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protein metals Protein-protein interface(s) links
Hydrolase PDB id
1fwf
Jmol
Contents
Protein chains
100 a.a. *
101 a.a. *
551 a.a. *
Metals
_NI ×2
Waters ×285
* Residue conservation analysis
PDB id:
1fwf
Name: Hydrolase
Title: Klebsiella aerogenes urease, c319d variant
Structure: Urease. Chain: a. Synonym: urea amidohydrolase. Engineered: yes. Mutation: yes. Urease. Chain: b. Synonym: urea amidohydrolase. Engineered: yes.
Source: Klebsiella aerogenes. Organism_taxid: 28451. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Nonamer (from PQS)
Resolution:
2.00Å     R-factor:   0.171    
Authors: M.A.Pearson,P.A.Karplus
Key ref:
M.A.Pearson et al. (1997). Structures of Cys319 variants and acetohydroxamate-inhibited Klebsiella aerogenes urease. Biochemistry, 36, 8164-8172. PubMed id: 9201965 DOI: 10.1021/bi970514j
Date:
23-Apr-97     Release date:   15-Oct-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P18316  (URE3_KLEAE) -  Urease subunit gamma
Seq:
Struc: 		100 a.a.
100 a.a.
Protein chain
Pfam   ArchSchema ?
P18315  (URE2_KLEAE) -  Urease subunit beta
Seq:
Struc: 		106 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
P18314  (URE1_KLEAE) -  Urease subunit alpha
Seq:
Struc: 		 
Seq:
Struc: 		567 a.a.
551 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, B, C: E.C.3.5.1.5  - Urease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Urea + H2O = CO2 + 2 NH3
Urea
 + H(2)O
 = CO(2)
 + 2 × NH(3)
      Cofactor: Nickel
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     nitrogen compound metabolic process   2 terms 
  Biochemical function     hydrolase activity     5 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi970514j Biochemistry 36:8164-8172 (1997)
PubMed id: 9201965  
 
 
Structures of Cys319 variants and acetohydroxamate-inhibited Klebsiella aerogenes urease.
M.A.Pearson, L.O.Michel, R.P.Hausinger, P.A.Karplus.
 
