1dvr

From Proteopedia

(Difference between revisions)

Revision as of 13:11, 13 October 2021

STRUCTURE OF A MUTANT ADENYLATE KINASE LIGATED WITH AN ATP-ANALOGUE SHOWING DOMAIN CLOSURE OVER ATP

Structural highlights

1dvr is a 2 chain structure with sequence from Atcc 18824. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Activity:	Adenylate kinase, with EC number 2.7.4.3
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[KAD2_YEAST] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. Adenylate kinase activity is critical for regulation of the phosphate utilization and the AMP de novo biosynthesis pathways.[HAMAP-Rule:MF_03168]^[1] ^[2] ^[3]

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

Structural studies on unligated and ligated adenylate kinases have shown that two domains, LID and NMPbind, close over the bound substrates, ATP and AMP, respectively. These motions can be, but need not be independent from each other. Up to now, the known structures display only the states "both domains open", "both closed" and "NMP bind closed". In spite of numerous cocrystallization attempts with ATP, a crystalline state "LID closed" has not yet been produced. These experiences suggested that LID closure depends on a bound AMP molecule, in contrast to enzyme kinetic studies indicating a random-bi-bi mechanism. Using an inactive mutant of yeast adenylate kinase together with the ATP analogue AMPPCF2P, however, we have now crystallized an adenylate kinase in the LID closed state. The structure was established at 2.36 A resolution; it indicates that the domain motions occur largely independent from each other in agreement with the kinetic studies. As a side-result, we report the protein environment of the fluorine atoms of the bound ATP analogue.

Structure of a mutant adenylate kinase ligated with an ATP-analogue showing domain closure over ATP.,Schlauderer GJ, Proba K, Schulz GE J Mol Biol. 1996 Feb 23;256(2):223-7. PMID:8594191^[4]

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

References

↑ Gauthier S, Coulpier F, Jourdren L, Merle M, Beck S, Konrad M, Daignan-Fornier B, Pinson B. Co-regulation of yeast purine and phosphate pathways in response to adenylic nucleotide variations. Mol Microbiol. 2008 Jun;68(6):1583-94. doi: 10.1111/j.1365-2958.2008.06261.x., Epub 2008 Apr 21. PMID:18433446 doi:http://dx.doi.org/10.1111/j.1365-2958.2008.06261.x
↑ Konrad M. Analysis and in vivo disruption of the gene coding for adenylate kinase (ADK1) in the yeast Saccharomyces cerevisiae. J Biol Chem. 1988 Dec 25;263(36):19468-74. PMID:2848829
↑ Bandlow W, Strobel G, Zoglowek C, Oechsner U, Magdolen V. Yeast adenylate kinase is active simultaneously in mitochondria and cytoplasm and is required for non-fermentative growth. Eur J Biochem. 1988 Dec 15;178(2):451-7. PMID:2850178
↑ Schlauderer GJ, Proba K, Schulz GE. Structure of a mutant adenylate kinase ligated with an ATP-analogue showing domain closure over ATP. J Mol Biol. 1996 Feb 23;256(2):223-7. PMID:8594191 doi:http://dx.doi.org/10.1006/jmbi.1996.0080

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/1dvr"

@@ Line 3: / Line 3: @@
 <StructureSection load='1dvr' size='340' side='right'caption='[[1dvr]], [[Resolution|resolution]] 2.36&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1dvr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DVR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DVR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1dvr]] is a 2 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=1DVR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DVR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATF:PHOSPHODIFLUOROMETHYLPHOSPHONIC+ACID-ADENYLATE+ESTER'>ATF</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATF:PHOSPHODIFLUOROMETHYLPHOSPHONIC+ACID-ADENYLATE+ESTER'>ATF</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </span></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=1dvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dvr OCA], [http://pdbe.org/1dvr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dvr RCSB], [http://www.ebi.ac.uk/pdbsum/1dvr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1dvr 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=1dvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dvr OCA], [https://pdbe.org/1dvr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dvr RCSB], [https://www.ebi.ac.uk/pdbsum/1dvr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dvr ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/KAD2_YEAST KAD2_YEAST]] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. Adenylate kinase activity is critical for regulation of the phosphate utilization and the AMP de novo biosynthesis pathways.[HAMAP-Rule:MF_03168]<ref>PMID:18433446</ref> <ref>PMID:2848829</ref> <ref>PMID:2850178</ref>
+[[https://www.uniprot.org/uniprot/KAD2_YEAST KAD2_YEAST]] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. Adenylate kinase activity is critical for regulation of the phosphate utilization and the AMP de novo biosynthesis pathways.[HAMAP-Rule:MF_03168]<ref>PMID:18433446</ref> <ref>PMID:2848829</ref> <ref>PMID:2850178</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]

1dvr

From Proteopedia

Revision as of 13:11, 13 October 2021

STRUCTURE OF A MUTANT ADENYLATE KINASE LIGATED WITH AN ATP-ANALOGUE SHOWING DOMAIN CLOSURE OVER ATP

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox