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PDBsum entry 12ca

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protein metals links
Lyase(oxo-acid) PDB id
12ca
Jmol
Contents
Protein chain
255 a.a. *
Metals
_HG
_ZN
Waters ×87
* Residue conservation analysis
PDB id:
12ca
Name: Lyase(oxo-acid)
Title: Altering the mouth of a hydrophobic pocket. Structure and kinetics of human carbonic anhydrase ii mutants at residue val-121
Structure: Carbonic anhydrase ii. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606
Resolution:
2.40Å     R-factor:   0.170    
Authors: S.K.Nair,D.W.Christianson
Key ref: S.K.Nair et al. (1991). Altering the mouth of a hydrophobic pocket. Structure and kinetics of human carbonic anhydrase II mutants at residue Val-121. J Biol Chem, 266, 17320-17325. PubMed id: 1910042
Date:
01-Oct-91     Release date:   15-Oct-92    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00918  (CAH2_HUMAN) -  Carbonic anhydrase 2
Seq:
Struc:
260 a.a.
255 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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     extracellular space   11 terms 
  Biological process     angiotensin-mediated signaling pathway   21 terms 
  Biochemical function     protein binding     5 terms  

 

 
    Added reference    
 
 
J Biol Chem 266:17320-17325 (1991)
PubMed id: 1910042  
 
 
Altering the mouth of a hydrophobic pocket. Structure and kinetics of human carbonic anhydrase II mutants at residue Val-121.
S.K.Nair, T.L.Calderone, D.W.Christianson, C.A.Fierke.
 