  ABSTRACT  
 
Cys319 is located on a mobile flap covering the active site of Klebsiella aerogenes urease but does not play an essential role in catalysis. Four urease variants altered at position C319 range from having high activity (C319A) to no measurable activity (C319Y), indicating Cys is not required at this position, but its presence is highly influential [Martin, P. R., & Hausinger, R. P. (1992) J. Biol. Chem. 267, 20024-20027]. Here, we present 2.0 A resolution crystal structures of C319A, C319S, C319D, and C319Y proteins and the C319A variant inhibited by acetohydroxamic acid. These structures show changes in the hydration of the active site nickel ions and in the position and flexibility of the active site flap. The C319Y protein exhibits an alternate conformation of the flap, explaining its lack of activity. The changes in hydration and conformation suggest that there are suboptimal protein-solvent and protein-protein interactions in the empty urease active site which contribute to urease catalysis. Specifically, we hypothesize that the suboptimal interactions may provide a significant source of substrate binding energy, and such hidden energy may be a common phenomenon for enzymes that contain mobile active site loops and undergo an induced fit. The acetohydroxamic acid-bound structure reveals a chelate interaction similar to those seen in other metalloenzymes and in a small molecule nickel complex. The inhibitor binding mode supports the proposed mode of urea binding. We complement these structural studies with extended functional studies of C319A urease to show that it has enhanced stability and resistance to inhibition by buffers containing nickel ions. The near wild-type activity and enhanced stability of the C319A variant make it useful for further studies of urease structure-function relationships.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20890717 J.Lv, Y.Jiang, Q.Yu, and S.Lu (2011).
Structural and functional role of nickel ions in urease by molecular dynamics simulation.
  J Biol Inorg Chem, 16, 125-135.  
20680216 C.Kozoni, E.Manolopoulou, M.Siczek, T.Lis, E.K.Brechin, and C.J.Milios (2010).
Polynuclear manganese amino acid complexes.
  Dalton Trans, 39, 7943-7950.  
20886006 H.Carlsson, and E.Nordlander (2010).
Computational modeling of the mechanism of urease.
  Bioinorg Chem Appl, 0, 0.  
20635345 R.Lam, V.Romanov, K.Johns, K.P.Battaile, J.Wu-Brown, J.L.Guthrie, R.P.Hausinger, E.F.Pai, and N.Y.Chirgadze (2010).
Crystal structure of a truncated urease accessory protein UreF from Helicobacter pylori.
  Proteins, 78, 2839-2848.
PDB code: 3cxn
  20046957 E.L.Carter, N.Flugga, J.L.Boer, S.B.Mulrooney, and R.P.Hausinger (2009).
Interplay of metal ions and urease.
  Metallomics, 1, 207-221.  
19030615 A.Banerjee, R.Singh, D.Chopra, E.Colacio, and K.K.Rajak (2008).
Mixed bridged dinuclear Ni(II) complexes: synthesis, structure, magnetic properties and DFT study.
  Dalton Trans, 0, 6539-6545.  
18823937 S.Quiroz-Valenzuela, S.C.Sukuru, R.P.Hausinger, L.A.Kuhn, and W.T.Heller (2008).
The structure of urease activation complexes examined by flexibility analysis, mutagenesis, and small-angle X-ray scattering.
  Arch Biochem Biophys, 480, 51-57.  
18443695 W.Z.Lee, H.S.Tseng, M.Y.Ku, and T.S.Kuo (2008).
Dinickel complexes of disubstituted benzoate polydentate ligands: mimics for the active site of urease.
  Dalton Trans, 0, 2538-2541.  
17510959 M.Salomone-Stagni, B.Zambelli, F.Musiani, and S.Ciurli (2007).
A model-based proposal for the role of UreF as a GTPase-activating protein in the urease active site biosynthesis.
  Proteins, 68, 749-761.  
16773613 G.Estiu, D.Suárez, and K.M.Merz (2006).
Quantum mechanical and molecular dynamics simulations of ureases and Zn beta-lactamases.
  J Comput Chem, 27, 1240-1262.  
16584179 G.Estiu, and K.M.Merz (2006).
Catalyzed decomposition of urea. Molecular dynamics simulations of the binding of urea to urease.
  Biochemistry, 45, 4429-4443.  
17041056 J.K.Kim, S.B.Mulrooney, and R.P.Hausinger (2006).
The UreEF fusion protein provides a soluble and functional form of the UreF urease accessory protein.
  J Bacteriol, 188, 8413-8420.  
16937256 L.Zhang, S.B.Mulrooney, A.F.Leung, Y.Zeng, B.B.Ko, R.P.Hausinger, and H.Sun (2006).
Inhibition of urease by bismuth(III): implications for the mechanism of action of bismuth drugs.
  Biometals, 19, 503-511.  
16199586 J.K.Kim, S.B.Mulrooney, and R.P.Hausinger (2005).
Biosynthesis of active Bacillus subtilis urease in the absence of known urease accessory proteins.
  J Bacteriol, 187, 7150-7154.  
15627389 E.I.Tarun, D.B.Rubinov, and D.I.Metelitza (2004).
Inhibition of soybean urease by triketone oximes.
  Biochemistry (Mosc), 69, 1344-1352.  
15090490 R.P.Hausinger (2004).
Metabolic versatility of prokaryotes for urea decomposition.
  J Bacteriol, 186, 2520-2522.  
14749331 Z.Chang, J.Kuchar, and R.P.Hausinger (2004).
Chemical cross-linking and mass spectrometric identification of sites of interaction for UreD, UreF, and urease.
  J Biol Chem, 279, 15305-15313.  
12829270 S.B.Mulrooney, and R.P.Hausinger (2003).
Nickel uptake and utilization by microorganisms.
  FEMS Microbiol Rev, 27, 239-261.  
11775695 D.Walther, C.Fugger, H.Schreer, R.Kilian, and H.Görls (2001).
Reversible fixation of carbon dioxide at nickel(0) centers: a route for large organometallic rings, dimers, and tetramers.
  Chemistry, 7, 5214-5221.  
11395407 J.A.Gerlt, and P.C.Babbitt (2001).
Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies.
  Annu Rev Biochem, 70, 209-246.  
11015224 A.Soriano, G.J.Colpas, and R.P.Hausinger (2000).
UreE stimulation of GTP-dependent urease activation in the UreD-UreF-UreG-urease apoprotein complex.
  Biochemistry, 39, 12435-12440.  
10913264 M.A.Pearson, I.S.Park, R.A.Schaller, L.O.Michel, P.A.Karplus, and R.P.Hausinger (2000).
Kinetic and structural characterization of urease active site variants.
  Biochemistry, 39, 8575-8584.
PDB codes: 1ejr 1ejs 1ejt 1eju 1ejv
10820010 M.J.Todd, and R.P.Hausinger (2000).
Fluoride inhibition of Klebsiella aerogenes urease: mechanistic implications of a pseudo-uncompetitive, slow-binding inhibitor.
  Biochemistry, 39, 5389-5396.  
10500143 A.Soriano, and R.P.Hausinger (1999).
GTP-dependent activation of urease apoprotein in complex with the UreD, UreF, and UreG accessory proteins.
  Proc Natl Acad Sci U S A, 96, 11140-11144.  
10373003 K.Pawłowski, B.Zhang, L.Rychlewski, and A.Godzik (1999).
The Helicobacter pylori genome: from sequence analysis to structural and functional predictions.
  Proteins, 36, 20-30.  
10226043 M.J.Maroney (1999).
Structure/function relationships in nickel metallobiochemistry.
  Curr Opin Chem Biol, 3, 188-199.  
  10368287 S.Benini, W.R.Rypniewski, K.S.Wilson, S.Miletti, S.Ciurli, and S.Mangani (1999).
A new proposal for urease mechanism based on the crystal structures of the native and inhibited enzyme from Bacillus pasteurii: why urea hydrolysis costs two nickels.
  Structure, 7, 205-216.
PDB codes: 2ubp 3ubp
9558361 M.A.Pearson, R.A.Schaller, L.O.Michel, P.A.Karplus, and R.P.Hausinger (1998).
Chemical rescue of Klebsiella aerogenes urease variants lacking the carbamylated-lysine nickel ligand.
  Biochemistry, 37, 6214-6220.
PDB codes: 1a5k 1a5l 1a5m 1a5n 1a5o
  9667931 S.W.Ragsdale (1998).
Nickel biochemistry.
  Curr Opin Chem Biol, 2, 208-215.  
9914255 U.Ermler, W.Grabarse, S.Shima, M.Goubeaud, and R.K.Thauer (1998).
Active sites of transition-metal enzymes with a focus on nickel.
  Curr Opin Struct Biol, 8, 749-758.  
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.