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5ot0

From Proteopedia

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The thermostable L-asparaginase from Thermococcus kodakarensis

Structural highlights

5ot0 is a 6 chain structure with sequence from Thermococcus kodakarensis KOD1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.18Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q5JIW4_THEKO

Publication Abstract from PubMed

L-Asparaginases catalyse the hydrolysis of asparagine to aspartic acid and ammonia. In addition, L-asparaginase is involved in the biosynthesis of amino acids such as lysine, methionine and threonine. These enzymes have been used as chemotherapeutic agents for the treatment of acute lymphoblastic leukaemia and other haematopoietic malignancies since the tumour cells cannot synthesize sufficient L-asparagine and are thus killed by deprivation of this amino acid. L-Asparaginases are also used in the food industry and have potential in the development of biosensors, for example for asparagine levels in leukaemia. The thermostable type I L-asparaginase from Thermococcus kodakarensis (TkA) is composed of 328 amino acids and forms homodimers in solution, with the highest catalytic activity being observed at pH 9.5 and 85 degrees C. It has a Km value of 5.5 mM for L-asparagine, with no glutaminase activity being observed. The crystal structure of TkA has been determined at 2.18 A resolution, confirming the presence of two alpha/beta domains connected by a short linker region. The N-terminal domain contains a highly flexible beta-hairpin which adopts `open' and `closed' conformations in different subunits of the solved TkA structure. In previously solved L-asparaginase structures this beta-hairpin was only visible when in the `closed' conformation, whilst it is characterized with good electron density in all of the subunits of the TkA structure. A phosphate anion resides at the active site, which is formed by residues from both of the neighbouring monomers in the dimer. The high thermostability of TkA is attributed to the high arginine and salt-bridge content when compared with related mesophilic enzymes.

Structure and function of the thermostable L-asparaginase from Thermococcus kodakarensis.,Guo J, Coker AR, Wood SP, Cooper JB, Chohan SM, Rashid N, Akhtar M Acta Crystallogr D Struct Biol. 2017 Nov 1;73(Pt 11):889-895. doi:, 10.1107/S2059798317014711. Epub 2017 Oct 20. PMID:29095161^[1]

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

References

↑ Guo J, Coker AR, Wood SP, Cooper JB, Chohan SM, Rashid N, Akhtar M. Structure and function of the thermostable L-asparaginase from Thermococcus kodakarensis. Acta Crystallogr D Struct Biol. 2017 Nov 1;73(Pt 11):889-895. doi:, 10.1107/S2059798317014711. Epub 2017 Oct 20. PMID:29095161 doi:http://dx.doi.org/10.1107/S2059798317014711

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5ot0"

@@ Line 1: / Line 1: @@
 ==The thermostable L-asparaginase from Thermococcus kodakarensis==
-<StructureSection load='5ot0' size='340' side='right' caption='[[5ot0]], [[Resolution|resolution]] 2.18&Aring;' scene=''>
+<StructureSection load='5ot0' size='340' side='right'caption='[[5ot0]], [[Resolution|resolution]] 2.18&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ot0]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OT0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OT0 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ot0]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OT0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OT0 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.18&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TK1656 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=5ot0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ot0 OCA], [http://pdbe.org/5ot0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ot0 RCSB], [http://www.ebi.ac.uk/pdbsum/5ot0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ot0 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=5ot0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ot0 OCA], [https://pdbe.org/5ot0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ot0 RCSB], [https://www.ebi.ac.uk/pdbsum/5ot0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ot0 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q5JIW4_THEKO Q5JIW4_THEKO]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 17: / Line 19: @@
 </div>
 <div class="pdbe-citations 5ot0" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Asparaginase 3D structures|Asparaginase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Akhtar, M]]
+[[Category: Large Structures]]
-[[Category: Chohan, S M]]
+[[Category: Thermococcus kodakarensis KOD1]]
-[[Category: Coker, A R]]
+[[Category: Akhtar M]]
-[[Category: Cooper, J B]]
+[[Category: Chohan SM]]
-[[Category: Guo, J]]
+[[Category: Coker AR]]
-[[Category: Rashid, N]]
+[[Category: Cooper JB]]
-[[Category: Wood, S P]]
+[[Category: Guo J]]
-[[Category: Homodimer]]
+[[Category: Rashid N]]
-[[Category: Hydrolase]]
+[[Category: Wood SP]]
-[[Category: Leukaemia]]
-[[Category: Thermostable]]

5ot0

From Proteopedia

Current revision

The thermostable L-asparaginase from Thermococcus kodakarensis

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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