3fb4

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of adenylate kinase from Marinibacillus marinus

Structural highlights

3fb4 is a 1 chain structure with sequence from Jeotgalibacillus marinus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q6B341_9BACL Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth (By similarity).[HAMAP-Rule:MF_00235]

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

Adenylate kinases (AKs; EC 2.7.4.3) are essential members of the NMP kinase family that maintain cellular homeostasis by the interconversion of AMP, ADP and ATP. AKs play a critical role in adenylate homeostasis across all domains of life and have been used extensively as prototypes for the study of protein adaptation and the relationship of protein dynamics and stability to function. To date, kinetic studies of psychrophilic AKs have not been performed. In order to broaden understanding of extremophilic adaptation, the kinetic parameters of adenylate kinase from the psychrophile Marinibacillus marinus were examined and the crystal structure of this cold-adapted enzyme was determined at 2.0 A resolution. As expected, the overall structure and topology of the psychrophilic M. marinus AK are similar to those of mesophilic and thermophilic AKs. The thermal denaturation midpoint of M. marinus AK (321.1 K) is much closer to that of the mesophile Bacillus subtilis (320.7 K) than the more closely related psychrophile B. globisporus (316.4 K). In addition, the enzymatic properties of M. marinus AK are quite close to those of the mesophilic AK and suggests that M. marinus experiences temperature ranges in which excellent enzyme function over a broad temperature range (293-313 K) has been retained for the success of the organism. Even transient loss of AK function is lethal and as a consequence AK must be robust and be well adapted to the environment of the host organism.

Structure and biochemical characterization of an adenylate kinase originating from the psychrophilic organism Marinibacillus marinus.,Davlieva M, Shamoo Y Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Aug 1;65(Pt, 8):751-6. Epub 2009 Jul 21. PMID:19652331^[1]

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

References

↑ Davlieva M, Shamoo Y. Structure and biochemical characterization of an adenylate kinase originating from the psychrophilic organism Marinibacillus marinus. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Aug 1;65(Pt, 8):751-6. Epub 2009 Jul 21. PMID:19652331 doi:10.1107/S1744309109024348

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/3fb4"

Categories: Jeotgalibacillus marinus | Large Structures | Davlieva MG | Shamoo Y

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:3fb4.jpg|left|200px]]
-<!--
+==Crystal structure of adenylate kinase from Marinibacillus marinus==
-The line below this paragraph, containing "STRUCTURE_3fb4", creates the "Structure Box" on the page.
+<StructureSection load='3fb4' size='340' side='right'caption='[[3fb4]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3fb4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Jeotgalibacillus_marinus Jeotgalibacillus marinus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FB4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FB4 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</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>
-{{STRUCTURE_3fb4|  PDB=3fb4  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3fb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fb4 OCA], [https://pdbe.org/3fb4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fb4 RCSB], [https://www.ebi.ac.uk/pdbsum/3fb4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fb4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q6B341_9BACL Q6B341_9BACL] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth (By similarity).[HAMAP-Rule:MF_00235]
+== 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/fb/3fb4_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=3fb4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Adenylate kinases (AKs; EC 2.7.4.3) are essential members of the NMP kinase family that maintain cellular homeostasis by the interconversion of AMP, ADP and ATP. AKs play a critical role in adenylate homeostasis across all domains of life and have been used extensively as prototypes for the study of protein adaptation and the relationship of protein dynamics and stability to function. To date, kinetic studies of psychrophilic AKs have not been performed. In order to broaden understanding of extremophilic adaptation, the kinetic parameters of adenylate kinase from the psychrophile Marinibacillus marinus were examined and the crystal structure of this cold-adapted enzyme was determined at 2.0 A resolution. As expected, the overall structure and topology of the psychrophilic M. marinus AK are similar to those of mesophilic and thermophilic AKs. The thermal denaturation midpoint of M. marinus AK (321.1 K) is much closer to that of the mesophile Bacillus subtilis (320.7 K) than the more closely related psychrophile B. globisporus (316.4 K). In addition, the enzymatic properties of M. marinus AK are quite close to those of the mesophilic AK and suggests that M. marinus experiences temperature ranges in which excellent enzyme function over a broad temperature range (293-313 K) has been retained for the success of the organism. Even transient loss of AK function is lethal and as a consequence AK must be robust and be well adapted to the environment of the host organism.
-===Crystal structure of adenylate kinase from Marinibacillus marinus===
+Structure and biochemical characterization of an adenylate kinase originating from the psychrophilic organism Marinibacillus marinus.,Davlieva M, Shamoo Y Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Aug 1;65(Pt, 8):751-6. Epub 2009 Jul 21. PMID:19652331<ref>PMID:19652331</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3fb4" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19652331}}, adds the Publication Abstract to the page
+*[[Adenylate kinase 3D structures|Adenylate kinase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19652331 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19652331}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Jeotgalibacillus marinus]]
-FB4 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Marinibacillus_marinus Marinibacillus marinus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FB4 OCA].
+[[Category: Large Structures]]
+[[Category: Davlieva MG]]
-==Reference==
+[[Category: Shamoo Y]]
-<ref group="xtra">PMID:19652331</ref><references group="xtra"/>
-[[Category: Adenylate kinase]]
-[[Category: Marinibacillus marinus]]
-[[Category: Davlieva, M G.]]
-[[Category: Shamoo, Y.]]
-[[Category: Adenylate kinase]]
-[[Category: Atp-binding]]
-[[Category: Kinase]]
-[[Category: Nucleotide-binding]]
-[[Category: Phosphotransferase]]
-[[Category: Psychrophile]]
-[[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 30 09:22:12 2009''

3fb4

From Proteopedia

Current revision

Crystal structure of adenylate kinase from Marinibacillus marinus

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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