2gu4: Difference between revisions

Revision as of 18:35, 21 February 2008

E. coli methionine aminopeptidase in complex with NleP, 1: 0.5, di-metalated

OverviewOverview

Methionine aminopeptidase (MetAP) removes the amino-terminal methionine residue from newly synthesized proteins, and it is a target for the development of antibacterial and anticancer agents. Available x-ray structures of MetAP, as well as other metalloaminopeptidases, show an active site containing two adjacent divalent metal ions bridged by a water molecule or hydroxide ion. The predominance of dimetalated structures leads naturally to proposed mechanisms of catalysis involving both metal ions. However, kinetic studies indicate that in many cases, only a single metal ion is required for full activity. By limiting the amount of metal ion present during crystal growth, we have now obtained a crystal structure for a complex of Escherichia coli MetAP with norleucine phosphonate, a transition-state analog, and only a single Mn(II) ion bound at the active site in the position designated M1, and three related structures of the same complex that show the transition from the mono-Mn(II) form to the di-Mn(II) form. An unliganded structure was also solved. In view of the full kinetic competence of the monometalated MetAP, the much weaker binding constant for occupancy of the M2 site compared with the M1 site, and the newly determined structures, we propose a revised mechanism of peptide bond hydrolysis by E. coli MetAP. We also suggest that the crystallization of dimetalated forms of metallohydrolases may, in some cases, be a misleading experimental artifact, and caution must be taken when structures are generated to aid in elucidation of reaction mechanisms or to support structure-aided drug design efforts.

About this StructureAbout this Structure

2GU4 is a Single protein structure of sequence from Escherichia coli with , and as ligands. Active as Methionyl aminopeptidase, with EC number 3.4.11.18 Full crystallographic information is available from OCA.

ReferenceReference

Structural basis of catalysis by monometalated methionine aminopeptidase., Ye QZ, Xie SX, Ma ZQ, Huang M, Hanzlik RP, Proc Natl Acad Sci U S A. 2006 Jun 20;103(25):9470-5. Epub 2006 Jun 12. PMID:16769889

Page seeded by OCA on Thu Feb 21 17:35:23 2008

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OCA

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-[[Image:2gu4.gif|left|200px]]<br /><applet load="2gu4" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:2gu4.gif|left|200px]]<br /><applet load="2gu4" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="2gu4, resolution 1.800&Aring;" />
 '''E. coli methionine aminopeptidase in complex with NleP, 1: 0.5, di-metalated'''<br />
 ==Overview==
-Methionine aminopeptidase (MetAP) removes the amino-terminal methionine, residue from newly synthesized proteins, and it is a target for the, development of antibacterial and anticancer agents. Available x-ray, structures of MetAP, as well as other metalloaminopeptidases, show an, active site containing two adjacent divalent metal ions bridged by a water, molecule or hydroxide ion. The predominance of dimetalated structures, leads naturally to proposed mechanisms of catalysis involving both metal, ions. However, kinetic studies indicate that in many cases, only a single, metal ion is required for full activity. By limiting the amount of metal, ion present during crystal growth, we have now obtained a crystal, structure for a complex of Escherichia coli MetAP with norleucine, phosphonate, a transition-state analog, and only a single Mn(II) ion bound, at the active site in the position designated M1, and three related, structures of the same complex that show the transition from the, mono-Mn(II) form to the di-Mn(II) form. An unliganded structure was also, solved. In view of the full kinetic competence of the monometalated MetAP, the much weaker binding constant for occupancy of the M2 site compared, with the M1 site, and the newly determined structures, we propose a, revised mechanism of peptide bond hydrolysis by E. coli MetAP. We also, suggest that the crystallization of dimetalated forms of metallohydrolases, may, in some cases, be a misleading experimental artifact, and caution, must be taken when structures are generated to aid in elucidation of, reaction mechanisms or to support structure-aided drug design efforts.
+Methionine aminopeptidase (MetAP) removes the amino-terminal methionine residue from newly synthesized proteins, and it is a target for the development of antibacterial and anticancer agents. Available x-ray structures of MetAP, as well as other metalloaminopeptidases, show an active site containing two adjacent divalent metal ions bridged by a water molecule or hydroxide ion. The predominance of dimetalated structures leads naturally to proposed mechanisms of catalysis involving both metal ions. However, kinetic studies indicate that in many cases, only a single metal ion is required for full activity. By limiting the amount of metal ion present during crystal growth, we have now obtained a crystal structure for a complex of Escherichia coli MetAP with norleucine phosphonate, a transition-state analog, and only a single Mn(II) ion bound at the active site in the position designated M1, and three related structures of the same complex that show the transition from the mono-Mn(II) form to the di-Mn(II) form. An unliganded structure was also solved. In view of the full kinetic competence of the monometalated MetAP, the much weaker binding constant for occupancy of the M2 site compared with the M1 site, and the newly determined structures, we propose a revised mechanism of peptide bond hydrolysis by E. coli MetAP. We also suggest that the crystallization of dimetalated forms of metallohydrolases may, in some cases, be a misleading experimental artifact, and caution must be taken when structures are generated to aid in elucidation of reaction mechanisms or to support structure-aided drug design efforts.
 ==About this Structure==
-GU4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with MN, NA and NLP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Methionyl_aminopeptidase Methionyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.18 3.4.11.18] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2GU4 OCA].
+GU4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=MN:'>MN</scene>, <scene name='pdbligand=NA:'>NA</scene> and <scene name='pdbligand=NLP:'>NLP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Methionyl_aminopeptidase Methionyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.18 3.4.11.18] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GU4 OCA].
 ==Reference==
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 [[Category: Methionyl aminopeptidase]]
 [[Category: Single protein]]
-[[Category: Ye, Q.Z.]]
+[[Category: Ye, Q Z.]]
 [[Category: MN]]
 [[Category: NA]]
@@ Line 25: / Line 25: @@
 [[Category: mononuclear]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 11:23:33 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:35:23 2008''