1zin: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1zin]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZIN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZIN FirstGlance]. <br>
<table><tr><td colspan='2'>[[1zin]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZIN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZIN FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AP5:BIS(ADENOSINE)-5-PENTAPHOSPHATE'>AP5</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.6&#8491;</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AP5:BIS(ADENOSINE)-5-PENTAPHOSPHATE'>AP5</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1zin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zin OCA], [https://pdbe.org/1zin PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zin RCSB], [https://www.ebi.ac.uk/pdbsum/1zin PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zin 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=1zin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zin OCA], [https://pdbe.org/1zin PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zin RCSB], [https://www.ebi.ac.uk/pdbsum/1zin PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zin ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/KAD_GEOSE KAD_GEOSE]] 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 (By similarity).  
[https://www.uniprot.org/uniprot/KAD_GEOSE KAD_GEOSE] 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 (By similarity).
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1zin 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=1zin ConSurf].
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<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A, Mn2+ Ap5A, and Mg2+ Ap5A have been determined by X-ray crystallography to resolutions of 1.6 A, 1.85 A, and 1.96 A, respectively. The protein's lid domain is partially open, being both rotated and translated away from bound Ap5A. The flexibility of the lid domain in the ternary state and its ability to transfer force directly to the the active site is discussed in light of our proposed entropic mechanism for catalytic turnover. The bound Zn2+ atom is demonstrably structural in nature, with no contacts other than its ligating cysteine residues within 5 A. The B. stearothermophilus adenylate kinase lid appears to be a truncated zinc finger domain, lacking the DNA binding finger, which we have termed a zinc knuckle domain. In the Mg2+ Ap5A and Mn2+ Ap5A structures, Mg2+ and Mn2+ demonstrate six coordinate octahedral geometry. The interactions of the Mg2+-coordinated water molecules with the protein and Ap5A phosphate chain demonstrate their involvement in catalyzing phosphate transfer. The protein selects for beta-y (preferred by Mg2+) rather than alpha-gamma (preferred by Mn2+) metal ion coordination by forcing the ATP phosphate chain to have an extended conformation.
Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A, Mg2+ Ap5A, and Mn2+ Ap5A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg2+ and Mn2+.,Berry MB, Phillips GN Jr Proteins. 1998 Aug 15;32(3):276-88. PMID:9715904<ref>PMID:9715904</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1zin" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Adenylate kinase 3D structures|Adenylate kinase 3D structures]]
*[[Adenylate kinase 3D structures|Adenylate kinase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Adenylate kinase]]
[[Category: Geobacillus stearothermophilus]]
[[Category: Geobacillus stearothermophilus]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Berry, M B]]
[[Category: Berry MB]]
[[Category: Phillips, G N]]
[[Category: Phillips Jr GN]]
[[Category: Phosphotransferase]]
[[Category: Zinc finger]]

Latest revision as of 12:05, 14 February 2024

ADENYLATE KINASE WITH BOUND AP5AADENYLATE KINASE WITH BOUND AP5A

Structural highlights

1zin is a 1 chain structure with sequence from Geobacillus stearothermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.6Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

KAD_GEOSE 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 (By similarity).

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1zin, resolution 1.60Å

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