (blue) and 8 (orange). (C) Binding mode of acetic acid in the -CA active site, with zinc–ligand interactions shown as solid lines and hydrogen bonds as dashed lines. The binding site is composed of two molecules, with one molecule shown in green and the other one in brown.
Figure 4.
Figure 4 Proposed mechanism for -CA. (A) Bicarbonate bound in the active site, in a position similar to that seen for the acetic acid molecule, forming hydrogen bonds with Gly224, Asp162 and Glu151. (B) This molecule decomposes into CO[2], which continues to interact with Gln151' and hydroxide. (C) CO[2] diffuses out of the active site leaving a hydroxide ion bound to the zinc. This ion then accepts a proton from a buffer molecule in bulk solvent, leaving water bound at the active site zinc (D).
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 1407-1418) copyright 2000.  
  Figures were selected by an automated process.  

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
21212893 O.Amata, T.Marino, N.Russo, and M.Toscano (2011).
Catalytic activity of a ζ-class zinc and cadmium containing carbonic anhydrase. Compared work mechanisms.
  Phys Chem Chem Phys, 13, 3468-3477.  
19679198 J.F.Domsic, and R.McKenna (2010).
Sequestration of carbon dioxide by the hydrophobic pocket of the carbonic anhydrases.
  Biochim Biophys Acta, 1804, 326-331.  
19747990 J.G.Ferry (2010).
The gamma class of carbonic anhydrases.
  Biochim Biophys Acta, 1804, 374-381.  
20659325 L.Syrjänen, M.Tolvanen, M.Hilvo, A.Olatubosun, A.Innocenti, A.Scozzafava, J.Leppiniemi, B.Niederhauser, V.P.Hytönen, T.A.Gorr, S.Parkkila, and C.T.Supuran (2010).
Characterization of the first beta-class carbonic anhydrase from an arthropod (Drosophila melanogaster) and phylogenetic analysis of beta-class carbonic anhydrases in invertebrates.
  BMC Biochem, 11, 28.  
19818877 T.K.Hurst, D.Wang, R.B.Thompson, and C.A.Fierke (2010).
Carbonic anhydrase II-based metal ion sensing: Advances and new perspectives.
  Biochim Biophys Acta, 1804, 393-403.  
19383148 A.K.Weber, and R.Pirow (2009).
Physiological responses of Daphnia pulex to acid stress.
  BMC Physiol, 9, 9.  
19218391 C.Kalloniati, D.Tsikou, V.Lampiri, M.N.Fotelli, H.Rennenberg, I.Chatzipavlidis, C.Fasseas, P.Katinakis, and E.Flemetakis (2009).
Characterization of a Mesorhizobium loti alpha-type carbonic anhydrase and its role in symbiotic nitrogen fixation.
  J Bacteriol, 191, 2593-2600.  
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
19296112 S.Elleuche, and S.Pöggeler (2009).
Evolution of carbonic anhydrases in fungi.
  Curr Genet, 55, 211-222.  
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
19017644 Y.Q.Wang, A.Feechan, B.W.Yun, R.Shafiei, A.Hofmann, P.Taylor, P.Xue, F.Q.Yang, Z.S.Xie, J.A.Pallas, C.C.Chu, and G.J.Loake (2009).
S-Nitrosylation of AtSABP3 Antagonizes the Expression of Plant Immunity.
  J Biol Chem, 284, 2131-2137.  
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.  
18322527 Y.Xu, L.Feng, P.D.Jeffrey, Y.Shi, and F.M.Morel (2008).
Structure and metal exchange in the cadmium carbonic anhydrase of marine diatoms.
  Nature, 452, 56-61.
PDB codes: 3bob 3boc 3boe 3boh 3boj
17407539 N.Fabre, I.M.Reiter, N.Becuwe-Linka, B.Genty, and D.Rumeau (2007).
Characterization and expression analysis of genes encoding alpha and beta carbonic anhydrases in Arabidopsis.
  Plant Cell Environ, 30, 617-629.  
17347907 N.N.Rudenko, L.K.Ignatova, and B.N.Ivanov (2007).
Multiple sources of carbonic anhydrase activity in pea thylakoids: soluble and membrane-bound forms.
  Photosynth Res, 91, 81-89.  
16321983 A.S.Covarrubias, T.Bergfors, T.A.Jones, and M.Högbom (2006).
Structural mechanics of the pH-dependent activity of beta-carbonic anhydrase from Mycobacterium tuberculosis.
  J Biol Chem, 281, 4993-4999.
PDB code: 2a5v
16863473 B.W.Clare, and C.T.Supuran (2006).
A perspective on quantitative structure-activity relationships and carbonic anhydrase inhibitors.
  Expert Opin Drug Metab Toxicol, 2, 113-137.  
