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3b2x

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Crystal Structure of E. coli Aminopeptidase N in complex with Lysine

Structural highlights

3b2x is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.5Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AMPN_ECOLI Aminopeptidase N is involved in the degradation of intracellular peptides generated by protein breakdown during normal growth as well as in response to nutrient starvation.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Aminopeptidase N from Escherichia coli is a M1 class aminopeptidase with the active-site region related to that of thermolysin. The enzyme has unusual specificity, cleaving adjacent to the large, nonpolar amino acids Phe and Tyr but also cleaving next to the polar residues Lys and Arg. To try to understand the structural basis for this pattern of hydrolysis, the structure of the enzyme was determined in complex with the amino acids l-arginine, l-lysine, l-phenylalanine, l-tryptophan, and l-tyrosine. These amino acids all bind with their backbone atoms close to the active-site zinc ion and their side chain occupying the S1 subsite. This subsite is in the form of a cylinder, about 10 A in cross-section and 12 A in length. The bottom of the cylinder includes the zinc ion and a number of polar side chains that make multiple hydrogen-bonding and other interactions with the alpha-amino group and the alpha-carboxylate of the bound amino acid. The walls of the S1 cylinder are hydrophobic and accommodate the nonpolar or largely nonpolar side chains of Phe and Tyr. The top of the cylinder is polar in character and includes bound water molecules. The epsilon-amino group of the bound lysine side chain and the guanidinium group of arginine both make multiple hydrogen bonds to this part of the S1 site. At the same time, the hydrocarbon part of the lysine and arginine side chains is accommodated within the nonpolar walls of the S1 cylinder. This combination of hydrophobic and hydrophilic binding surfaces explains the ability of ePepN to cleave Lys, Arg, Phe, and Tyr. Another favored substrate has Ala at the P1 position. The short, nonpolar side chain of this residue can clearly be bound within the hydrophobic part of the S1 cylinder, but the reason for its facile hydrolysis remains uncertain.

Structural Basis for the Unusual Specificity of Escherichia coli Aminopeptidase N.,Addlagatta A, Gay L, Matthews BW Biochemistry. 2008 Apr 17;. PMID:18416562^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Addlagatta A, Gay L, Matthews BW. Structural Basis for the Unusual Specificity of Escherichia coli Aminopeptidase N. Biochemistry. 2008 Apr 17;. PMID:18416562 doi:10.1021/bi7022333

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3b2x"

Categories: Escherichia coli | Large Structures | Addlagatta A | Gay L | Matthews BW

@@ Line 1: / Line 1: @@
 ==Crystal Structure of E. coli Aminopeptidase N in complex with Lysine==
-<StructureSection load='3b2x' size='340' side='right' caption='[[3b2x]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+<StructureSection load='3b2x' size='340' side='right'caption='[[3b2x]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3b2x]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B2X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B2X FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3b2x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B2X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B2X FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3b2p|3b2p]], [[2hpo|2hpo]], [[2hpt|2hpt]], [[3b34|3b34]], [[3b37|3b37]], [[3b3b|3b3b]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Aminopeptidase N ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3b2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b2x OCA], [https://pdbe.org/3b2x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b2x RCSB], [https://www.ebi.ac.uk/pdbsum/3b2x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b2x ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3b2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b2x OCA], [http://pdbe.org/3b2x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3b2x RCSB], [http://www.ebi.ac.uk/pdbsum/3b2x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3b2x ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/AMPN_ECOLI AMPN_ECOLI]] Aminopeptidase N is involved in the degradation of intracellular peptides generated by protein breakdown during normal growth as well as in response to nutrient starvation.
+[https://www.uniprot.org/uniprot/AMPN_ECOLI AMPN_ECOLI] Aminopeptidase N is involved in the degradation of intracellular peptides generated by protein breakdown during normal growth as well as in response to nutrient starvation.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b2/3b2x_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b2/3b2x_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 31: / Line 29: @@
 </div>
 <div class="pdbe-citations 3b2x" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Aminopeptidase 3D structures|Aminopeptidase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Membrane alanyl aminopeptidase]]
+[[Category: Large Structures]]
-[[Category: Addlagatta, A]]
+[[Category: Addlagatta A]]
-[[Category: Gay, L]]
+[[Category: Gay L]]
-[[Category: Matthews, B W]]
+[[Category: Matthews BW]]
-[[Category: Aminopeptidase n]]
-[[Category: Hydrolase]]
-[[Category: Lysin]]
-[[Category: Membrane]]
-[[Category: Metal-binding]]
-[[Category: Metalloprotease]]
-[[Category: Protease]]
-[[Category: Thermolysin]]

3b2x

From Proteopedia

Current revision

Crystal Structure of E. coli Aminopeptidase N in complex with Lysine

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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