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PDBsum entry 1k6w

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protein metals links
Hydrolase PDB id
1k6w
Jmol
Contents
Protein chain
423 a.a. *
Metals
_FE
Waters ×426
* Residue conservation analysis
PDB id:
1k6w
Name: Hydrolase
Title: The structure of escherichia coli cytosine deaminase
Structure: Cytosine deaminase. Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PDB file)
Resolution:
1.75Å     R-factor:   0.155     R-free:   0.172
Authors: G.C.Ireton,G.Mcdermott,M.E.Black,B.L.Stoddard
Key ref:
G.C.Ireton et al. (2002). The structure of Escherichia coli cytosine deaminase. J Mol Biol, 315, 687-697. PubMed id: 11812140 DOI: 10.1006/jmbi.2001.5277
Date:
17-Oct-01     Release date:   06-Feb-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P25524  (CODA_ECOLI) -  Cytosine deaminase
Seq:
Struc:
427 a.a.
423 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.5.4.1  - Cytosine deaminase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Cytosine + H2O = uracil + NH3
Cytosine
+ H(2)O
= uracil
+ NH(3)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytosol   1 term 
  Biological process     cytosine metabolic process   2 terms 
  Biochemical function     isoguanine deaminase activity     8 terms  

 

 
    Added reference    
 
 
DOI no: 10.1006/jmbi.2001.5277 J Mol Biol 315:687-697 (2002)
PubMed id: 11812140  
 
 
The structure of Escherichia coli cytosine deaminase.
G.C.Ireton, G.McDermott, M.E.Black, B.L.Stoddard.
 
