2c49: Difference between revisions
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< | ==Crystal Structure of Methanocaldococcus jannaschii Nucleoside Kinase - An Archaeal Member of the Ribokinase Family== | ||
<StructureSection load='2c49' size='340' side='right'caption='[[2c49]], [[Resolution|resolution]] 1.92Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2c49]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C49 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C49 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]] 1.92Å</td></tr> | |||
-- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=2c49 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c49 OCA], [https://pdbe.org/2c49 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c49 RCSB], [https://www.ebi.ac.uk/pdbsum/2c49 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c49 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/NK_METJA NK_METJA] Catalyzes the phosphorylation of a wide range of nucleosides to yield nucleoside monophosphates. Shows the highest activity for inosine, guanosine and cytidine, but very poor kinase activity with adenosine, thymidine, uridine and xanthosine. ATP is the best phosphate donor, but can also use ITP and GTP. Shows extremely low activity with fructose-6-phosphate.<ref>PMID:17021658</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/c4/2c49_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=2c49 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Nucleoside kinase from the hyperthermophilic archaeon Methanocaldococcus jannaschii (MjNK) is a member of the ribokinase family. In the presence of ATP and Mg(2+), MjNK is able to catalyze the phosphorylation of a variety of nucleosides, including inosine, cytidine, guanosine and adenosine. Here, the crystal structure of MjNK, the first structure of an archaeal representative of the ribokinase family, is presented. The structure was solved using the multiple-wavelength anomalous dispersion technique. Three-dimensional structures of the unliganded enzyme and a complex of MjNK, an ATP analogue and adenosine were determined to 1.7 and 1.9 A resolution, respectively. Each subunit comprises an alpha/beta-domain and a smaller lid domain and has an overall fold characteristic of the ribokinase superfamily. MjNK shares highest structural similarity to the ribokinases from Escherichia coli and Thermotoga maritima. Similar to ribokinase and other superfamily members, the lid domain of MjNK undergoes a significant conformational change upon substrate binding. In the crystal structure of the MjNK complex, subunit A adopts a closed conformation and subunit B an open conformation. In subunit A all substrates and Mg(2+) were observed, whereas in subunit B only the ATP analogue could be clearly identified in the electron density. The structures of MjNK and E. coli ribokinase (EcRK) were compared with respect to putative determinants of thermal stability. Relative to EcRK, MjNK shows an increased charged and a decreased hydrophobic accessible surface area, as well as a higher fraction of charged residues, ionic networks and large aromatic clusters, characteristics that are frequently observed in enzymes from hyperthermophiles. | |||
Structure of Methanocaldococcus jannaschii nucleoside kinase: an archaeal member of the ribokinase family.,Arnfors L, Hansen T, Schonheit P, Ladenstein R, Meining W Acta Crystallogr D Biol Crystallogr. 2006 Sep;62(Pt 9):1085-97. Epub 2006, Aug 19. PMID:16929110<ref>PMID:16929110</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2c49" style="background-color:#fffaf0;"></div> | |||
== References == | |||
--> | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Large Structures]] | ||
[[Category: Methanocaldococcus jannaschii]] | [[Category: Methanocaldococcus jannaschii]] | ||
[[Category: Arnfors L]] | |||
[[Category: Arnfors | [[Category: Hansen T]] | ||
[[Category: Hansen | [[Category: Ladenstein R]] | ||
[[Category: Ladenstein | [[Category: Meining W]] | ||
[[Category: Meining | [[Category: Schoenheit P]] | ||
[[Category: Schoenheit | |||
Latest revision as of 12:21, 9 May 2024
Crystal Structure of Methanocaldococcus jannaschii Nucleoside Kinase - An Archaeal Member of the Ribokinase FamilyCrystal Structure of Methanocaldococcus jannaschii Nucleoside Kinase - An Archaeal Member of the Ribokinase Family
Structural highlights
FunctionNK_METJA Catalyzes the phosphorylation of a wide range of nucleosides to yield nucleoside monophosphates. Shows the highest activity for inosine, guanosine and cytidine, but very poor kinase activity with adenosine, thymidine, uridine and xanthosine. ATP is the best phosphate donor, but can also use ITP and GTP. Shows extremely low activity with fructose-6-phosphate.[1] 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 PubMedNucleoside kinase from the hyperthermophilic archaeon Methanocaldococcus jannaschii (MjNK) is a member of the ribokinase family. In the presence of ATP and Mg(2+), MjNK is able to catalyze the phosphorylation of a variety of nucleosides, including inosine, cytidine, guanosine and adenosine. Here, the crystal structure of MjNK, the first structure of an archaeal representative of the ribokinase family, is presented. The structure was solved using the multiple-wavelength anomalous dispersion technique. Three-dimensional structures of the unliganded enzyme and a complex of MjNK, an ATP analogue and adenosine were determined to 1.7 and 1.9 A resolution, respectively. Each subunit comprises an alpha/beta-domain and a smaller lid domain and has an overall fold characteristic of the ribokinase superfamily. MjNK shares highest structural similarity to the ribokinases from Escherichia coli and Thermotoga maritima. Similar to ribokinase and other superfamily members, the lid domain of MjNK undergoes a significant conformational change upon substrate binding. In the crystal structure of the MjNK complex, subunit A adopts a closed conformation and subunit B an open conformation. In subunit A all substrates and Mg(2+) were observed, whereas in subunit B only the ATP analogue could be clearly identified in the electron density. The structures of MjNK and E. coli ribokinase (EcRK) were compared with respect to putative determinants of thermal stability. Relative to EcRK, MjNK shows an increased charged and a decreased hydrophobic accessible surface area, as well as a higher fraction of charged residues, ionic networks and large aromatic clusters, characteristics that are frequently observed in enzymes from hyperthermophiles. Structure of Methanocaldococcus jannaschii nucleoside kinase: an archaeal member of the ribokinase family.,Arnfors L, Hansen T, Schonheit P, Ladenstein R, Meining W Acta Crystallogr D Biol Crystallogr. 2006 Sep;62(Pt 9):1085-97. Epub 2006, Aug 19. PMID:16929110[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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