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PDBsum entry 1qrg

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protein metals links
Lyase PDB id
1qrg
Jmol
Contents
Protein chain
206 a.a. *
Metals
_ZN
Waters ×75
* Residue conservation analysis
PDB id:
1qrg
Name: Lyase
Title: A closer look and the active site of gamma-carbonic anhydras resolution crystallographic studies of the carbonic anhydra methanosarcina thermophila
Structure: Carbonic anhydrase. Chain: a. Engineered: yes
Source: Methanosarcina thermophila. Organism_taxid: 2210. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Trimer (from PDB file)
Resolution:
1.72Å     R-factor:   0.191     R-free:   0.227
Authors: T.M.Iverson,B.E.Alber,C.Kisker,J.G.Ferry,D.C.Rees
Key ref:
T.M.Iverson et al. (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. PubMed id: 10924115 DOI: 10.1021/bi000204s
Date:
13-Jun-99     Release date:   25-Jun-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P40881  (CAH_METTE) -  Carbonic anhydrase
Seq:
Struc:
247 a.a.
206 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)
+ H(2)O
      Cofactor: Zinc
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     lyase activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi000204s Biochemistry 39:9222-9231 (2000)
PubMed id: 10924115  
 
 
A closer look at the active site of gamma-class carbonic anhydrases: high-resolution crystallographic studies of the carbonic anhydrase from Methanosarcina thermophila.
T.M.Iverson, B.E.Alber, C.Kisker, J.G.Ferry, D.C.Rees.
 
  ABSTRACT  
 
The prototype of the gamma-class of carbonic anhydrase has been characterized from the methanogenic archaeon Methanosarcina thermophila. Previously reported kinetic studies of the gamma-class carbonic anhydrase are consistent with this enzyme having a reaction mechanism similar to that of the mammalian alpha-class carbonic anhydrase. However, the overall folds of these two enzymes are dissimilar, and apart from the zinc-coordinating histidines, the active site residues bear little resemblance to one another. The crystal structures of zinc-containing and cobalt-substituted gamma-class carbonic anhydrases from M. thermophila are reported here between 1.46 and 1.95 A resolution in the unbound form and cocrystallized with either SO(4)(2)(-) or HCO(3)(-). Relative to the tetrahedral coordination geometry seen at the active site in the alpha-class of carbonic anhydrases, the active site of the gamma-class enzyme contains additional metal-bound water ligands, so the overall coordination geometry is trigonal bipyramidal for the zinc-containing enzyme and octahedral for the cobalt-substituted enzyme. Ligands bound to the active site all make contacts with the side chain of Glu 62 in manners that suggest the side chain is likely protonated. In the uncomplexed zinc-containing enzyme, the side chains of Glu 62 and Glu 84 appear to share a proton; additionally, Glu 84 exhibits multiple conformations. This suggests that Glu 84 may act as a proton shuttle, which is an important aspect of the reaction mechanism of alpha-class carbonic anhydrases. A hydrophobic pocket on the surface of the enzyme may participate in the trapping of CO(2) at the active site. On the basis of the coordination geometry at the active site, ligand binding modes, the behavior of the side chains of Glu 62 and Glu 84, and analogies to the well-characterized alpha-class of carbonic anhydrases, a more-defined reaction mechanism is proposed for the gamma-class of carbonic anhydrases.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
19679199 R.L.Mikulski, and D.N.Silverman (2010).
Proton transfer in catalysis and the role of proton shuttles in carbonic anhydrase.
  Biochim Biophys Acta, 1804, 422-426.  
20023030 S.A.Zimmerman, J.F.Tomb, and J.G.Ferry (2010).
Characterization of CamH from Methanosarcina thermophila, founding member of a subclass of the {gamma} class of carbonic anhydrases.
  J Bacteriol, 192, 1353-1360.  
18378593 J.G.Ferry, and D.J.Lessner (2008).
Methanogenesis in marine sediments.
  Ann N Y Acad Sci, 1125, 147-157.  
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
17993516 S.S.Cot, A.K.So, and G.S.Espie (2008).
A multiprotein bicarbonate dehydration complex essential to carboxysome function in cyanobacteria.
  J Bacteriol, 190, 936-945.  
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.  
17427958 I.Elder, Z.Fisher, P.J.Laipis, C.Tu, R.McKenna, and D.N.Silverman (2007).
Structural and kinetic analysis of proton shuttle residues in the active site of human carbonic anhydrase III.
  Proteins, 68, 337-343.
PDB codes: 2hfw 2hfx 2hfy 3uyn 3uyq
16821039 K.N.Sas, L.Kovács, O.Zsíros, Z.Gombos, G.Garab, L.Hemmingsen, and E.Danielsen (2006).
Fast cadmium inhibition of photosynthesis in cyanobacteria in vivo and in vitro studies using perturbed angular correlation of gamma-rays.
  J Biol Inorg Chem, 11, 725-734.  
16407270 S.Sunderhaus, N.V.Dudkina, L.Jänsch, J.Klodmann, J.Heinemeyer, M.Perales, E.Zabaleta, E.J.Boekema, and H.P.Braun (2006).
Carbonic anhydrase subunits form a matrix-exposed domain attached to the membrane arm of mitochondrial complex I in plants.
  J Biol Chem, 281, 6482-6488.  
14662760 B.C.Tripp, C.B.Bell, F.Cruz, C.Krebs, and J.G.Ferry (2004).
A role for iron in an ancient carbonic anhydrase.
  J Biol Chem, 279, 6683-6687.  
15604675 G.Parisi, M.Perales, M.S.Fornasari, A.Colaneri, N.González-Schain, D.Gómez-Casati, S.Zimmermann, A.Brennicke, A.Araya, J.G.Ferry, J.Echave, and E.Zabaleta (2004).
Gamma carbonic anhydrases in plant mitochondria.
  Plant Mol Biol, 55, 193-207.  
15316916 H.Oku, T.Ohyama, A.Hiroki, K.Yamada, K.Fukuyama, H.Kawaguchi, and R.Katakai (2004).
Addition of a peptide fragment on an alpha-helical depsipeptide induces alpha/3(10)-conjugated helix: synthesis, crystal structure, and CD spectra of Boc-Leu-Leu-Ala-(Leu-Leu-Lac)3-Leu-Leu-OEt.
  Biopolymers, 75, 242-254.  
15821992 M.Perales, G.Parisi, M.S.Fornasari, A.Colaneri, F.Villarreal, N.González-Schain, J.Echave, D.Gómez-Casati, H.P.Braun, A.Araya, and E.Zabaleta (2004).
Gamma carbonic anhydrase like complex interact with plant mitochondrial complex I.
  Plant Mol Biol, 56, 947-957.  
15231846 V.E.Pye, A.P.Tingey, R.L.Robson, and P.C.Moody (2004).
The structure and mechanism of serine acetyltransferase from Escherichia coli.
  J Biol Chem, 279, 40729-40736.
PDB code: 1t3d
11880627 J.S.Richardson, and D.C.Richardson (2002).
Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation.
  Proc Natl Acad Sci U S A, 99, 2754-2759.  
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.  
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
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.  
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.