  ABSTRACT  
 
Cytosine deaminase (CD) catalyzes the deamination of cytosine, producing uracil. This enzyme is present in prokaryotes and fungi (but not multicellular eukaryotes) and is an important member of the pyrimidine salvage pathway in those organisms. The same enzyme also catalyzes the conversion of 5-fluorocytosine to 5-fluorouracil; this activity allows the formation of a cytotoxic chemotherapeutic agent from a non-cytotoxic precursor. The enzyme is of widespread interest both for antimicrobial drug design and for gene therapy applications against tumors. The structure of Escherichia coli CD has been determined in the presence and absence of a bound mechanism-based inhibitor. The enzyme forms an (alphabeta)(8) barrel structure with structural similarity to adenosine deaminase, a relationship that is undetectable at the sequence level, and no similarity to bacterial cytidine deaminase. The enzyme is packed into a hexameric assembly stabilized by a unique domain-swapping interaction between enzyme subunits. The active site is located in the mouth of the enzyme barrel and contains a bound iron ion that coordinates a hydroxyl nucleophile. Substrate binding involves a significant conformational change that sequesters the reaction complex from solvent.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. (a) Cytosine deaminase catalyzes conversion of cytosine to uracil and ammonia. The reaction proceeds through the stereospecific addition of a metal-bound hydroxyl group to the substrate, forming a tetrahedral transition state intermediate that decomposes through the elimination of ammonia. (b) 2-Hydroxypyrimidine (also called pyrimidine-2-one in its tautomeric keto form) is enzymatically converted to a hydrated adduct that accumulates as a mechanism-based, tightly bound active site inhibitor. The structure of bCD was solved in the presence of this inhibitor as described in the text. (c) 5-Fluorocytosine is also deaminated by bCD to form 5-fluoruracil, a potent cytotoxic chemotherapy agent.
Figure 4.
Figure 4. Schematic of enzyme active site with distances of contacts between protein side-chains, the catalytic metal ion and bound ligand. (a) Unbound apo-enzyme. (b) Enzyme complexed with 4-(R)-hydroxyl-3,4-dihydropyrimidine, a tightly bound substrate complex formed by the enzymatic hydration of 2-hydroxypyrimidine. (c) active site and substrate-binding interactions for cytosine deaminase (from Xiang et al., 1997[10]). The two common features of the cytosine deaminase and cytidine deaminase active site are a bound metal ion that coordinates the hydroxyl nucleophile, and a glutamic acid residue (red side-chain) that acts as a general acid/base.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 315, 687-697) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21338418 J.E.Martin, and J.A.Imlay (2011).
The alternative aerobic ribonucleotide reductase of Escherichia coli, NrdEF, is a manganese-dependent enzyme that enables cell replication during periods of iron starvation.
  Mol Microbiol, 80, 319-334.  
20529317 G.Garau, L.Muzzolini, P.Tornaghi, and M.Degano (2010).
Active site plasticity revealed from the structure of the enterobacterial N-ribohydrolase RihA bound to a competitive inhibitor.
  BMC Struct Biol, 10, 14.  
20088569 G.J.Lohman, and J.Stubbe (2010).
Inactivation of Lactobacillus leichmannii ribonucleotide reductase by 2',2'-difluoro-2'-deoxycytidine 5'-triphosphate: covalent modification.
  Biochemistry, 49, 1404-1417.  
  20634983 K.Shameer, G.Pugalenthi, K.K.Kandaswamy, P.N.Suganthan, G.Archunan, and R.Sowdhamini (2010).
Insights into Protein Sequence and Structure-Derived Features Mediating 3D Domain Swapping Mechanism using Support Vector Machine Based Approach.
  Bioinform Biol Insights, 4, 33-42.  
19201959 C.Scott, C.J.Jackson, C.W.Coppin, R.G.Mourant, M.E.Hilton, T.D.Sutherland, R.J.Russell, and J.G.Oakeshott (2009).
