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PDBsum entry 1krb
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protein metals Protein-protein interface(s) links
Hydrolase PDB id
1krb

 

 

 

 

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Contents
Protein chains
100 a.a. *
101 a.a. *
566 a.a. *
Metals
_NI ×2
Waters ×152
* Residue conservation analysis
PDB id:
1krb
Name: Hydrolase
Title: Crystal structure of klebsiella aerogenes urease, its apoenzyme and two active site mutants
Structure: Urease. Chain: a. Mutation: yes. Urease. Chain: b. Mutation: yes. Urease. Chain: c. Mutation: yes
Source: Klebsiella aerogenes. Organism_taxid: 28451. Organ: bean. Organ: bean
Biol. unit: Nonamer (from PQS)
Resolution:
2.50Å     R-factor:   0.179    
Authors: E.Jabri,P.A.Karplus
Key ref:
E.Jabri and P.A.Karplus (1996). Structures of the Klebsiella aerogenes urease apoenzyme and two active-site mutants. Biochemistry, 35, 10616-10626. PubMed id: 8718850 DOI: 10.1021/bi960424z
Date:
20-Jun-95     Release date:   15-Oct-95    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P18316  (URE3_KLEAE) -  Urease subunit gamma from Klebsiella aerogenes
Seq:
Struc: 		100 a.a.
100 a.a.
Protein chain
Pfam   ArchSchema ?
P18315  (URE2_KLEAE) -  Urease subunit beta from Klebsiella aerogenes
Seq:
Struc: 		106 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
P18314  (URE1_KLEAE) -  Urease subunit alpha from Klebsiella aerogenes
Seq:
Struc: 		 
Seq:
Struc: 		567 a.a.
566 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C: E.C.3.5.1.5  - urease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: urea + 2 H2O + H+ = hydrogencarbonate + 2 NH4+
urea
 + 2 × H2O
 + H(+)
 = hydrogencarbonate
 + 2 × NH4(+)
      Cofactor: Ni(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1021/bi960424z Biochemistry 35:10616-10626 (1996)
PubMed id: 8718850  
 
 
Structures of the Klebsiella aerogenes urease apoenzyme and two active-site mutants.
E.Jabri, P.A.Karplus.
 
  ABSTRACT  
 
Urease from Klebsiella aerogenes [Jabri et al. (1995) Science 268, 998-1004] is an (alpha beta gamma)3 trimer with each alpha-subunit having an (alpha beta)8-barrel domain containing a binickel active center. Here we examine structure-function relations for urease in more detail through structural analysis of the urease apoenzyme at 2.3 A resolution and mutants of two key catalytic residues (H219A and H320A) at 2.5 A resolution. With the exception of the active site, in which a water molecule takes the place of the missing carbamate and nickel atoms, the structure of the apoenzyme is nearly identical to that of the holoenzyme, suggesting a high degree of preorganization which helps explain the tight binding of nickel. In the structure of H219A, the major change involves a conformational shift and ordering of the active site flap, but a small shift in the side chain of Asp alpha 221 could contribute to the lower activity of H219A. In the H320A structure, the catalytic water, primarily a Ni-2 ligand in the holoenzyme, shifts into a bridging position. This shift shows that the nickel ligation is rather sensitive to the environment and the change in ligation may contribute to the 10(5)-fold lower activity of H320A. In addition, these results show that urease is resilient to the loss of nickel ions and mutations. Analysis of the urease tertiary/quaternary structure suggests that the stability of this enzyme may be largely due to its burial of an unusually large fraction of its residues: 50% in the gamma-subunit, 30% in the beta-subunit, and 60% in the alpha-subunit.
 

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.  
20207756 E.L.Carter, and R.P.Hausinger (2010).
Characterization of the Klebsiella aerogenes urease accessory protein UreD in fusion with the maltose binding protein.
  J Bacteriol, 192, 2294-2304.  
20442959 H.Kaluarachchi, K.C.Chan Chung, and D.B.Zamble (2010).
Microbial nickel proteins.
  Nat Prod Rep, 27, 681-694.  
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
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.  
17249815 A.N.Alexandrova, and W.L.Jorgensen (2007).
Why urea eliminates ammonia rather than hydrolyzes in aqueous solution.
  J Phys Chem B, 111, 720-730.  
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.  
16283299 M.J.Wagemaker, D.C.Eastwood, C.van der Drift, M.S.Jetten, K.Burton, L.J.Van Griensven, and H.J.Op den Camp (2006).
Expression of the urease gene of Agaricus bisporus: a tool for studying fruit body formation and post-harvest development.
  Appl Microbiol Biotechnol, 71, 486-492.  
16284925 L.L.Lin, W.H.Hsu, W.Y.Hsu, S.C.Kan, and H.Y.Hu (2005).
Phylogenetic analysis and biochemical characterization of a thermostable dihydropyrimidinase from alkaliphilic Bacillus sp. TS-23.
  Antonie Van Leeuwenhoek, 88, 189-197.  
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.  
12837777 Z.Xu, Y.Liu, Y.Yang, W.Jiang, E.Arnold, and J.Ding (2003).
Crystal structure of D-Hydantoinase from Burkholderia pickettii at a resolution of 2.7 Angstroms: insights into the molecular basis of enzyme thermostability.
  J Bacteriol, 185, 4038-4049.
PDB code: 1nfg
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.  
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
10411639 M.Houimel, J.P.Mach, I.Corthésy-Theulaz, B.Corthésy, and I.Fisch (1999).
New inhibitors of Helicobacter pylori urease holoenzyme selected from phage-displayed peptide libraries.
  Eur J Biochem, 262, 774-780.  
  10548053 N.Nagano, E.G.Hutchinson, and J.M.Thornton (1999).
Barrel structures in proteins: automatic identification and classification including a sequence analysis of TIM barrels.
  Protein Sci, 8, 2072-2084.  
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
9761912 S.Benini, S.Ciurli, W.R.Rypniewski, K.S.Wilson, and S.Mangani (1998).
Crystallization and preliminary high-resolution X-ray diffraction analysis of native and beta-mercaptoethanol-inhibited urease from Bacillus pasteurii.
  Acta Crystallogr D Biol Crystallogr, 54, 409-412.  
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.  
9095194 K.Diederichs, and P.A.Karplus (1997).
Improved R-factors for diffraction data analysis in macromolecular crystallography.
  Nat Struct Biol, 4, 269-275.  
9201965 M.A.Pearson, L.O.Michel, R.P.Hausinger, and P.A.Karplus (1997).
Structures of Cys319 variants and acetohydroxamate-inhibited Klebsiella aerogenes urease.
  Biochemistry, 36, 8164-8172.
PDB codes: 1fwa 1fwb 1fwc 1fwd 1fwe 1fwf 1fwg 1fwh 1fwj
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.

 

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