2vkq

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (15:23, 13 December 2023) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2vkq.jpg|left|200px]]
 
-
{{Structure
+
==Crystal structure of human cytosolic 5'-nucleotidase III (cN-III, NT5C3) in complex with beryllium trifluoride==
-
|PDB= 2vkq |SIZE=350|CAPTION= <scene name='initialview01'>2vkq</scene>, resolution 2.50&Aring;
+
<StructureSection load='2vkq' size='340' side='right'caption='[[2vkq]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-
|SITE= <scene name='pdbsite=AC1:Bef+Binding+Site+For+Chain+A'>AC1</scene> and <scene name='pdbsite=AC2:Mg+Binding+Site+For+Chain+A'>AC2</scene>
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>
+
<table><tr><td colspan='2'>[[2vkq]] is a 1 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=2VKQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VKQ FirstGlance]. <br>
-
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/5'-nucleotidase 5'-nucleotidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.5 3.1.3.5] </span>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vkq OCA], [https://pdbe.org/2vkq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vkq RCSB], [https://www.ebi.ac.uk/pdbsum/2vkq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vkq ProSAT]</span></td></tr>
-
|RELATEDENTRY=[[2jga|2JGA]], [[2cn1|2CN1]]
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2vkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vkq OCA], [http://www.ebi.ac.uk/pdbsum/2vkq PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2vkq RCSB]</span>
+
== Disease ==
-
}}
+
[https://www.uniprot.org/uniprot/5NT3A_HUMAN 5NT3A_HUMAN] Hemolytic anemia due to pyrimidine 5' nucleotidase deficiency. The disease is caused by variants affecting the gene represented in this entry.
-
 
+
== Function ==
-
'''CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'-NUCLEOTIDASE III (CN-III, NT5C3) IN COMPLEX WITH BERYLLIUM TRIFLUORIDE'''
+
[https://www.uniprot.org/uniprot/5NT3A_HUMAN 5NT3A_HUMAN] Nucleotidase which shows specific activity towards cytidine monophosphate (CMP) and 7-methylguanosine monophosphate (m(7)GMP) (PubMed:24603684). CMP seems to be the preferred substrate (PubMed:15968458).<ref>PMID:15968458</ref> <ref>PMID:24603684</ref>
-
 
+
== Evolutionary Conservation ==
-
 
+
[[Image:Consurf_key_small.gif|200px|right]]
-
==Overview==
+
Check<jmol>
-
Cytosolic 5'-nucleotidase II catalyzes the dephosphorylation of 6-hydroxypurine nucleoside 5'-monophosphates and regulates the IMP and GMP pools within the cell. It possesses phosphotransferase activity and thereby also catalyzes the reverse reaction. Both reactions are allosterically activated by adenine-based nucleotides and 2,3-bisphosphoglycerate. We have solved structures of cytosolic 5'-nucleotidase II as native protein (2.2 Angstrom) and in complex with adenosine (1.5 Angstrom) and beryllium trifluoride (2.15 Angstrom) The tetrameric enzyme is structurally similar to enzymes of the haloacid dehalogenase (HAD) superfamily, including mitochondrial 5'(3')-deoxyribonucleotidase and cytosolic 5'-nucleotidase III but possesses additional regulatory regions that contain two allosteric effector sites. At effector site 1 located near a subunit interface we modeled diadenosine tetraphosphate with one adenosine moiety in each subunit. This efficiently glues the tetramer subunits together in pairs. The model shows why diadenosine tetraphosphate but not diadenosine triphosphate activates the enzyme and supports a role for cN-II during apoptosis when the level of diadenosine tetraphosphate increases. We have also modeled 2,3-bisphosphoglycerate in effector site 1 using one phosphate site from each subunit. By comparing the structure of cytosolic 5'-nucleotidase II with that of mitochondrial 5'(3')-deoxyribonucleotidase in complex with dGMP, we identified residues involved in substrate recognition.
+
<jmolCheckbox>
-
 
