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PDBsum entry 1y7w

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
1y7w
Jmol
Contents
Protein chains
274 a.a. *
Ligands
ACY ×2
Metals
_NA ×2
_ZN ×3
Waters ×527
* Residue conservation analysis
PDB id:
1y7w
Name: Lyase
Title: Crystal structure of a halotolerant carbonic anhydrase from salina
Structure: Halotolerant alpha-type carbonic anhydrase (dca i chain: a, b. Engineered: yes
Source: Dunaliella salina. Organism_taxid: 3046. Gene: dca ii. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.86Å     R-factor:   0.167     R-free:   0.202
Authors: L.Premkumar,H.M.Greenblatt,U.K.Bageshwar,T.Savchenko,I.Gokhm J.L.Sussman,A.Zamir,Israel Structural Proteomics Center (Is
Key ref:
L.Premkumar et al. (2005). Three-dimensional structure of a halotolerant algal carbonic anhydrase predicts halotolerance of a mammalian homolog. Proc Natl Acad Sci U S A, 102, 7493-7498. PubMed id: 15894606 DOI: 10.1073/pnas.0502829102
Date:
10-Dec-04     Release date:   03-May-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
No UniProt id for this chain
Struc: 274 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)
Bound ligand (Het Group name = ACY)
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     one-carbon metabolic process   1 term 
  Biochemical function     carbonate dehydratase activity     2 terms  

 

 
    Added reference    
 
 
DOI no: 10.1073/pnas.0502829102 Proc Natl Acad Sci U S A 102:7493-7498 (2005)
PubMed id: 15894606  
 
 
Three-dimensional structure of a halotolerant algal carbonic anhydrase predicts halotolerance of a mammalian homolog.
L.Premkumar, H.M.Greenblatt, U.K.Bageshwar, T.Savchenko, I.Gokhman, J.L.Sussman, A.Zamir.
 
  ABSTRACT  
 
Protein molecular adaptation to drastically shifting salinities was studied in dCA II, an alpha-type carbonic anhydrase (EC 4.2.1.1) from the exceptionally salt-tolerant unicellular green alga Dunaliella salina. The salt-inducible, extracellular dCA II is highly salt-tolerant and thus differs from its mesophilic homologs. The crystal structure of dCA II, determined at 1.86-A resolution, is globally similar to other alpha-type carbonic anhydrases except for two extended alpha-helices and an added Na-binding loop. Its unusual electrostatic properties include a uniformly negative surface electrostatic potential of lower magnitude than that observed in the highly acidic halophilic proteins and an exceptionally low positive potential at a site adjoining the catalytic Zn(2+) compared with mesophilic homologs. The halotolerant dCA II also differs from typical halophilic proteins in retaining conformational stability and solubility in low to high salt concentrations. The crucial role of electrostatic features in dCA II halotolerance is strongly supported by the ability to predict the unanticipated halotolerance of the murine CA XIV isozyme, which was confirmed biochemically. A proposal for the functional significance of the halotolerance of CA XIV in the kidney is presented.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Ribbon diagram of the dCA II structure. The regions corresponding to CRs (blue), VRs (green), and VCRs (red), as defined in the text, are mapped onto the dCA II structure. Marked are the catalytic Zn2+ and insertions and deletions in VCRs including L1 (the Zn binding loop), L4 (the Na-binding loop), and L5 as well as the two extended -helices (E and G). N and C termini are indicated.
Figure 3.
Fig. 3. Electrostatic properties and effect of salt on enzymatic activity of mCA XIV. (a) The surface electrostatic potentials, the decrease in electrostatic free energy on transfer from 3.0 to 0.1 M NaCl, and surface density of acidic and basic residues are as described in Fig. 2. (b and c) Assays of CO[2] hydration activity (b) and ester hydrolysis activity (c) of dCA II (green), mCA XIV (yellow), or hCA I (red) were performed as described in Materials and Methods. Controls indicate enzyme activity in the absence of salt. For esterase activity, 0.5 mM p-nitrophenyl acetate was used as substrate. Pot, electrostatic potential.
 
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19823944 J.Li, Y.Lu, L.Xue, and H.Xie (2010).
A structurally novel salt-regulated promoter of duplicated carbonic anhydrase gene 1 from Dunaliella salina.
  Mol Biol Rep, 37, 1143-1154.  
20088880 K.Wada, M.Irie, H.Suzuki, and K.Fukuyama (2010).
Crystal structure of the halotolerant gamma-glutamyltranspeptidase from Bacillus subtilis in complex with glutamate reveals a unique architecture of the solvent-exposed catalytic pocket.
  FEBS J, 277, 1000-1009.
PDB code: 3a75
20050917 K.Yoshimune, Y.Shirakihara, M.Wakayama, and I.Yumoto (2010).
Crystal structure of salt-tolerant glutaminase from Micrococcus luteus K-3 in the presence and absence of its product L-glutamate and its activator Tris.
  FEBS J, 277, 738-748.
PDB codes: 3if5 3ih8 3ih9 3iha 3ihb
20000704 M.Toth, C.Smith, H.Frase, S.Mobashery, and S.Vakulenko (2010).
An antibiotic-resistance enzyme from a deep-sea bacterium.
  J Am Chem Soc, 132, 816-823.
PDB code: 3lez
20224780 S.Saari, M.Hilvo, P.Pan, G.Gros, N.Hanke, A.Waheed, W.S.Sly, and S.Parkkila (2010).
The most recently discovered carbonic anhydrase, CA XV, is expressed in the thick ascending limb of Henle and in the collecting ducts of mouse kidney.
  PLoS One, 5, e9624.  
20016684 X.Tadeo, B.López-Méndez, T.Trigueros, A.Laín, D.Castaño, and O.Millet (2009).
Structural basis for the aminoacid composition of proteins from halophilic archea.
  PLoS Biol, 7, e1000257.
PDB code: 2kac
18177372 C.Ye, K.Gao, and M.Giordano (2008).
The odd behaviour of carbonic anhydrase in the terrestrial cyanobacterium Nostoc flagelliforme during hydration-dehydration cycles.
  Environ Microbiol, 10, 1018-1023.  
19021134 J.Gao, and C.J.Cassady (2008).
Negative ion production from peptides and proteins by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.
  Rapid Commun Mass Spectrom, 22, 4066-4072.  
18312415 L.Niiranen, B.Altermark, B.O.Brandsdal, H.K.Leiros, R.Helland, A.O.Smalås, and N.P.Willassen (2008).
Effects of salt on the kinetics and thermodynamic stability of endonuclease I from Vibrio salmonicida and Vibrio cholerae.
  FEBS J, 275, 1593-1605.
PDB code: 2vnd
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.  
17573429 S.Marino, K.Hayakawa, K.Hatada, M.Benfatto, A.Rizzello, M.Maffia, and L.Bubacco (2007).
Structural features that govern enzymatic activity in carbonic anhydrase from a low-temperature adapted fish, Chionodraco hamatus.
  Biophys J, 93, 2781-2790.  
17310272 S.Srimathi, G.Jayaraman, G.Feller, B.Danielsson, and P.R.Narayanan (2007).
Intrinsic halotolerance of the psychrophilic alpha-amylase from Pseudoalteromonas haloplanktis.
  Extremophiles, 11, 505-515.  
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 code is shown on the right.