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3mn8

From Proteopedia

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Structure of Drosophila melanogaster carboxypeptidase D isoform 1B short

Structural highlights

3mn8 is a 4 chain structure with sequence from Drosophila melanogaster. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.7Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CBPD_DROME Metallocarboxypeptidase that catalyzes the release of C-terminal arginine or lysine residues from peptides and proteins (PubMed:12393882, PubMed:16556608, PubMed:20386952, PubMed:20600119, PubMed:31309630). Functionally important for processing a broad range of proteins including growth factors, peptide hormones (such as Akh) and neuropeptides (PubMed:16556608, PubMed:20386952, PubMed:20600119, PubMed:27430952, PubMed:31309630). Consequently, it is involved in a wide range of processes including viability, memory formation, locomotive activity, wing formation, and peptide-regulated behaviors such as starvation-induced hyperactivity, appetitive gustatory preference, and cold and ethanol sensitivity (PubMed:20386952, PubMed:20600119, PubMed:27430952, PubMed:31309630). Key enzyme in neuropeptide processing (PubMed:31309630). Involved in regulation of memory formation, possibly via the insulin pathway in neurosecretory cells (PubMed:27430952).^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

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

Drosophila melanogaster silver gene is the ortholog of the coding gene of mammalian carboxypeptidase D (CPD). The silver gene gives rise to eight different splicing variants of differing length that can contain up to three homologous repeats. Among the protein variants encoded, the short form 1B alias DmCPD1Bs (D. melanogaster CPD variant 1B short) is necessary and sufficient for viability of the fruit fly. It has one single repeat, it is active against standard peptide substrates, and it is localized to the secretory pathway. In this work, the enzyme was found as a monomer in solution and as a homodimer in the crystal structure, which features a protomer with an N-terminal 311-residue catalytic domain of alpha/beta-hydrolase fold and a C-terminal 84-residue all-beta transthyretin-like domain. Overall, DmCPD1Bs conforms to the structure of N/E-type funnelins/M14B metallopeptidases, but it has two unique structural elements potentially involved in regulation of its activity: (i) two contiguous surface cysteines that may become palmitoylated and target the enzyme to membranes, thus providing control through localization, and (ii) a surface hot spot targetable by peptidases that would provide a regulatory mechanism through proteolytic inactivation. Given that the fruit fly possesses orthologs of only two out of the five proteolytically competent N/E-type funnelins found in higher vertebrates, DmCPD1Bs may represent a functional analog of at least one of the missing mammalian CPs.

Structure-function analysis of the short splicing variant carboxypeptidase encoded by Drosophila melanogaster silver.,Tanco S, Arolas JL, Guevara T, Lorenzo J, Aviles FX, Gomis-Ruth FX J Mol Biol. 2010 Aug 20;401(3):465-77. Epub 2010 Jun 25. PMID:20600119^[7]

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

References

↑ Sidyelyeva G, Fricker LD. Characterization of Drosophila carboxypeptidase D. J Biol Chem. 2002 Dec 20;277(51):49613-20. PMID:12393882 doi:10.1074/jbc.M209652200
↑ Sidyelyeva G, Baker NE, Fricker LD. Characterization of the molecular basis of the Drosophila mutations in carboxypeptidase D. Effect on enzyme activity and expression. J Biol Chem. 2006 May 12;281(19):13844-13852. PMID:16556608 doi:10.1074/jbc.M513499200
↑ Sidyelyeva G, Wegener C, Schoenfeld BP, Bell AJ, Baker NE, McBride SM, Fricker LD. Individual carboxypeptidase D domains have both redundant and unique functions in Drosophila development and behavior. Cell Mol Life Sci. 2010 Sep;67(17):2991-3004. PMID:20386952 doi:10.1007/s00018-010-0369-8
↑ Tanco S, Arolas JL, Guevara T, Lorenzo J, Aviles FX, Gomis-Ruth FX. Structure-function analysis of the short splicing variant carboxypeptidase encoded by Drosophila melanogaster silver. J Mol Biol. 2010 Aug 20;401(3):465-77. Epub 2010 Jun 25. PMID:20600119 doi:10.1016/j.jmb.2010.06.035
↑ Lu B, Zhao Y, Zhao J, Yao X, Shuai Y, Ma W, Zhong Y. The carboxypeptidase D homolog silver regulates memory formation via insulin pathway in Drosophila. Protein Cell. 2016 Aug;7(8):606-10. PMID:27430952 doi:10.1007/s13238-016-0291-4
↑ Pauls D, Hamarat Y, Trufasu L, Schendzielorz TM, Gramlich G, Kahnt J, Vanselow JT, Schlosser A, Wegener C. Drosophila carboxypeptidase D (SILVER) is a key enzyme in neuropeptide processing required to maintain locomotor activity levels and survival rate. Eur J Neurosci. 2019 Nov;50(9):3502-3519. PMID:31309630 doi:10.1111/ejn.14516
↑ Tanco S, Arolas JL, Guevara T, Lorenzo J, Aviles FX, Gomis-Ruth FX. Structure-function analysis of the short splicing variant carboxypeptidase encoded by Drosophila melanogaster silver. J Mol Biol. 2010 Aug 20;401(3):465-77. Epub 2010 Jun 25. PMID:20600119 doi:10.1016/j.jmb.2010.06.035