Catalytic improvement and evolution of atrazine chlorohydrolase.
  Appl Environ Microbiol, 75, 2184-2191.  
18781344 C.Y.Huang, C.C.Hsu, M.C.Chen, and Y.S.Yang (2009).
Effect of metal binding and posttranslational lysine carboxylation on the activity of recombinant hydantoinase.
  J Biol Inorg Chem, 14, 111-121.  
19051213 L.Marignol, R.Foley, T.D.Southgate, M.Coffey, D.Hollywood, and M.Lawler (2009).
Hypoxia response element-driven cytosine deaminase/5-fluorocytosine gene therapy system: a highly effective approach to overcome the dynamics of tumour hypoxia and enhance the radiosensitivity of prostate cancer cells in vitro.
  J Gene Med, 11, 169-179.  
19487291 M.Fuchita, A.Ardiani, L.Zhao, K.Serve, B.L.Stoddard, and M.E.Black (2009).
Bacterial cytosine deaminase mutants created by molecular engineering show improved 5-fluorocytosine-mediated cell killing in vitro and in vivo.
  Cancer Res, 69, 4791-4799.
PDB code: 3g77
19470646 P.M.Murphy, J.M.Bolduc, J.L.Gallaher, B.L.Stoddard, and D.Baker (2009).
Alteration of enzyme specificity by computational loop remodeling and design.
  Proc Natl Acad Sci U S A, 106, 9215-9220.
PDB code: 3e0l
19678710 T.T.Nguyen, A.A.Fedorov, L.Williams, E.V.Fedorov, Y.Li, C.Xu, S.C.Almo, and F.M.Raushel (2009).
The mechanism of the reaction catalyzed by uronate isomerase illustrates how an isomerase may have evolved from a hydrolase within the amidohydrolase superfamily.
  Biochemistry, 48, 8879-8890.
PDB codes: 3hk5 3hk7 3hk8 3hk9 3hka
18096851 L.L.Grochowski, and R.H.White (2008).
Promiscuous anaerobes: new and unconventional metabolism in methanogenic archaea.
  Ann N Y Acad Sci, 1125, 190-214.  
18291415 T.S.Stolworthy, A.M.Korkegian, C.L.Willmon, A.Ardiani, J.Cundiff, B.L.Stoddard, and M.E.Black (2008).
Yeast cytosine deaminase mutants with increased thermostability impart sensitivity to 5-fluorocytosine.
  J Mol Biol, 377, 854-869.  
17660279 J.L.Seffernick, A.Aleem, J.P.Osborne, G.Johnson, M.J.Sadowsky, and L.P.Wackett (2007).
Hydroxyatrazine N-ethylaminohydrolase (AtzB): an amidohydrolase superfamily enzyme catalyzing deamination and dechlorination.
  J Bacteriol, 189, 6989-6997.  
17567047 R.S.Hall, D.F.Xiang, C.Xu, and F.M.Raushel (2007).
N-Acetyl-D-glucosamine-6-phosphate deacetylase: substrate activation via a single divalent metal ion.
  Biochemistry, 46, 7942-7952.  
17640072 R.Tyagi, D.Kumaran, S.K.Burley, and S.Swaminathan (2007).
X-ray structure of imidazolonepropionase from Agrobacterium tumefaciens at 1.87 A resolution.
  Proteins, 69, 652-658.
PDB codes: 2gok 2puz
16894175 A.Alhapel, D.J.Darley, N.Wagener, E.Eckel, N.Elsner, and A.J.Pierik (2006).
Molecular and functional analysis of nicotinate catabolism in Eubacterium barkeri.
  Proc Natl Acad Sci U S A, 103, 12341-12346.  
16963440 M.Goto, H.Hayashi, I.Miyahara, K.Hirotsu, M.Yoshida, and T.Oikawa (2006).
Crystal structures of nonoxidative zinc-dependent 2,6-dihydroxybenzoate (gamma-resorcylate) decarboxylase from Rhizobium sp. strain MTP-10005.
  J Biol Chem, 281, 34365-34373.
PDB codes: 2dvt 2dvu 2dvx
16885454 N.Shapir, C.Pedersen, O.Gil, L.Strong, J.Seffernick, M.J.Sadowsky, and L.P.Wackett (2006).
TrzN from Arthrobacter aurescens TC1 Is a zinc amidohydrolase.
  J Bacteriol, 188, 5859-5864.  
16709014 S.Deorah, C.F.Lynch, Z.A.Sibenaller, and T.C.Ryken (2006).
Trends in brain cancer incidence and survival in the United States: Surveillance, Epidemiology, and End Results Program, 1973 to 2001.
  Neurosurg Focus, 20, E1.  
16990261 Y.Yu, Y.H.Liang, E.Brostromer, J.M.Quan, S.Panjikar, Y.H.Dong, and X.D.Su (2006).
A catalytic mechanism revealed by the crystal structures of the imidazolonepropionase from Bacillus subtilis.
  J Biol Chem, 281, 36929-36936.
PDB codes: 2bb0 2g3f
16187256 A.M.Elshafei, N.H.Ali, and L.A.Mohamed (2005).
Cytidine deaminase activity in Penicillium politans NRC-510.
