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4bg4

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Current revision

Crystal structure of Litopenaeus vannamei arginine kinase in a ternary analog complex with arginine, ADP-Mg and NO3

Structural highlights

4bg4 is a 2 chain structure with sequence from Penaeus vannamei. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.601Å
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

KARG0_PENVA Catalyzes the reversible transfer of high energy ATP gamma-phosphate group to L-arginine (PubMed:17496423, PubMed:27072556, PubMed:22750864, PubMed:23873077). Has nucleoside diphosphate kinase-like activity toward dTDP. Binds and phosphorylates dTDP using ATP as a phosphate donor. Does not phosphorylate dADP, dCDP, dGDP, dTMP or thymidine (PubMed:27072556).^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

Arginine kinase (AK) is a key enzyme for energetic balance in invertebrates. Although AK is a well-studied system that provides fast energy to invertebrates using the phosphagen phospho-arginine, the structural details on the AK-arginine binary complex interaction remain unclear. Herein, we determined two crystal structures of the Pacific whiteleg shrimp (Litopenaeus vannamei) arginine kinase, one in binary complex with arginine (LvAK-Arg) and a ternary transition state analog complex (TSAC). We found that the arginine guanidinium group makes ionic contacts with Glu225, Cys271 and a network of ordered water molecules. On the zwitterionic side of the amino acid, the backbone amide nitrogens of Gly64 and Val65 coordinate the arginine carboxylate. Glu314, one of proposed acid-base catalytic residues, did not interact with arginine in the binary complex. This residue is located in the flexible loop 310-320 that covers the active site and only stabilizes in the LvAK-TSAC. This is the first binary complex crystal structure of a guanidine kinase in complex with the guanidine substrate and could give insights into the nature of the early steps of phosphagen biosynthesis.

Crystal structure of shrimp arginine kinase in binary complex with arginine-a molecular view of the phosphagen precursor binding to the enzyme.,Lopez-Zavala AA, Garcia-Orozco KD, Carrasco-Miranda JS, Sugich-Miranda R, Velazquez-Contreras EF, Criscitiello MF, Brieba LG, Rudino-Pinera E, Sotelo-Mundo RR J Bioenerg Biomembr. 2013 Jul 20. PMID:23873077^[5]

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

References

↑ García-Orozco KD, Aispuro-Hernández E, Yepiz-Plascencia G, Calderón-de-la-Barca AM, Sotelo-Mundo RR. Molecular characterization of arginine kinase, an allergen from the shrimp Litopenaeus vannamei. Int Arch Allergy Immunol. 2007;144(1):23-8. PMID:17496423 doi:10.1159/000102610
↑ Lopez-Zavala AA, Sotelo-Mundo RR, Garcia-Orozco KD, Isac-Martinez F, Brieba LG, Rudino-Pinera E. Crystallization and X-ray diffraction studies of arginine kinase from the white Pacific shrimp Litopenaeus vannamei. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Jul 1;68(Pt 7):783-5. Epub, 2012 Jun 27. PMID:22750864 doi:10.1107/S1744309112020180
↑ Lopez-Zavala AA, Garcia-Orozco KD, Carrasco-Miranda JS, Sugich-Miranda R, Velazquez-Contreras EF, Criscitiello MF, Brieba LG, Rudino-Pinera E, Sotelo-Mundo RR. Crystal structure of shrimp arginine kinase in binary complex with arginine-a molecular view of the phosphagen precursor binding to the enzyme. J Bioenerg Biomembr. 2013 Jul 20. PMID:23873077 doi:10.1007/s10863-013-9521-0
↑ Lopez-Zavala AA, Sotelo-Mundo RR, Hernandez-Flores JM, Lugo-Sanchez ME, Sugich-Miranda R, Garcia-Orozco KD. Arginine kinase shows nucleoside diphosphate kinase-like activity toward deoxythymidine diphosphate. J Bioenerg Biomembr. 2016 Jun;48(3):301-8. PMID:27072556 doi:10.1007/s10863-016-9660-1
↑ Lopez-Zavala AA, Garcia-Orozco KD, Carrasco-Miranda JS, Sugich-Miranda R, Velazquez-Contreras EF, Criscitiello MF, Brieba LG, Rudino-Pinera E, Sotelo-Mundo RR. Crystal structure of shrimp arginine kinase in binary complex with arginine-a molecular view of the phosphagen precursor binding to the enzyme. J Bioenerg Biomembr. 2013 Jul 20. PMID:23873077 doi:10.1007/s10863-013-9521-0

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/4bg4"

@@ Line 3: / Line 3: @@
 <StructureSection load='4bg4' size='340' side='right'caption='[[4bg4]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4bg4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Litopenaeus_vannamei Litopenaeus vannamei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BG4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BG4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4bg4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Penaeus_vannamei Penaeus vannamei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BG4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BG4 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=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</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]] 1.601&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></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=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Arginine_kinase Arginine kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.3.3 2.7.3.3] </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=4bg4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bg4 OCA], [https://pdbe.org/4bg4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4bg4 RCSB], [https://www.ebi.ac.uk/pdbsum/4bg4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4bg4 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/KARG0_PENVA KARG0_PENVA] Catalyzes the reversible transfer of high energy ATP gamma-phosphate group to L-arginine (PubMed:17496423, PubMed:27072556, PubMed:22750864, PubMed:23873077). Has nucleoside diphosphate kinase-like activity toward dTDP. Binds and phosphorylates dTDP using ATP as a phosphate donor. Does not phosphorylate dADP, dCDP, dGDP, dTMP or thymidine (PubMed:27072556).<ref>PMID:17496423</ref> <ref>PMID:22750864</ref> <ref>PMID:23873077</ref> <ref>PMID:27072556</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Arginine kinase]]
 [[Category: Large Structures]]
-[[Category: Litopenaeus vannamei]]
+[[Category: Penaeus vannamei]]
-[[Category: Carrasco-Miranda, J S]]
+[[Category: Carrasco-Miranda JS]]
-[[Category: Criscitiello, M F]]
+[[Category: Criscitiello MF]]
-[[Category: GBrieba, L]]
+[[Category: GBrieba L]]
-[[Category: Garcia-Orozco, K D]]
+[[Category: Garcia-Orozco KD]]
-[[Category: Lopez-Zavala, A A]]
+[[Category: Lopez-Zavala AA]]
-[[Category: Rudino-Pinera, E]]
+[[Category: Rudino-Pinera E]]
-[[Category: Sotelo-Mundo, R R]]
+[[Category: Sotelo-Mundo RR]]
-[[Category: Sugich-Miranda, R]]
+[[Category: Sugich-Miranda R]]
-[[Category: Velazquez-Contreras, E F]]
+[[Category: Velazquez-Contreras EF]]
-[[Category: Binary complex]]
-[[Category: Transferase]]

4bg4

From Proteopedia

Current revision

Crystal structure of Litopenaeus vannamei arginine kinase in a ternary analog complex with arginine, ADP-Mg and NO3

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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