spacer
spacer

PDBsum entry 1g5c
Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Lyase PDB id
1g5c

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
169 a.a. *
158 a.a. *
Ligands
EPE ×3
Metals
_CA ×6
_ZN ×6
Waters ×413
* Residue conservation analysis
PDB id:
1g5c
Name: Lyase
Title: Crystal structure of the 'cab' type beta class carbonic anhydrase from methanobacterium thermoautotrophicum
Structure: Beta-carbonic anhydrase. Chain: a, b, c, d, e, f. Engineered: yes
Source: Methanothermobacter thermautotrophicus. Organism_taxid: 145262. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.10Å     R-factor:   0.211     R-free:   0.248
Authors: P.Strop,K.S.Smith,T.M.Iverson,J.G.Ferry,D.C.Rees
Key ref:
P.Strop et al. (2001). Crystal structure of the "cab"-type beta class carbonic anhydrase from the archaeon Methanobacterium thermoautotrophicum. J Biol Chem, 276, 10299-10305. PubMed id: 11096105 DOI: 10.1074/jbc.M009182200
Date:
31-Oct-00     Release date:   04-Apr-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q50565  (Q50565_METTH) -  Carbonic anhydrase from Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
Seq:
Struc: 		176 a.a.
169 a.a.*
Protein chains
Pfam   ArchSchema ?
Q50565  (Q50565_METTH) -  Carbonic anhydrase from Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
Seq:
Struc: 		176 a.a.
158 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F: E.C.4.2.1.1  - carbonic anhydrase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: hydrogencarbonate + H+ = CO2 + H2O
hydrogencarbonate
 + H(+)
 = CO2
 + H2O
      Cofactor: Zn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1074/jbc.M009182200 J Biol Chem 276:10299-10305 (2001)
PubMed id: 11096105  
 
 
Crystal structure of the "cab"-type beta class carbonic anhydrase from the archaeon Methanobacterium thermoautotrophicum.
P.Strop, K.S.Smith, T.M.Iverson, J.G.Ferry, D.C.Rees.
 
  ABSTRACT  
 
The structure of the "cab"-type beta class carbonic anhydrase from the archaeon Methanobacterium thermoautotrophicum (Cab) has been determined to 2.1-A resolution using the multiwavelength anomalous diffraction phasing technique. Cab exists as a dimer with a subunit fold similar to that observed in "plant"-type beta class carbonic anhydrases. The active site zinc is coordinated by protein ligands Cys(32), His(87), and Cys(90), with the tetrahedral coordination completed by a water molecule. The major difference between plant- and cab-type beta class carbonic anhydrases is in the organization of the hydrophobic pocket. The structure reveals a Hepes buffer molecule bound 8 A away from the active site zinc, which suggests a possible proton transfer pathway from the active site to the solvent.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Alignment of -CA sequences. Cab, M. thermoautotrophicum; PPnterm, P. purpureum N-terminal domain; PPcterm, P. purpureum C-terminal domain; P.S., P. sativum; ECcynT, E. coli. Zinc ligands are colored yellow, the conserved Asp/Arg pair is red, and residues differentiating cab-type and plant-type are blue. 		Figure 6.
Fig. 6. Stereo diagram showing the superposition of the active site of Cab , P. sativum, and P. purpureum -CAs including zinc, zinc-coordinating residues, and the conserved residues differentiating between cab- and plant-type -CA. A, Cab is shown in yellow; P. sativum -CA is shown in green. The coordinating water molecule in Cab is shown in red. B, Cab is shown in yellow; P. purpureum -CA is shown in blue. The coordinating water molecule in Cab is shown in red.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 10299-10305) copyright 2001.  
  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
21371693 Z.Sebestyén, K.Máthé, A.Buvári-Barcza, E.Vass, F.Ruff, J.Szemán, and L.Barcza (2011).
Diverse associations in the ternary systems of β-cyclodextrin, simple carbohydrates and phenyl derivatives of inorganic oxoacids.
  Carbohydr Res, 346, 833-838.  
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.  
20528692 J.G.Ferry (2010).
How to make a living by exhaling methane.
  Annu Rev Microbiol, 64, 453-473.  
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.  
19816790 M.K.Fasseas, D.Tsikou, E.Flemetakis, and P.Katinakis (2010).
Molecular and biochemical analysis of the beta class carbonic anhydrases in Caenorhabditis elegans.
  Mol Biol Rep, 37, 2941-2950.  
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.  
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
17222138 H.Park, B.Song, and F.M.Morel (2007).
Diversity of the cadmium-containing carbonic anhydrase in marine diatoms and natural waters.
  Environ Microbiol, 9, 403-413.  
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.  
16698543 M.J.Bennett, M.R.Sawaya, and D.Eisenberg (2006).
Deposition diseases and 3D domain swapping.
  Structure, 14, 811-824.  
15274929 C.L.Lawson, B.Benoff, T.Berger, H.M.Berman, and J.Carey (2004).
E. coli trp repressor forms a domain-swapped array in aqueous alcohol.
  Structure, 12, 1099-1108.
PDB code: 1mi7
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.  
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.  
12021428 Y.Liu, and D.Eisenberg (2002).
3D domain swapping: as domains continue to swap.
  Protein Sci, 11, 1285-1299.  
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.

 

spacer
spacer