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[[Image:1hi9.gif|left|200px]]<br /><applet load="1hi9" size="350" color="white" frame="true" align="right" spinBox="true"
caption="1hi9, resolution 2.40&Aring;" />
'''ZN-DEPENDENT D-AMINOPEPTIDASE DPPA FROM BACILLUS SUBTILIS, A SELF-COMPARTMENTALIZING PROTEASE.'''<br />


==Overview==
==Zn-dependent D-aminopeptidase DppA from Bacillus subtilis, a self-compartmentalizing protease.==
Bacillus subtilis DppA is a binuclear zinc-dependent, D-specific, aminopeptidase. The X-ray structure of the enzyme has been determined at, 2.4 A resolution by a three-wavelength MAD experiment. The structure, reveals that DppA is a new example of a 'self-compartmentalizing, protease', a family of proteolytic complexes. Proteasomes are the most, extensively studied representatives of this family. The DppA enzyme is, composed of identical 30 kDa subunits organized in a decamer with 52, point-group symmetry. A 20 A wide channel runs through the complex, giving, access to a central chamber holding the active sites. The structure shows, DppA to be a prototype of a new family of metalloaminopeptidases, characterized by the SXDXEG key sequence.
<StructureSection load='1hi9' size='340' side='right'caption='[[1hi9]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1hi9]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HI9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HI9 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=1hi9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hi9 OCA], [https://pdbe.org/1hi9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hi9 RCSB], [https://www.ebi.ac.uk/pdbsum/1hi9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hi9 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DPPA_BACSU DPPA_BACSU] Hydrolyzes N-terminal residues in D-amino acid containing peptides. Among the tested substrates, the highest activities are with D-Ala-D-Ala and D-Ala-Gly-Gly. The physiological role is not clear.
== 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/hi/1hi9_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1hi9 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Bacillus subtilis DppA is a binuclear zinc-dependent, D-specific aminopeptidase. The X-ray structure of the enzyme has been determined at 2.4 A resolution by a three-wavelength MAD experiment. The structure reveals that DppA is a new example of a 'self-compartmentalizing protease', a family of proteolytic complexes. Proteasomes are the most extensively studied representatives of this family. The DppA enzyme is composed of identical 30 kDa subunits organized in a decamer with 52 point-group symmetry. A 20 A wide channel runs through the complex, giving access to a central chamber holding the active sites. The structure shows DppA to be a prototype of a new family of metalloaminopeptidases characterized by the SXDXEG key sequence.


==About this Structure==
Structure of the Bacillus subtilis D-aminopeptidase DppA reveals a novel self-compartmentalizing protease.,Remaut H, Bompard-Gilles C, Goffin C, Frere JM, Van Beeumen J Nat Struct Biol. 2001 Aug;8(8):674-8. PMID:11473256<ref>PMID:11473256</ref>
1HI9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] with <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Known structural/functional Sites: <scene name='pdbsite=AC1:Zn+Binding+Site+For+Residue+A300'>AC1</scene>, <scene name='pdbsite=AC2:Zn+Binding+Site+For+Residue+A301'>AC2</scene>, <scene name='pdbsite=AC3:Zn+Binding+Site+For+Residue+B300'>AC3</scene>, <scene name='pdbsite=AC4:Zn+Binding+Site+For+Residue+B301'>AC4</scene>, <scene name='pdbsite=AC5:Zn+Binding+Site+For+Residue+C300'>AC5</scene>, <scene name='pdbsite=AC6:Zn+Binding+Site+For+Residue+C301'>AC6</scene>, <scene name='pdbsite=AC7:Zn+Binding+Site+For+Residue+D300'>AC7</scene>, <scene name='pdbsite=AC8:Zn+Binding+Site+For+Residue+D301'>AC8</scene>, <scene name='pdbsite=AC9:Zn+Binding+Site+For+Residue+E300'>AC9</scene> and <scene name='pdbsite=BC1:Zn+Binding+Site+For+Residue+E301'>BC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HI9 OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Structure of the Bacillus subtilis D-aminopeptidase DppA reveals a novel self-compartmentalizing protease., Remaut H, Bompard-Gilles C, Goffin C, Frere JM, Van Beeumen J, Nat Struct Biol. 2001 Aug;8(8):674-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11473256 11473256]
</div>
<div class="pdbe-citations 1hi9" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[ABC transporter 3D structures|ABC transporter 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Beeumen, J.Van.]]
[[Category: Bompard-Gilles C]]
[[Category: Bompard-Gilles, C.]]
[[Category: Frere JM]]
[[Category: Frere, J.M.]]
[[Category: Goffin C]]
[[Category: Goffin, C.]]
[[Category: Remaut H]]
[[Category: Remaut, H.]]
[[Category: Van Beeumen J]]
[[Category: ZN]]
[[Category: d-aminopeptidase]]
[[Category: decamer]]
[[Category: protease]]
[[Category: self-compartmentalizing]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb  3 09:49:23 2008''

Latest revision as of 11:56, 9 May 2024

Zn-dependent D-aminopeptidase DppA from Bacillus subtilis, a self-compartmentalizing protease.Zn-dependent D-aminopeptidase DppA from Bacillus subtilis, a self-compartmentalizing protease.

Structural highlights

1hi9 is a 5 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.4Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DPPA_BACSU Hydrolyzes N-terminal residues in D-amino acid containing peptides. Among the tested substrates, the highest activities are with D-Ala-D-Ala and D-Ala-Gly-Gly. The physiological role is not clear.

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

Bacillus subtilis DppA is a binuclear zinc-dependent, D-specific aminopeptidase. The X-ray structure of the enzyme has been determined at 2.4 A resolution by a three-wavelength MAD experiment. The structure reveals that DppA is a new example of a 'self-compartmentalizing protease', a family of proteolytic complexes. Proteasomes are the most extensively studied representatives of this family. The DppA enzyme is composed of identical 30 kDa subunits organized in a decamer with 52 point-group symmetry. A 20 A wide channel runs through the complex, giving access to a central chamber holding the active sites. The structure shows DppA to be a prototype of a new family of metalloaminopeptidases characterized by the SXDXEG key sequence.

Structure of the Bacillus subtilis D-aminopeptidase DppA reveals a novel self-compartmentalizing protease.,Remaut H, Bompard-Gilles C, Goffin C, Frere JM, Van Beeumen J Nat Struct Biol. 2001 Aug;8(8):674-8. PMID:11473256[1]

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

See Also

References

  1. ↑ Remaut H, Bompard-Gilles C, Goffin C, Frere JM, Van Beeumen J. Structure of the Bacillus subtilis D-aminopeptidase DppA reveals a novel self-compartmentalizing protease. Nat Struct Biol. 2001 Aug;8(8):674-8. PMID:11473256 doi:10.1038/90380

1hi9, resolution 2.40Å

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