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PDBsum entry 1koq

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protein metals Protein-protein interface(s) links
Lyase PDB id
1koq
Jmol
Contents
Protein chains
222 a.a. *
Metals
_ZN ×2
Waters ×147
* Residue conservation analysis
PDB id:
1koq
Name: Lyase
Title: Neisseria gonorrhoeae carbonic anhydrase
Structure: Carbonic anhydrase. Chain: a, b. Engineered: yes
Source: Neisseria gonorrhoeae. Organism_taxid: 485. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.90Å     R-factor:   0.206     R-free:   0.271
Authors: S.Huang,Y.Xue,L.Chirica,S.Lindskog,B.-H.Jonsson
Key ref:
S.Huang et al. (1998). Crystal structure of carbonic anhydrase from Neisseria gonorrhoeae and its complex with the inhibitor acetazolamide. J Mol Biol, 283, 301-310. PubMed id: 9761692 DOI: 10.1006/jmbi.1998.2077
Date:
22-Mar-98     Release date:   09-Dec-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q50940  (CAH_NEIGO) -  Carbonic anhydrase
Seq:
Struc:
252 a.a.
222 a.a.
Key:    PfamA domain  PfamB 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: Zn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     periplasmic space   1 term 
  Biological process     one-carbon metabolic process   1 term 
  Biochemical function     lyase activity     4 terms  

 

 
    Added reference    
 
 
DOI no: 10.1006/jmbi.1998.2077 J Mol Biol 283:301-310 (1998)
PubMed id: 9761692  
 
 
Crystal structure of carbonic anhydrase from Neisseria gonorrhoeae and its complex with the inhibitor acetazolamide.
S.Huang, Y.Xue, E.Sauer-Eriksson, L.Chirica, S.Lindskog, B.H.Jonsson.
 
  ABSTRACT  
 
The crystal structure of carbonic anhydrase from Neisseria gonorrhoeae has been solved to a resolution of 1.78 A by molecular replacement using human carbonic anhydrase II as a template. After refinement the R factor was 17.8% (Rfree=23.2%). There are two molecules per asymmetric unit (space group P21), but they have essentially identical structures. The fold of the N. gonorrhoeae enzyme is very similar to that of human isozyme II; 192 residues, 74 of which are identical in the two enzymes, have equivalent positions in the three-dimensional structures. This corresponds to 85% of the entire polypeptide chain of the bacterial enzyme. The only two cysteine residues in the bacterial enzyme, which has a periplasmic location in the cell, are connected by a disulfide bond. Most of the secondary structure elements present in human isozyme II are retained in N. gonorrhoeae carbonic anhydrase, but there are also differences, particularly in the few helical regions. Long deletions in the bacterial enzyme relative to human isozyme II have resulted in a considerable shortening of three surface loops. One of these deletions, corresponding to residues 128 to 139 in the human enzyme, leads to a widening of the entrance to the hydrophobic part of the active site cavity. Practically all the amino acid residues in the active site of human isozyme II are conserved in the N. gonorrhoeae enzyme and have similar structural positions. However, the imidazole ring of a histidine residue, which has been shown to function as a proton shuttle in the catalytic mechanism of the human enzyme, interacts with an extraneous entity, which has tentatively been identified as a 2-mercaptoethanol molecule from the crystallization medium. When this entity is removed by soaking the crystal in a different medium, the side-chain of His66 becomes quite mobile. The structure of a complex with the sulfonamide inhibitor, acetazolamide, has also been determined. Its position in the active site is very similar to that observed in human carbonic anhydrase II.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Schematic drawings of the structures of NGCA (left) and HCA II (right). The molecules are shown in a slightly different orientation from that in Figure 1. The N termini are in the upper left parts of the drawings. The zinc ions are shown as filled circles. Arrows indicate the three loops in HCA II which are deleted in NGCA. The Figure was produced with MOLSCRIPT [Kraulis 1991].
Figure 4.
Figure 4. Stereo diagram showing the Cys28---Cys181 disulfide bond in NGCA. Thin lines represent the corresponding residues in HCA II.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 283, 301-310) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21377464 J.A.Cuesta-Seijo, M.S.Borchert, J.C.Navarro-Poulsen, K.M.Schnorr, S.B.Mortensen, and L.Lo Leggio (2011).
Structure of a dimeric fungal α-type carbonic anhydrase.
  FEBS Lett, 585, 1042-1048.  
20945495 B.Kanbar, and E.Ozdemir (2010).
Thermal stability of carbonic anhydrase immobilized within polyurethane foam.
  Biotechnol Prog, 26, 1474-1480.  
20960531 G.Zanotti, and L.Cendron (2010).
Functional and structural aspects of Helicobacter pylori acidic stress response factors.
  IUBMB Life, 62, 715-723.  
19224556 Z.Liu, P.Bartlow, R.M.Dilmore, Y.Soong, Z.Pan, R.Koepsel, and M.Ataai (2009).
Production, purification, and characterization of a fusion protein of carbonic anhydrase from Neisseria gonorrhoeae and cellulose binding domain from Clostridium thermocellum.
  Biotechnol Prog, 25, 68-74.  
18599462 N.Shah, D.A.Kuntz, and D.R.Rose (2008).
Golgi alpha-mannosidase II cleaves two sugars sequentially in the same catalytic site.
  Proc Natl Acad Sci U S A, 105, 9570-9575.
PDB codes: 3cv5 3czn 3czs
18239688 T.Shutova, H.Kenneweg, J.Buchta, J.Nikitina, V.Terentyev, S.Chernyshov, B.Andersson, S.I.Allakhverdiev, V.V.Klimov, H.Dau, W.Junge, and G.Samuelsson (2008).
The photosystem II-associated Cah3 in Chlamydomonas enhances the O2 evolution rate by proton removal.
  EMBO J, 27, 782-791.  
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.  
17075950 B.D.Charette, R.G.Macdonald, S.Wetzel, D.B.Berkowitz, and H.Waldmann (2006).
Protein structure similarity clustering: dynamic treatment of PDB structures facilitates clustering.
  Angew Chem Int Ed Engl, 45, 7766-7770.  
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.  
11248679 B.Elleby, L.C.Chirica, C.Tu, M.Zeppezauer, and S.Lindskog (2001).
Characterization of carbonic anhydrase from Neisseria gonorrhoeae.
  Eur J Biochem, 268, 1613-1619.  
11341916 L.C.Chirica, B.Elleby, and S.Lindskog (2001).
Cloning, expression and some properties of alpha-carbonic anhydrase from Helicobacter pylori.
  Biochim Biophys Acta, 1544, 55-63.  
10978542 K.S.Smith, and J.G.Ferry (2000).
Prokaryotic carbonic anhydrases.
  FEMS Microbiol Rev, 24, 335-366.  
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.