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vk/2vkq_consurf.spt"</scriptWhenChecked>
-
==About this Structure==
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
2VKQ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKQ OCA].
+
<text>to colour the structure by Evolutionary Conservation</text>
-
 
+
</jmolCheckbox>
-
==Reference==
+
</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=2vkq ConSurf].
-
Crystal structure of human cytosolic 5'-nucleotidase II: insights into allosteric regulation and substrate recognition., Wallden K, Stenmark P, Nyman T, Flodin S, Graslund S, Loppnau P, Bianchi V, Nordlund P, J Biol Chem. 2007 Jun 15;282(24):17828-36. Epub 2007 Apr 3. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17405878 17405878]
+
<div style="clear:both"></div>
-
[[Category: 5'-nucleotidase]]
+
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Arrowsmith, C H.]]
+
[[Category: Arrowsmith CH]]
-
[[Category: Berg]]
+
[[Category: Berglund H]]
-
[[Category: Berglund, H.]]
+
[[Category: Busam R]]
-
[[Category: Busam, R.]]
+
[[Category: Collins R]]
-
[[Category: Collins, R.]]
+
[[Category: Dahlgren LG]]
-
[[Category: Dahlgren, L G.]]
+
[[Category: Edwards A]]
-
[[Category: Den]]
+
[[Category: Flodin S]]
-
[[Category: Edwards, A.]]
+
[[Category: Flores A]]
-
[[Category: Flodin, S.]]
+
[[Category: Graslund S]]
-
[[Category: Flores, A.]]
+
[[Category: Hammarstrom M]]
-
[[Category: Graslund, S.]]
+
[[Category: Herman MD]]
-
[[Category: Hammarstrom, M.]]
+
[[Category: Johansson A]]
-
[[Category: Herman, M D.]]
+
[[Category: Johansson I]]
-
[[Category: Johansson, A.]]
+
[[Category: Kallas A]]
-
[[Category: Johansson, I.]]
+
[[Category: Karlberg T]]
-
[[Category: Kallas, A.]]
+
[[Category: Kotenyova T]]
-
[[Category: Karlberg, T.]]
+
[[Category: Lehtio L]]
-
[[Category: Kotenyova, T.]]
+
[[Category: Moche M]]
-
[[Category: Lehtio, L.]]
+
[[Category: Nilsson ME]]
-
[[Category: Moche, M.]]
+
[[Category: Nordlund P]]
-
[[Category: Nilsson, M E.]]
+
[[Category: Nyman T]]
-
[[Category: Nordlund, P.]]
+
[[Category: Persson C]]
-
[[Category: Nyman, T.]]
+
[[Category: Sagemark J]]
-
[[Category: Persson, C.]]
+
[[Category: Thorsell AG]]
-
[[Category: Sagemark, J.]]
+
[[Category: Tresaugues L]]
-
[[Category: Sgc, Structural GenomicsConsortium.]]
+
[[Category: Wallden K]]
-
[[Category: Thorsell, A G.]]
+
[[Category: Weigelt J]]
-
[[Category: Tresaugues, L.]]
+
[[Category: Welin M]]
-
[[Category: Van, S.]]
+
[[Category: Van den Berg S]]
-
[[Category: Wallden, K.]]
+
-
[[Category: Weigelt, J.]]
+
-
[[Category: Welin, M.]]
+
-
[[Category: alternative splicing]]
+
-
[[Category: cytoplasm]]
+
-
[[Category: disease mutation]]
+
-
[[Category: endoplasmic reticulum]]
+
-
[[Category: hemolytic anemia]]
+
-
[[Category: hydrolase]]
+
-
[[Category: nucleotidase]]
+
-
[[Category: nucleotide metabolism]]
+
-
[[Category: nucleotide-binding]]
+
-
[[Category: phosphotransferase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:13:19 2008''
+

Current revision

Crystal structure of human cytosolic 5'-nucleotidase III (cN-III, NT5C3) in complex with beryllium trifluoride

PDB ID 2vkq

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2vkq"
Personal tools