1krb: Difference between revisions

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CRYSTAL STRUCTURE OF KLEBSIELLA AEROGENES UREASE, ITS APOENZYME AND TWO ACTIVE SITE MUTANTS

OverviewOverview

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.

About this StructureAbout this Structure

1KRB is a Protein complex structure of sequences from Klebsiella aerogenes with and as ligands. Active as Urease, with EC number 3.5.1.5 Full crystallographic information is available from OCA.

ReferenceReference

Structures of the Klebsiella aerogenes urease apoenzyme and two active-site mutants., Jabri E, Karplus PA, Biochemistry. 1996 Aug 20;35(33):10616-26. PMID:8718850

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-[[Image:1krb.jpg|left|200px]]<br /><applet load="1krb" size="450" color="white" frame="true" align="right" spinBox="true"
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 caption="1krb, resolution 2.5&Aring;" />
 '''CRYSTAL STRUCTURE OF KLEBSIELLA AEROGENES UREASE, ITS APOENZYME AND TWO ACTIVE SITE MUTANTS'''<br />
 ==Overview==
-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.
+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.
 ==About this Structure==
-KRB is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Klebsiella_aerogenes Klebsiella aerogenes] with NI and CO2 as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Urease Urease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.5 3.5.1.5] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KRB OCA].
+KRB is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Klebsiella_aerogenes Klebsiella aerogenes] with <scene name='pdbligand=NI:'>NI</scene> and <scene name='pdbligand=CO2:'>CO2</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Urease Urease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.5 3.5.1.5] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KRB OCA].
 ==Reference==
@@ Line 15: / Line 15: @@
 [[Category: Urease]]
 [[Category: Jabri, E.]]
-[[Category: Karplus, P.A.]]
+[[Category: Karplus, P A.]]
 [[Category: CO2]]
 [[Category: NI]]
@@ Line 21: / Line 21: @@
 [[Category: nickel metalloenzyme]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:44:06 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:37:07 2008''