2c4e

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of Methanocaldococcus jannaschii Nucleoside Kinase - An Archaeal Member of the Ribokinase Family

Structural highlights

2c4e is a 1 chain structure with sequence from Methanocaldococcus jannaschii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.7Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[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 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^[2]

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

References

↑ Hansen T, Arnfors L, Ladenstein R, Schönheit P. The phosphofructokinase-B (MJ0406) from Methanocaldococcus jannaschii represents a nucleoside kinase with a broad substrate specificity. Extremophiles. 2007 Jan;11(1):105-14. PMID:17021658 doi:10.1007/s00792-006-0018-1
↑ Arnfors L, Hansen T, Schonheit P, Ladenstein R, Meining W. Structure of Methanocaldococcus jannaschii nucleoside kinase: an archaeal member of the ribokinase family. Acta Crystallogr D Biol Crystallogr. 2006 Sep;62(Pt 9):1085-97. Epub 2006, Aug 19. PMID:16929110 doi:10.1107/S0907444906024826

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2c4e"

@@ Line 1: / Line 1: @@
-==CRYSTAL STRUCTURE OF METHANOCALDOCOCCUS JANNASCHII NUCLEOSIDE KINASE - AN ARCHAEAL MEMBER OF THE RIBOKINASE FAMILY==
-<StructureSection load='2c4e' size='340' side='right' caption='[[2c4e]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+==Crystal Structure of Methanocaldococcus jannaschii Nucleoside Kinase - An Archaeal Member of the Ribokinase Family==
+<StructureSection load='2c4e' size='340' side='right'caption='[[2c4e]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2c4e]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C4E FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2c4e]] is a 1 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=2C4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C4E FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.7&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2c49|2c49]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2c4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c4e OCA], [http://pdbe.org/2c4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2c4e RCSB], [http://www.ebi.ac.uk/pdbsum/2c4e PDBsum]</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=2c4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c4e OCA], [https://pdbe.org/2c4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c4e RCSB], [https://www.ebi.ac.uk/pdbsum/2c4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c4e 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/c4/2c4e_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c4/2c4e_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/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=2c4e ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 30: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 43067]]
+[[Category: Large Structures]]
-[[Category: Arnfors, L]]
+[[Category: Methanocaldococcus jannaschii]]
-[[Category: Hansen, T]]
+[[Category: Arnfors L]]
-[[Category: Ladenstein, R]]
+[[Category: Hansen T]]
-[[Category: Meining, W]]
+[[Category: Ladenstein R]]
-[[Category: Schoenheit, P]]
+[[Category: Meining W]]
-[[Category: Hyperthermophile]]
+[[Category: Schoenheit P]]
-[[Category: Nucleoside kinase]]
-[[Category: Ribokinase family]]
-[[Category: Ribokinase fold]]
-[[Category: Transferase]]

2c4e

From Proteopedia

Current revision

Crystal Structure of Methanocaldococcus jannaschii Nucleoside Kinase - An Archaeal Member of the Ribokinase Family

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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