1ukz

From Proteopedia

(Difference between revisions)

Current revision

SUBSTRATE SPECIFICITY AND ASSEMBLY OF CATALYTIC CENTER DERIVED FROM TWO STRUCTURES OF LIGATED URIDYLATE KINASE

Structural highlights

1ukz is a 1 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

KCY_YEAST Catalyzes the phosphorylation of pyrimidine nucleoside monophosphates at the expense of ATP. Plays an important role in de novo pyrimidine nucleotide biosynthesis. Has preference for UMP and dUMP as phosphate acceptors, but can also use CMP, dCMP, AMP, GMP, dGMP and dTMP. ATP and dATP are the best phosphate donors, but can also use GTP, dGTP, dCTP, and dTTP to some degree.^[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

Two crystal structures of ligated uridylate kinase from Saccharomyces cerevisiae were determined by X-ray analyses. The ligands were ADP and AMP. Cocrystallization with ATP yielded crystals with ADP at the ATP site and a mixture of AMP and ADP at the NMP site. Cocrystallization with ADP gave rise to a distinct crystal type with ADP at the ATP site, but only AMP at the NMP site. In both cases, the substrates are kept in place by favorable crystal contacts. The structures have been refined to R-factors of 17.8% and 19.6% at resolutions of 2.1 A and 1.9 A, respectively. A comparison with the related cytosolic adenylate kinase from pig disclosed large induced-fit movements on substrate binding and the disassembly of the catalytic center in the absence of substrates. The relatively high side-activity of uridylate kinase for AMP is explained by the finding that the binding pocket is sized for an AMP, but constructed to bind UMP together with a water molecule.

Substrate specificity and assembly of the catalytic center derived from two structures of ligated uridylate kinase.,Muller-Dieckmann HJ, Schulz GE J Mol Biol. 1995 Mar 3;246(4):522-30. PMID:7877173^[5]

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

References

↑ Schricker R, Magdolen V, Kaniak A, Wolf K, Bandlow W. The adenylate kinase family in yeast: identification of URA6 as a multicopy suppressor of deficiency in major AMP kinase. Gene. 1992 Dec 1;122(1):111-8. PMID:1333436
↑ Ma JJ, Huang SH, Jong AY. Purification and characterization of Saccharomyces cerevisiae uridine monophosphate kinase. J Biol Chem. 1990 Nov 5;265(31):19122-7. PMID:2172245
↑ Jong A, Yeh Y, Ma JJ. Characteristics, substrate analysis, and intracellular location of Saccharomyces cerevisiae UMP kinase. Arch Biochem Biophys. 1993 Jul;304(1):197-204. PMID:8391780 doi:http://dx.doi.org/S0003-9861(83)71339-1
↑ Choi WJ, Campbell JL, Kuo CL, Jong AY. The Saccharomyces cerevisiae SOC8-1 gene and its relationship to a nucleotide kinase. J Biol Chem. 1989 Sep 15;264(26):15593-9. PMID:2549068
↑ Muller-Dieckmann HJ, Schulz GE. Substrate specificity and assembly of the catalytic center derived from two structures of ligated uridylate kinase. J Mol Biol. 1995 Mar 3;246(4):522-30. PMID:7877173

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/1ukz"

Categories: Large Structures | Saccharomyces cerevisiae | Mueller-Dieckmann H-J | Schulz GE

@@ Line 3: / Line 3: @@
 <StructureSection load='1ukz' size='340' side='right'caption='[[1ukz]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ukz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UKZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UKZ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ukz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UKZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UKZ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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]] 1.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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=1ukz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ukz OCA], [https://pdbe.org/1ukz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ukz RCSB], [https://www.ebi.ac.uk/pdbsum/1ukz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ukz ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/KCY_YEAST KCY_YEAST]] Catalyzes the phosphorylation of pyrimidine nucleoside monophosphates at the expense of ATP. Plays an important role in de novo pyrimidine nucleotide biosynthesis. Has preference for UMP and dUMP as phosphate acceptors, but can also use CMP, dCMP, AMP, GMP, dGMP and dTMP. ATP and dATP are the best phosphate donors, but can also use GTP, dGTP, dCTP, and dTTP to some degree.<ref>PMID:1333436</ref> <ref>PMID:2172245</ref> <ref>PMID:8391780</ref> <ref>PMID:2549068</ref>
+[https://www.uniprot.org/uniprot/KCY_YEAST KCY_YEAST] Catalyzes the phosphorylation of pyrimidine nucleoside monophosphates at the expense of ATP. Plays an important role in de novo pyrimidine nucleotide biosynthesis. Has preference for UMP and dUMP as phosphate acceptors, but can also use CMP, dCMP, AMP, GMP, dGMP and dTMP. ATP and dATP are the best phosphate donors, but can also use GTP, dGTP, dCTP, and dTTP to some degree.<ref>PMID:1333436</ref> <ref>PMID:2172245</ref> <ref>PMID:8391780</ref> <ref>PMID:2549068</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 14: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/uk/1ukz_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 35: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
 [[Category: Large Structures]]
-[[Category: Mueller-Dieckmann, H J]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Schulz, G E]]
+[[Category: Mueller-Dieckmann H-J]]
-[[Category: Transferase]]
+[[Category: Schulz GE]]

1ukz

From Proteopedia

Current revision

SUBSTRATE SPECIFICITY AND ASSEMBLY OF CATALYTIC CENTER DERIVED FROM TWO STRUCTURES OF LIGATED URIDYLATE KINASE

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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