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| | ==Free serine kinase (E30A mutant) in complex with ADP== | | ==Free serine kinase (E30A mutant) in complex with ADP== |
| - | <StructureSection load='5x0g' size='340' side='right' caption='[[5x0g]], [[Resolution|resolution]] 1.90Å' scene=''> | + | <StructureSection load='5x0g' size='340' side='right'caption='[[5x0g]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5x0g]] is a 1 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=5X0G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X0G FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5x0g]] is a 1 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=5X0G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X0G FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7WF:2-HYDROXY-3-[4-(2-HYDROXY-3-SULFOPROPYL)PIPERAZIN-1-YL]PROPANE-1-SULFONIC+ACID'>7WF</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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]] 1.9Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5x0b|5x0b]], [[5x0e|5x0e]], [[5x0f|5x0f]], [[5x0j|5x0j]], [[5x0k|5x0k]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7WF:2-HYDROXY-3-[4-(2-HYDROXY-3-SULFOPROPYL)PIPERAZIN-1-YL]PROPANE-1-SULFONIC+ACID'>7WF</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TK0378 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</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=5x0g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x0g OCA], [https://pdbe.org/5x0g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x0g RCSB], [https://www.ebi.ac.uk/pdbsum/5x0g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x0g ProSAT]</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=5x0g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x0g OCA], [http://pdbe.org/5x0g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x0g RCSB], [http://www.ebi.ac.uk/pdbsum/5x0g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x0g ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/SERK_THEKO SERK_THEKO] Free serine kinase that uses ADP to phosphorylate L-serine to yield O-phospho-L-serine and AMP.<ref>PMID:27857065</ref> <ref>PMID:28358477</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Fujihashi, M]] | + | [[Category: Large Structures]] |
| - | [[Category: Miki, K]] | + | [[Category: Thermococcus kodakarensis KOD1]] |
| - | [[Category: Nagata, R]] | + | [[Category: Fujihashi M]] |
| - | [[Category: Cysteine biosynthesis]] | + | [[Category: Miki K]] |
| - | [[Category: Thermococcus kodakarensis]] | + | [[Category: Nagata R]] |
| - | [[Category: Transferase]]
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| Structural highlights
Function
SERK_THEKO Free serine kinase that uses ADP to phosphorylate L-serine to yield O-phospho-L-serine and AMP.[1] [2]
Publication Abstract from PubMed
A free serine kinase (SerK) is involved in L-cysteine biosynthesis in the hyperthermophilic archaeon Thermococcus kodakarensis. The enzyme converts ADP and L-serine (Ser) into AMP and O-phospho-L-serine (Sep), which is a precursor of L-cysteine. SerK is the first identified enzyme that phosphorylates free serine, while serine/threonine protein kinases have been well studied. SerK displays low sequence similarities to known kinases, suggesting that its reaction mechanism is different from those of known kinases. Here, we determined the crystal structures of SerK from T. kodakarensis (Tk-SerK). The overall structure is divided into two domains. A large cleft is found between the two domains in the AMP complex and in the ADP complex. The cleft is closed in the ternary product complex (Sep, AMP, and Tk-SerK), and may also be in the ternary substrate complex (Ser, ADP, and Tk-SerK). The closure may reorient the carboxyl group of E30 near to the Ogamma atom of Ser. The Ogamma atom is considered to be deprotonated by E30 and to attack the beta-phosphate of ADP to form Sep. The substantial decrease in the activity of the E30A mutant is consistent with this mechanism. Our structures also revealed the residues that contribute to the ligand binding. The conservation of these residues in uncharacterized proteins from bacteria may raise the possibility of the presence of free Ser kinases not only in archaea but also in bacteria.
Structural Study on the Reaction Mechanism of a Free Serine Kinase Involved in Cysteine Biosynthesis.,Nagata R, Fujihashi M, Kawamura H, Sato T, Fujita T, Atomi H, Miki K ACS Chem Biol. 2017 Mar 30. doi: 10.1021/acschembio.7b00064. PMID:28358477[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Makino Y, Sato T, Kawamura H, Hachisuka SI, Takeno R, Imanaka T, Atomi H. An archaeal ADP-dependent serine kinase involved in cysteine biosynthesis and serine metabolism. Nat Commun. 2016 Nov 18;7:13446. PMID:27857065 doi:10.1038/ncomms13446
- ↑ Nagata R, Fujihashi M, Kawamura H, Sato T, Fujita T, Atomi H, Miki K. Structural Study on the Reaction Mechanism of a Free Serine Kinase Involved in Cysteine Biosynthesis. ACS Chem Biol. 2017 Mar 30. doi: 10.1021/acschembio.7b00064. PMID:28358477 doi:http://dx.doi.org/10.1021/acschembio.7b00064
- ↑ Nagata R, Fujihashi M, Kawamura H, Sato T, Fujita T, Atomi H, Miki K. Structural Study on the Reaction Mechanism of a Free Serine Kinase Involved in Cysteine Biosynthesis. ACS Chem Biol. 2017 Mar 30. doi: 10.1021/acschembio.7b00064. PMID:28358477 doi:http://dx.doi.org/10.1021/acschembio.7b00064
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