  ABSTRACT  
 
Eleven amino acid substitutions at Val-121 of human carbonic anhydrase II including Gly, Ala, Ser, Leu, Ile, Lys, and Arg, were constructed by site-directed mutagenesis. This residue is at the mouth of the hydrophobic pocket in the enzyme active site. The CO2 hydrase activity and the p-nitrophenyl esterase activity of these CAII variants correlate with the hydrophobicity of the residue, suggesting that the hydrophobic character of this residue is important for catalysis. The effects of these mutations on the steady-state kinetics for CO2 hydration occur mainly in kcat/Km and Km, consistent with involvement of this residue in CO2 association. The Val-121----Ala mutant, which exhibits about one-third normal CO2 hydrase activity, has been studied by x-ray crystallographic methods. No significant changes in the mutant enzyme conformation are evident relative to the wild-type enzyme. Since Val-121 is at the mouth of the hydrophobic pocket, its substitution by the methyl side chain of alanine makes the pocket mouth significantly wider than that of the wild-type enzyme. Hence, although a moderately wide (and deep) pocket is important for substrate association, a wider mouth to this pocket does not seriously compromise the catalytic approach of CO2 toward nucleophilic zinc-bound hydroxide.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21212893 O.Amata, T.Marino, N.Russo, and M.Toscano (2011).
Catalytic activity of a ΞΆ-class zinc and cadmium containing carbonic anhydrase. Compared work mechanisms.
  Phys Chem Chem Phys, 13, 3468-3477.  
19520834 B.Sjöblom, M.Polentarutti, and K.Djinovic-Carugo (2009).
Structural study of X-ray induced activation of carbonic anhydrase.
  Proc Natl Acad Sci U S A, 106, 10609-10613.
PDB codes: 2vva 2vvb
19185003 S.B.Moparthi, P.Hammarström, and U.Carlsson (2009).
A nonessential role for Arg 55 in cyclophilin18 for catalysis of proline isomerization during protein folding.
  Protein Sci, 18, 475-479.  
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.  
17665409 G.E.Höst, J.Razkin, L.Baltzer, and B.H.Jonsson (2007).
Combined enzyme and substrate design: grafting of a cooperative two-histidine catalytic motif into a protein targeted at the scissile bond in a designed ester substrate.
  Chembiochem, 8, 1570-1576.  
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.  
17441142 V.M.Krishnamurthy, B.R.Bohall, C.Y.Kim, D.T.Moustakas, D.W.Christianson, and G.M.Whitesides (2007).
Thermodynamic parameters for the association of fluorinated benzenesulfonamides with bovine carbonic anhydrase II.
  Chem Asian J, 2, 94.  
17263415 V.M.Krishnamurthy, V.Semetey, P.J.Bracher, N.Shen, and G.M.Whitesides (2007).
Dependence of effective molarity on linker length for an intramolecular protein-ligand system.
  J Am Chem Soc, 129, 1312-1320.  
16416502 K.Okrasa, and R.J.Kazlauskas (2006).
Manganese-substituted carbonic anhydrase as a new peroxidase.
  Chemistry, 12, 1587-1596.  
  17077484 L.Buetow, A.Dawson, and W.N.Hunter (2006).
The nucleotide-binding site of Aquifex aeolicus LpxC.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1082-1086.
PDB code: 2j65
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
11375495 A.González, G.Larsson, R.Persson, and E.Cedergren-Zeppezauer (2001).
Atomic resolution structure of Escherichia coli dUTPase determined ab initio.
  Acta Crystallogr D Biol Crystallogr, 57, 767-774.
PDB codes: 1eu5 1euw
11330997 C.A.DiTusa, K.A.McCall, T.Christensen, M.Mahapatro, C.A.Fierke, and E.J.Toone (2001).
Thermodynamics of metal ion binding. 2. Metal ion binding by carbonic anhydrase variants.
  Biochemistry, 40, 5345-5351.  
11330996 C.A.DiTusa, T.Christensen, K.A.McCall, C.A.Fierke, and E.J.Toone (2001).
Thermodynamics of metal ion binding. 1. Metal ion binding by wild-type carbonic anhydrase.
  Biochemistry, 40, 5338-5344.  
11258876 D.Andersson, P.Hammarström, and U.Carlsson (2001).
Cofactor-induced refolding: refolding of molten globule carbonic anhydrase induced by Zn(II) and Co(II).
  Biochemistry, 40, 2653-2661.  
11148046 J.E.Jackman, C.R.Raetz, and C.A.Fierke (2001).
Site-directed mutagenesis of the bacterial metalloamidase UDP-(3-O-acyl)-N-acetylglucosamine deacetylase (LpxC). Identification of the zinc binding site.
  Biochemistry, 40, 514-523.  
11371461 M.Persson, J.R.Harbridge, P.Hammarström, R.Mitri, L.G.Mårtensson, U.Carlsson, G.R.Eaton, and S.S.Eaton (2001).
Comparison of electron paramagnetic resonance methods to determine distances between spin labels on human carbonic anhydrase II.
  Biophys J, 80, 2886-2897.  
10998050 B.Elleby, B.Sjöblom, C.Tu, D.N.Silverman, and S.Lindskog (2000).
Enhancement of catalytic efficiency by the combination of site-specific mutations in a carbonic anhydrase-related protein.
  Eur J Biochem, 267, 5908-5915.  
10747009 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.
PDB code: 1ekj
  10794421 R.E.Burton, J.A.Hunt, C.A.Fierke, and T.G.Oas (2000).
Novel disulfide engineering in human carbonic anhydrase II using the PAIRWISE side-chain geometry database.
  Protein Sci, 9, 776-785.  
10336637 B.Elleby, B.Sjöblom, and S.Lindskog (1999).
Changing the efficiency and specificity of the esterase activity of human carbonic anhydrase II by site-specific mutagenesis.
  Eur J Biochem, 262, 516-521.  
10872443 D.W.Christianson, and J.D.Cox (1999).
Catalysis by metal-activated hydroxide in zinc and manganese metalloenzymes.
  Annu Rev Biochem, 68, 33-57.  
10413479 J.A.Hunt, M.Ahmed, and C.A.Fierke (1999).
Metal binding specificity in carbonic anhydrase is influenced by conserved hydrophobic core residues.
  Biochemistry, 38, 9054-9062.  
10026271 J.E.Jackman, C.R.Raetz, and C.A.Fierke (1999).
UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase of Escherichia coli is a zinc metalloenzyme.
  Biochemistry, 38, 1902-1911.  
9778351 A.Peracchi, A.Karpeisky, L.Maloney, L.Beigelman, and D.Herschlag (1998).
A core folding model for catalysis by the hammerhead ribozyme accounts for its extraordinary sensitivity to abasic mutations.
  Biochemistry, 37, 14765-14775.  
8987973 J.E.Jackman, K.M.Merz, and C.A.Fierke (1996).
Disruption of the active site solvent network in carbonic anhydrase II decreases the efficiency of proton transfer.
  Biochemistry, 35, 16421-16428.  
7758465 C.Engstrand, B.H.Jonsson, and S.Lindskog (1995).
Catalytic and inhibitor-binding properties of some active-site mutants of human carbonic anhydrase I.
  Eur J Biochem, 229, 696-702.  
7669898 M.Lindgren, M.Svensson, P.O.Freskgård, U.Carlsson, P.Jonasson, L.G.Mårtensson, and B.H.Jonsson (1995).
Characterization of a folding intermediate of human carbonic anhydrase II: probing local mobility by electron paramagnetic resonance.
  Biophys J, 69, 202-213.  
7696308 M.Persson, G.Aronsson, N.Bergenhem, P.O.Freskgård, B.H.Jonsson, B.P.Surin, M.D.Spangfort, and U.Carlsson (1995).
GroEL/ES-mediated refolding of human carbonic anhydrase II: role of N-terminal helices as recognition motifs for GroEL.
  Biochim Biophys Acta, 1247, 195-200.  
  7757009 T.P.Lo, M.E.Murphy, J.G.Guillemette, M.Smith, and G.D.Brayer (1995).
Replacements in a conserved leucine cluster in the hydrophobic heme pocket of cytochrome c.
  Protein Sci, 4, 198-208.
PDB codes: 1csu 1csv 1csw 1csx
8306976 A.Liljas, K.Håkansson, B.H.Jonsson, and Y.Xue (1994).
Inhibition and catalysis of carbonic anhydrase. Recent crystallographic analyses.
  Eur J Biochem, 219, 1.  
8477723 S.K.Nair, and D.W.Christianson (1993).
Crystallographic studies of azide binding to human carbonic anhydrase II.
  Eur J Biochem, 213, 507-515.  
8451242 Y.Xue, J.Vidgren, L.A.Svensson, A.Liljas, B.H.Jonsson, and S.Lindskog (1993).
Crystallographic analysis of Thr-200-->His human carbonic anhydrase II and its complex with the substrate, HCO3-.
  Proteins, 15, 80-87.
PDB code: 1bic
8436138 Z.Liang, Y.Xue, G.Behravan, B.H.Jonsson, and S.Lindskog (1993).
Importance of the conserved active-site residues Tyr7, Glu106 and Thr199 for the catalytic function of human carbonic anhydrase II.
  Eur J Biochem, 211, 821-827.  
1542674 D.E.Roth, P.J.Venta, R.E.Tashian, and W.S.Sly (1992).
Molecular basis of human carbonic anhydrase II deficiency.
  Proc Natl Acad Sci U S A, 89, 1804-1808.  
1323835 N.X.Krueger, and H.Saito (1992).
A human transmembrane protein-tyrosine-phosphatase, PTP zeta, is expressed in brain and has an N-terminal receptor domain homologous to carbonic anhydrases.
  Proc Natl Acad Sci U S A, 89, 7417-7421.  
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.