  J Basic Microbiol, 45, 335-343.  
15895087 J.C.Meier, C.Henneberger, I.Melnick, C.Racca, R.J.Harvey, U.Heinemann, V.Schmieden, and R.Grantyn (2005).
RNA editing produces glycine receptor alpha3(P185L), resulting in high agonist potency.
  Nat Neurosci, 8, 736-744.  
15809227 M.A.Langlois, R.C.Beale, S.G.Conticello, and M.S.Neuberger (2005).
Mutational comparison of the single-domained APOBEC3C and double-domained APOBEC3F/G anti-retroviral cytidine deaminases provides insight into their DNA target site specificities.
  Nucleic Acids Res, 33, 1913-1923.  
  16511045 M.J.Ku, W.H.Lee, K.H.Nam, K.H.Rhee, K.S.Lee, E.E.Kim, M.H.Yu, and K.Y.Hwang (2005).
Crystallization and preliminary X-ray crystallographic analysis of the tRNA-specific adenosine deaminase from Streptococcus pyogenes.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 375-377.  
14557261 F.Vincent, D.Yates, E.Garman, G.J.Davies, and J.A.Brannigan (2004).
The three-dimensional structure of the N-acetylglucosamine-6-phosphate deacetylase, NagA, from Bacillus subtilis: a member of the urease superfamily.
  J Biol Chem, 279, 2809-2816.
PDB codes: 1un7 2vhl
15358859 H.Fukatsu, Y.Hashimoto, M.Goda, H.Higashibata, and M.Kobayashi (2004).
Amine-synthesizing enzyme N-substituted formamide deformylase: screening, purification, characterization, and gene cloning.
  Proc Natl Acad Sci U S A, 101, 13726-13731.  
14685275 R.C.Deo, E.F.Schmidt, A.Elhabazi, H.Togashi, S.K.Burley, and S.M.Strittmatter (2004).
Structural bases for CRMP function in plexin-dependent semaphorin3A signaling.
  EMBO J, 23, 9.
PDB code: 1kcx
14736882 W.L.Lai, L.Y.Chou, C.Y.Ting, R.Kirby, Y.C.Tsai, A.H.Wang, and S.H.Liaw (2004).
The functional role of the binuclear metal center in D-aminoacylase: one-metal activation and second-metal attenuation.
  J Biol Chem, 279, 13962-13967.
PDB codes: 1rjp 1rjq 1rjr 1rk5 1rk6 1v4y 1v51
12906827 G.C.Ireton, M.E.Black, and B.L.Stoddard (2003).
The 1.14 A crystal structure of yeast cytosine deaminase: evolution of nucleotide salvage enzymes and implications for genetic chemotherapy.
  Structure, 11, 961-972.
PDB codes: 1ox7 1p6o
14579323 L.N.Kinch, Y.Qi, T.J.Hubbard, and N.V.Grishin (2003).
CASP5 target classification.
  Proteins, 53, 340-351.  
12644833 P.M.Deckert, C.Renner, L.S.Cohen, A.Jungbluth, G.Ritter, J.R.Bertino, L.J.Old, and S.Welt (2003).
A33scFv-cytosine deaminase: a recombinant protein construct for antibody-directed enzyme-prodrug therapy.
  Br J Cancer, 88, 937-939.  
12486048 S.B.Mulrooney, and R.P.Hausinger (2003).
Metal ion dependence of recombinant Escherichia coli allantoinase.
  J Bacteriol, 185, 126-134.  
12454005 S.H.Liaw, S.J.Chen, T.P.Ko, C.S.Hsu, C.J.Chen, A.H.Wang, and Y.C.Tsai (2003).
Crystal structure of D-aminoacylase from Alcaligenes faecalis DA1. A novel subset of amidohydrolases and insights into the enzyme mechanism.
  J Biol Chem, 278, 4957-4962.
PDB code: 1m7j
12637534 T.P.Ko, J.J.Lin, C.Y.Hu, Y.H.Hsu, A.H.Wang, and S.H.Liaw (2003).
Crystal structure of yeast cytosine deaminase. Insights into enzyme mechanism and evolution.
  J Biol Chem, 278, 19111-19117.
PDB code: 1uaq
  12686722 W.A.Denny (2003).
Prodrugs for Gene-Directed Enzyme-Prodrug Therapy (Suicide Gene Therapy).
  J Biomed Biotechnol, 2003, 48-70.  
12777821 Y.H.Hsu, C.Y.Hu, J.J.Lin, and S.H.Liaw (2003).
Crystallization and preliminary crystallographic analysis of yeast cytosine deaminase.
  Acta Crystallogr D Biol Crystallogr, 59, 950-952.  
12045112 B.L.Bass (2002).
RNA editing by adenosine deaminases that act on RNA.
  Annu Rev Biochem, 71, 817-846.  
12218024 N.Shapir, J.P.Osborne, G.Johnson, M.J.Sadowsky, and L.P.Wackett (2002).
Purification, substrate range, and metal center of AtzC: the N-isopropylammelide aminohydrolase involved in bacterial atrazine metabolism.
  J Bacteriol, 184, 5376-5384.  
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.