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3n2w

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Crystal structure of the N-terminal beta-aminopeptidase BapA from Sphingosinicella xenopeptidilytica

Structural highlights

3n2w is a 4 chain structure with sequence from Sphingosinicella xenopeptidilytica. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.45Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BAPA_SPHXN Beta-aminopeptidase that can cleave synthetic beta-peptides which consist of backbone-elongated beta-amino acid residues that are not processed by common proteolytic enzymes. Can cleave the beta-peptides beta-homoVal-beta-homoAla-beta-homoLeu and beta-homoAla-beta-homoLeu. Requires a beta-amino acid at the N-terminus of peptide substrates and cleaves the peptide bond between the N-terminal beta-amino acid and the amino acid at the second position of tripeptidic substrates of the general structure H-betahXaa-Ile-betahTyr-OH according to the following preferences with regard to the side chain of the N-terminal beta-amino acid: aliphatic and aromatic > OH-containing > hydrogen, basic and polar.^[1] ^[2]

Publication Abstract from PubMed

The beta-aminopeptidase BapA from Sphingosinicella xenopeptidilytica belongs to the N-terminal nucleophile (Ntn) hydrolases of the DmpA-like family and has the unprecedented property of cleaving N-terminal beta-amino acid residues from peptides. We determined the crystal structures of the native (alphabeta)(4) heterooctamer and of the 153 kDa precursor homotetramer at a resolution of 1.45 and 1.8 A, respectively. These structures together with mutational analyses strongly support mechanisms for autoproteolysis and catalysis that involve residues Ser250, Ser288, and Glu290. The autoproteolytic mechanism is different from the one so far described for Ntn hydrolases. The structures together with functional data also provide insight into the discriminating features of the active site cleft that determine substrate specificity.

Autoproteolytic and catalytic mechanisms for the beta-aminopeptidase BapA--a member of the Ntn hydrolase family.,Merz T, Heck T, Geueke B, Mittl PR, Briand C, Seebach D, Kohler HP, Grutter MG Structure. 2012 Nov 7;20(11):1850-60. doi: 10.1016/j.str.2012.07.017. Epub 2012, Sep 12. PMID:22980995^[3]

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

References

↑ Geueke B, Namoto K, Seebach D, Kohler HP. A novel beta-peptidyl aminopeptidase (BapA) from strain 3-2W4 cleaves peptide bonds of synthetic beta-tri- and beta-dipeptides. J Bacteriol. 2005 Sep;187(17):5910-7. PMID:16109932 doi:http://dx.doi.org/187/17/5910
↑ Geueke B, Heck T, Limbach M, Nesatyy V, Seebach D, Kohler HP. Bacterial beta-peptidyl aminopeptidases with unique substrate specificities for beta-oligopeptides and mixed beta,alpha-oligopeptides. FEBS J. 2006 Dec;273(23):5261-72. Epub 2006 Oct 25. PMID:17064315 doi:http://dx.doi.org/10.1111/j.1742-4658.2006.05519.x
↑ Merz T, Heck T, Geueke B, Mittl PR, Briand C, Seebach D, Kohler HP, Grutter MG. Autoproteolytic and catalytic mechanisms for the beta-aminopeptidase BapA--a member of the Ntn hydrolase family. Structure. 2012 Nov 7;20(11):1850-60. doi: 10.1016/j.str.2012.07.017. Epub 2012, Sep 12. PMID:22980995 doi:http://dx.doi.org/10.1016/j.str.2012.07.017

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3n2w"

@@ Line 3: / Line 3: @@
 <StructureSection load='3n2w' size='340' side='right'caption='[[3n2w]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3n2w]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ccug_52537 Ccug 52537]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N2W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N2W FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3n2w]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingosinicella_xenopeptidilytica Sphingosinicella xenopeptidilytica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N2W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N2W FirstGlance]. <br>
-</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=SO4:SULFATE+ION'>SO4</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]] 1.45&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3n33|3n33]], [[3n5i|3n5i]]</div></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=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bapA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=364098 CCUG 52537])</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=3n2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n2w OCA], [https://pdbe.org/3n2w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3n2w RCSB], [https://www.ebi.ac.uk/pdbsum/3n2w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3n2w ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/BAPA_SPHXN BAPA_SPHXN]] Beta-aminopeptidase that can cleave synthetic beta-peptides which consist of backbone-elongated beta-amino acid residues that are not processed by common proteolytic enzymes. Can cleave the beta-peptides beta-homoVal-beta-homoAla-beta-homoLeu and beta-homoAla-beta-homoLeu. Requires a beta-amino acid at the N-terminus of peptide substrates and cleaves the peptide bond between the N-terminal beta-amino acid and the amino acid at the second position of tripeptidic substrates of the general structure H-betahXaa-Ile-betahTyr-OH according to the following preferences with regard to the side chain of the N-terminal beta-amino acid: aliphatic and aromatic > OH-containing > hydrogen, basic and polar.<ref>PMID:16109932</ref> <ref>PMID:17064315</ref>
+[https://www.uniprot.org/uniprot/BAPA_SPHXN BAPA_SPHXN] Beta-aminopeptidase that can cleave synthetic beta-peptides which consist of backbone-elongated beta-amino acid residues that are not processed by common proteolytic enzymes. Can cleave the beta-peptides beta-homoVal-beta-homoAla-beta-homoLeu and beta-homoAla-beta-homoLeu. Requires a beta-amino acid at the N-terminus of peptide substrates and cleaves the peptide bond between the N-terminal beta-amino acid and the amino acid at the second position of tripeptidic substrates of the general structure H-betahXaa-Ile-betahTyr-OH according to the following preferences with regard to the side chain of the N-terminal beta-amino acid: aliphatic and aromatic > OH-containing > hydrogen, basic and polar.<ref>PMID:16109932</ref> <ref>PMID:17064315</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 27: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Ccug 52537]]
 [[Category: Large Structures]]
-[[Category: Geueke, B]]
+[[Category: Sphingosinicella xenopeptidilytica]]
-[[Category: Gruetter, M G]]
+[[Category: Geueke B]]
-[[Category: Heck, T]]
+[[Category: Gruetter MG]]
-[[Category: Kohler, H P]]
+[[Category: Heck T]]
-[[Category: Merz, T]]
+[[Category: Kohler H-P]]
-[[Category: Alpha-beta-beta-alpha sandwich]]
+[[Category: Merz T]]
-[[Category: Beta-aminopeptidase]]
-[[Category: Beta-peptide]]
-[[Category: Hydrolase]]
-[[Category: Ntn hydrolase]]

3n2w

From Proteopedia

Current revision

Crystal structure of the N-terminal beta-aminopeptidase BapA from Sphingosinicella xenopeptidilytica

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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