16407248 M.R.Sawaya, G.C.Cannon, S.Heinhorst, S.Tanaka, E.B.Williams, T.O.Yeates, and C.A.Kerfeld (2006).
The structure of beta-carbonic anhydrase from the carboxysomal shell reveals a distinct subclass with one active site for the price of two.
  J Biol Chem, 281, 7546-7555.
PDB code: 2fgy
15753099 A.Suarez Covarrubias, A.M.Larsson, M.Högbom, J.Lindberg, T.Bergfors, C.Björkelid, S.L.Mowbray, T.Unge, and T.A.Jones (2005).
Structure and function of carbonic anhydrases from Mycobacterium tuberculosis.
  J Biol Chem, 280, 18782-18789.
PDB codes: 1ylk 1ym3
14997539 M.S.Sujatha, and P.V.Balaji (2004).
Identification of common structural features of binding sites in galactose-specific proteins.
  Proteins, 55, 44-65.  
12596267 T.Hamelryck (2003).
Efficient identification of side-chain patterns using a multidimensional index tree.
  Proteins, 51, 96.  
12193617 B.Kusian, D.Sültemeyer, and B.Bowien (2002).
Carbonic anhydrase is essential for growth of Ralstonia eutropha at ambient CO(2) concentrations.
  J Bacteriol, 184, 5018-5026.  
12185253 D.H.Slaymaker, D.A.Navarre, D.Clark, O.del Pozo, G.B.Martin, and D.F.Klessig (2002).
The tobacco salicylic acid-binding protein 3 (SABP3) is the chloroplast carbonic anhydrase, which exhibits antioxidant activity and plays a role in the hypersensitive defense response.
  Proc Natl Acad Sci U S A, 99, 11640-11645.  
12107142 K.S.Smith, C.Ingram-Smith, and J.G.Ferry (2002).
Roles of the conserved aspartate and arginine in the catalytic mechanism of an archaeal beta-class carbonic anhydrase.
  J Bacteriol, 184, 4240-4245.  
12056894 S.Huang, B.Sjöblom, A.E.Sauer-Eriksson, and B.H.Jonsson (2002).
Organization of an efficient carbonic anhydrase: implications for the mechanism based on structure-function studies of a T199P/C206S mutant.
  Biochemistry, 41, 7628-7635.
PDB codes: 1lg5 1lg6 1lgd
11241598 H.Strasdeit (2001).
The First Cadmium-Specific Enzyme.
  Angew Chem Int Ed Engl, 40, 707-709.  
11316870 J.D.Cronk, J.A.Endrizzi, M.R.Cronk, J.W.O'neill, and K.Y.Zhang (2001).
Crystal structure of E. coli beta-carbonic anhydrase, an enzyme with an unusual pH-dependent activity.
  Protein Sci, 10, 911-922.
PDB codes: 1i6o 1i6p
11256616 A.Liljas, and M.Laurberg (2000).
A wheel invented three times. The molecular structures of the three carbonic anhydrases.
  EMBO Rep, 1, 16-17.  
10924116 B.C.Tripp, and J.G.Ferry (2000).
A structure-function study of a proton transport pathway in the gamma-class carbonic anhydrase from Methanosarcina thermophila.
  Biochemistry, 39, 9232-9240.  
11015190 E.H.Cox, G.L.McLendon, F.M.Morel, T.W.Lane, R.C.Prince, I.J.Pickering, and G.N.George (2000).
The active site structure of Thalassiosira weissflogii carbonic anhydrase 1.
  Biochemistry, 39, 12128-12130.  
10957638 J.D.Cronk, J.W.O'Neill, M.R.Cronk, J.A.Endrizzi, and K.Y.Zhang (2000).
Cloning, crystallization and preliminary characterization of a beta-carbonic anhydrase from Escherichia coli.
  Acta Crystallogr D Biol Crystallogr, 56, 1176-1179.  
11073902 K.S.Smith, N.J.Cosper, C.Stalhandske, R.A.Scott, and J.G.Ferry (2000).
Structural and kinetic characterization of an archaeal beta-class carbonic anhydrase.
  J Bacteriol, 182, 6605-6613.  
10996087 S.J.Ferguson (2000).
Proton transfer: it's a stringent process.
  Curr Biol, 10, R627-R630.  
10924115 T.M.Iverson, B.E.Alber, C.Kisker, J.G.Ferry, and D.C.Rees (2000).
A closer look at the active site of gamma-class carbonic anhydrases: high-resolution crystallographic studies of the carbonic anhydrase from Methanosarcina thermophila.
  Biochemistry, 39, 9222-9231.
PDB codes: 1qq0 1qre 1qrf 1qrg 1qrl 1qrm
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.