1xfd

From Proteopedia

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Current revision

Structure of a human A-type Potassium Channel Accelerating factor DPPX, a member of the dipeptidyl aminopeptidase family

Structural highlights

1xfd is a 4 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

DPP6_HUMAN Autosomal dominant primary microcephaly;Idiopathic ventricular fibrillation, non Brugada type. The disease is caused by variants affecting the gene represented in this entry. A genetic variation 340 bases upstream from the ATG start site of the DPP6 gene is the cause of familial paroxysmal ventricular fibrillation type 2. The disease is caused by variants affecting the gene represented in this entry.

Function

DPP6_HUMAN Promotes cell surface expression of the potassium channel KCND2 (PubMed:15454437, PubMed:19441798). Modulates the activity and gating characteristics of the potassium channel KCND2 (PubMed:18364354). Has no dipeptidyl aminopeptidase activity (PubMed:8103397, PubMed:15476821).^[1] ^[2] ^[3] ^[4]

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

It has recently been reported that dipeptidyl aminopeptidase X (DPPX) interacts with the voltage-gated potassium channel Kv4 and that co-expression of DPPX together with Kv4 pore forming alpha-subunits, and potassium channel interacting proteins (KChIPs), reconstitutes properties of native A-type potassium channels in vitro. Here we report the X-ray crystal structure of the extracellular domain of human DPPX determined at 3.0A resolution. This structure reveals the potential for a surface electrostatic change based on the protonation state of histidine. Subtle changes in extracellular pH might modulate the interaction of DPPX with Kv4.2 and possibly with other proteins. We propose models of DPPX interaction with the voltage-gated potassium channel complex. The dimeric structure of DPPX is highly homologous to the related protein DPP-IV. Comparison of the active sites of DPPX and DPP-IV reveals loss of the catalytic serine residue but the presence of an additional serine near the "active" site. However, the arrangement of residues is inconsistent with that of canonical serine proteases and DPPX is unlikely to function as a protease (dipeptidyl aminopeptidase).

Structure of a human A-type potassium channel interacting protein DPPX, a member of the dipeptidyl aminopeptidase family.,Strop P, Bankovich AJ, Hansen KC, Garcia KC, Brunger AT J Mol Biol. 2004 Oct 29;343(4):1055-65. PMID:15476821^[5]

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

References

↑ Jerng HH, Qian Y, Pfaffinger PJ. Modulation of Kv4.2 channel expression and gating by dipeptidyl peptidase 10 (DPP10). Biophys J. 2004 Oct;87(4):2380-96. PMID:15454437 doi:http://dx.doi.org/10.1529/biophysj.104.042358
↑ Soh H, Goldstein SA. I SA channel complexes include four subunits each of DPP6 and Kv4.2. J Biol Chem. 2008 May 30;283(22):15072-7. doi: 10.1074/jbc.M706964200. Epub 2008 , Mar 25. PMID:18364354 doi:http://dx.doi.org/10.1074/jbc.M706964200
↑ Yokotani N, Doi K, Wenthold RJ, Wada K. Non-conservation of a catalytic residue in a dipeptidyl aminopeptidase IV-related protein encoded by a gene on human chromosome 7. Hum Mol Genet. 1993 Jul;2(7):1037-9. doi: 10.1093/hmg/2.7.1037. PMID:8103397 doi:http://dx.doi.org/10.1093/hmg/2.7.1037
↑ Strop P, Bankovich AJ, Hansen KC, Garcia KC, Brunger AT. Structure of a human A-type potassium channel interacting protein DPPX, a member of the dipeptidyl aminopeptidase family. J Mol Biol. 2004 Oct 29;343(4):1055-65. PMID:15476821 doi:10.1016/j.jmb.2004.09.003
↑ Strop P, Bankovich AJ, Hansen KC, Garcia KC, Brunger AT. Structure of a human A-type potassium channel interacting protein DPPX, a member of the dipeptidyl aminopeptidase family. J Mol Biol. 2004 Oct 29;343(4):1055-65. PMID:15476821 doi:10.1016/j.jmb.2004.09.003

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1xfd"

@@ Line 3: / Line 3: @@
 <StructureSection load='1xfd' size='340' side='right'caption='[[1xfd]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1xfd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XFD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1XFD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1xfd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XFD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XFD FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</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]] 3&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DPPX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1xfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xfd OCA], [http://pdbe.org/1xfd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xfd RCSB], [http://www.ebi.ac.uk/pdbsum/1xfd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xfd ProSAT]</span></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=1xfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xfd OCA], [https://pdbe.org/1xfd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xfd RCSB], [https://www.ebi.ac.uk/pdbsum/1xfd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xfd ProSAT]</span></td></tr>
 </table>
+== Disease ==
+[https://www.uniprot.org/uniprot/DPP6_HUMAN DPP6_HUMAN] Autosomal dominant primary microcephaly;Idiopathic ventricular fibrillation, non Brugada type. The disease is caused by variants affecting the gene represented in this entry. A genetic variation 340 bases upstream from the ATG start site of the DPP6 gene is the cause of familial paroxysmal ventricular fibrillation type 2.  The disease is caused by variants affecting the gene represented in this entry.
+== Function ==
+[https://www.uniprot.org/uniprot/DPP6_HUMAN DPP6_HUMAN] Promotes cell surface expression of the potassium channel KCND2 (PubMed:15454437, PubMed:19441798). Modulates the activity and gating characteristics of the potassium channel KCND2 (PubMed:18364354). Has no dipeptidyl aminopeptidase activity (PubMed:8103397, PubMed:15476821).<ref>PMID:15454437</ref> <ref>PMID:18364354</ref> <ref>PMID:8103397</ref> <ref>PMID:15476821</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 13: / Line 17: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xf/1xfd_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>
@@ Line 31: / Line 35: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Bankovich, A J]]
+[[Category: Bankovich AJ]]
-[[Category: Brunger, A T]]
+[[Category: Brunger AT]]
-[[Category: Garcia, K C]]
+[[Category: Garcia KC]]
-[[Category: Hansen, K C]]
+[[Category: Hansen KC]]
-[[Category: Strop, P]]
+[[Category: Strop P]]
-[[Category: Dpp6]]
-[[Category: Dppx]]
-[[Category: Kaf]]
-[[Category: Kv]]
-[[Category: Kv4]]
-[[Category: Membrane protein]]

1xfd

From Proteopedia

Current revision

Structure of a human A-type Potassium Channel Accelerating factor DPPX, a member of the dipeptidyl aminopeptidase family

Structural highlights

Disease

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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