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/3mn8"

@@ Line 1: / Line 1: @@
 ==Structure of Drosophila melanogaster carboxypeptidase D isoform 1B short==
-<StructureSection load='3mn8' size='340' side='right' caption='[[3mn8]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+<StructureSection load='3mn8' size='340' side='right'caption='[[3mn8]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3mn8]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MN8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3MN8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3mn8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MN8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MN8 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GEM:(2-GUANIDINOETHYLMERCAPTO)SUCCINIC+ACID'>GEM</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.7&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1qmu|1qmu]], [[1h8l|1h8l]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GEM:(2-GUANIDINOETHYLMERCAPTO)SUCCINIC+ACID'>GEM</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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">svr-RF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 Drosophila melanogaster])</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=3mn8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mn8 OCA], [https://pdbe.org/3mn8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3mn8 RCSB], [https://www.ebi.ac.uk/pdbsum/3mn8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3mn8 ProSAT]</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=3mn8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mn8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3mn8 RCSB], [http://www.ebi.ac.uk/pdbsum/3mn8 PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/CBPD_DROME CBPD_DROME] Metallocarboxypeptidase that catalyzes the release of C-terminal arginine or lysine residues from peptides and proteins (PubMed:12393882, PubMed:16556608, PubMed:20386952, PubMed:20600119, PubMed:31309630). Functionally important for processing a broad range of proteins including growth factors, peptide hormones (such as Akh) and neuropeptides (PubMed:16556608, PubMed:20386952, PubMed:20600119, PubMed:27430952, PubMed:31309630). Consequently, it is involved in a wide range of processes including viability, memory formation, locomotive activity, wing formation, and peptide-regulated behaviors such as starvation-induced hyperactivity, appetitive gustatory preference, and cold and ethanol sensitivity (PubMed:20386952, PubMed:20600119, PubMed:27430952, PubMed:31309630). Key enzyme in neuropeptide processing (PubMed:31309630). Involved in regulation of memory formation, possibly via the insulin pathway in neurosecretory cells (PubMed:27430952).<ref>PMID:12393882</ref> <ref>PMID:16556608</ref> <ref>PMID:20386952</ref> <ref>PMID:20600119</ref> <ref>PMID:27430952</ref> <ref>PMID:31309630</ref>
 == 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/mn/3mn8_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mn/3mn8_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=3mn8 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3mn8" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Carboxypeptidase|Carboxypeptidase]]
+*[[Carboxypeptidase 3D structures|Carboxypeptidase 3D structures]]
 == References ==
 <references/>
@@ Line 34: / Line 37: @@
 </StructureSection>
 [[Category: Drosophila melanogaster]]
-[[Category: Arolas, J L]]
+[[Category: Large Structures]]
-[[Category: Aviles, F X]]
+[[Category: Arolas JL]]
-[[Category: Gomis-Ruth, F X]]
+[[Category: Aviles FX]]
-[[Category: Guevara, T]]
+[[Category: Gomis-Ruth FX]]
-[[Category: Lorenzo, J]]
+[[Category: Guevara T]]
-[[Category: Tanco, S]]
+[[Category: Lorenzo J]]
-[[Category: All-beta transthyretin-like domain]]
+[[Category: Tanco S]]
-[[Category: C-terminal]]
-[[Category: Catalytic domain of alpha/beta-hydrolase fold]]
-[[Category: Hydrolase]]

3mn8

From Proteopedia

Current revision

Structure of Drosophila melanogaster carboxypeptidase D isoform 1B short

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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