2dqm: Difference between revisions
New page: left|200px<br /><applet load="2dqm" size="450" color="white" frame="true" align="right" spinBox="true" caption="2dqm, resolution 1.60Å" /> '''Crystal Structure of... |
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[[Image:2dqm.gif|left|200px]]<br /><applet load="2dqm" size=" | [[Image:2dqm.gif|left|200px]]<br /><applet load="2dqm" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="2dqm, resolution 1.60Å" /> | caption="2dqm, resolution 1.60Å" /> | ||
'''Crystal Structure of Aminopeptidase N complexed with bestatin'''<br /> | '''Crystal Structure of Aminopeptidase N complexed with bestatin'''<br /> | ||
==Overview== | ==Overview== | ||
Aminopeptidase N from Escherichia coli is a broad specificity zinc | Aminopeptidase N from Escherichia coli is a broad specificity zinc exopeptidase belonging to aminopeptidase clan MA, family M1. The structures of the ligand-free form and the enzyme-bestatin complex were determined at 1.5- and 1.6-A resolution, respectively. The enzyme is composed of four domains: an N-terminal beta-domain (Met(1)-Asp(193)), a catalytic domain (Phe(194)-Gly(444)), a middle beta-domain (Thr(445)-Trp(546)), and a C-terminal alpha-domain (Ser(547)-Ala(870)). The structure of the catalytic domain exhibits similarity to thermolysin, and a metal-binding motif (HEXXHX(18)E) is found in the domain. The zinc ion is coordinated by His(297), His(301), Glu(320), and a water molecule. The groove on the catalytic domain that contains the active site is covered by the C-terminal alpha-domain, and a large cavity is formed inside the protein. However, there exists a small hole at the center of the C-terminal alpha-domain. The N terminus of bestatin is recognized by Glu(121) and Glu(264), which are located in the N-terminal and catalytic domains, respectively. Glu(298) and Tyr(381), located near the zinc ion, are considered to be involved in peptide cleavage. A difference revealed between the ligand-free form and the enzyme-bestatin complex indicated that Met(260) functions as a cushion to accept substrates with different N-terminal residue sizes, resulting in the broad substrate specificity of this enzyme. | ||
==About this Structure== | ==About this Structure== | ||
2DQM 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 ZN, SO4 and BES as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Membrane_alanyl_aminopeptidase Membrane alanyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.2 3.4.11.2] Full crystallographic information is available from [http:// | 2DQM 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=ZN:'>ZN</scene>, <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=BES:'>BES</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Membrane_alanyl_aminopeptidase Membrane alanyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.2 3.4.11.2] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQM OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: inhibitor complex]] | [[Category: inhibitor complex]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:01:31 2008'' | ||
Revision as of 18:01, 21 February 2008
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Crystal Structure of Aminopeptidase N complexed with bestatin
OverviewOverview
Aminopeptidase N from Escherichia coli is a broad specificity zinc exopeptidase belonging to aminopeptidase clan MA, family M1. The structures of the ligand-free form and the enzyme-bestatin complex were determined at 1.5- and 1.6-A resolution, respectively. The enzyme is composed of four domains: an N-terminal beta-domain (Met(1)-Asp(193)), a catalytic domain (Phe(194)-Gly(444)), a middle beta-domain (Thr(445)-Trp(546)), and a C-terminal alpha-domain (Ser(547)-Ala(870)). The structure of the catalytic domain exhibits similarity to thermolysin, and a metal-binding motif (HEXXHX(18)E) is found in the domain. The zinc ion is coordinated by His(297), His(301), Glu(320), and a water molecule. The groove on the catalytic domain that contains the active site is covered by the C-terminal alpha-domain, and a large cavity is formed inside the protein. However, there exists a small hole at the center of the C-terminal alpha-domain. The N terminus of bestatin is recognized by Glu(121) and Glu(264), which are located in the N-terminal and catalytic domains, respectively. Glu(298) and Tyr(381), located near the zinc ion, are considered to be involved in peptide cleavage. A difference revealed between the ligand-free form and the enzyme-bestatin complex indicated that Met(260) functions as a cushion to accept substrates with different N-terminal residue sizes, resulting in the broad substrate specificity of this enzyme.
About this StructureAbout this Structure
2DQM is a Single protein structure of sequence from Escherichia coli with , and as ligands. Active as Membrane alanyl aminopeptidase, with EC number 3.4.11.2 Full crystallographic information is available from OCA.
ReferenceReference
Crystal structure of aminopeptidase N (proteobacteria alanyl aminopeptidase) from Escherichia coli and conformational change of methionine 260 involved in substrate recognition., Ito K, Nakajima Y, Onohara Y, Takeo M, Nakashima K, Matsubara F, Ito T, Yoshimoto T, J Biol Chem. 2006 Nov 3;281(44):33664-76. Epub 2006 Aug 2. PMID:16885166
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