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5yg8

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Revision as of 08:29, 22 November 2023

Crystal structure of ribose-1,5-bisphosphate isomerase from Pyrococcus horikoshii OT3 in complex with ribulose-1,5-bisphosphate, AMP and GMP

Structural highlights

5yg8 is a 3 chain structure with sequence from Pyrococcus horikoshii OT3. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.8Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

R15PI_PYRHO Catalyzes the isomerization of ribose 1,5-bisphosphate (R15P) to ribulose 1,5-bisphosphate (RuBP), the CO(2) acceptor and substrate for RubisCO. Functions in an archaeal AMP degradation pathway, together with AMP phosphorylase and RubisCO (By similarity).

Publication Abstract from PubMed

The homologues of the regulatory subunits of eukaryotic translation initiation factor 2B (eIF2B) are assumed to be present in archaea. Likewise, an ORF, PH0208 in Pyrococcus horikoshii OT3 have been proposed to encode one of the homologues of regulatory subunits of eIF2B. However, PH0208 protein also shares sequence similarity with a functionally non-related enzyme, ribose-1,5-bisphosphate isomerase (R15Pi), involved in conversion of ribose-1,5-bisphosphate (R15P) to ribulose-1,5-bisphosphate (RuBP) in an AMP-dependent manner. Herein, we have determined the crystal structure of PH0208 protein in order to decipher its true function. Although structurally similar to the regulatory subunits of eIF2B, the ability to bind R15P and RuBP suggests that PH0208 would function as R15Pi. Additionally, this study for the first time reports the binding sites of AMP and GMP in R15Pi. The AMP binding site in PH0208 protein clarified the role of AMP in providing structural stability to R15Pi. The binding of GMP to the 'AMP binding site' in addition to its own binding site indicates that GMP might also execute a similar function, though with less specificity. Furthermore, we have utilized the resemblance between PH0208 and the regulatory subunits of eIF2B to propose a model for the regulatory mechanism of eIF2B in eukaryotes.

A presumed homologue of the regulatory subunits of eIF2B functions as ribose-1,5-bisphosphate isomerase in Pyrococcus horikoshii OT3.,Gogoi P, Kanaujia SP Sci Rep. 2018 Jan 30;8(1):1891. doi: 10.1038/s41598-018-20418-w. PMID:29382938^[1]

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

References

↑ Gogoi P, Kanaujia SP. A presumed homologue of the regulatory subunits of eIF2B functions as ribose-1,5-bisphosphate isomerase in Pyrococcus horikoshii OT3. Sci Rep. 2018 Jan 30;8(1):1891. doi: 10.1038/s41598-018-20418-w. PMID:29382938 doi:http://dx.doi.org/10.1038/s41598-018-20418-w

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5yg8"

Categories: Large Structures | Pyrococcus horikoshii OT3 | Gogoi P | Kanaujia SP

@@ Line 3: / Line 3: @@
 <StructureSection load='5yg8' size='340' side='right'caption='[[5yg8]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5yg8]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YG8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YG8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5yg8]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YG8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YG8 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=RUB:RIBULOSE-1,5-DIPHOSPHATE'>RUB</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]] 2.8&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribose_1,5-bisphosphate_isomerase Ribose 1,5-bisphosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.29 5.3.1.29] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=RUB:RIBULOSE-1,5-DIPHOSPHATE'>RUB</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5yg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yg8 OCA], [http://pdbe.org/5yg8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yg8 RCSB], [http://www.ebi.ac.uk/pdbsum/5yg8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yg8 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=5yg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yg8 OCA], [https://pdbe.org/5yg8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yg8 RCSB], [https://www.ebi.ac.uk/pdbsum/5yg8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yg8 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/R15PI_PYRHO R15PI_PYRHO]] Catalyzes the isomerization of ribose 1,5-bisphosphate (R15P) to ribulose 1,5-bisphosphate (RuBP), the CO(2) acceptor and substrate for RubisCO. Functions in an archaeal AMP degradation pathway, together with AMP phosphorylase and RubisCO (By similarity).
+[https://www.uniprot.org/uniprot/R15PI_PYRHO R15PI_PYRHO] Catalyzes the isomerization of ribose 1,5-bisphosphate (R15P) to ribulose 1,5-bisphosphate (RuBP), the CO(2) acceptor and substrate for RubisCO. Functions in an archaeal AMP degradation pathway, together with AMP phosphorylase and RubisCO (By similarity).
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Ribose 1,5-bisphosphate isomerase]]
+[[Category: Pyrococcus horikoshii OT3]]
-[[Category: Gogoi, P]]
+[[Category: Gogoi P]]
-[[Category: Kanaujia, S P]]
+[[Category: Kanaujia SP]]
-[[Category: 5-bisphosphate]]
-[[Category: Isomerase]]
-[[Category: Nmp degradation pathway]]
-[[Category: Ribose-1]]
-[[Category: Rossmann-like fold]]

5yg8

From Proteopedia

Revision as of 08:29, 22 November 2023

Crystal structure of ribose-1,5-bisphosphate isomerase from Pyrococcus horikoshii OT3 in complex with ribulose-1,5-bisphosphate, AMP and GMP

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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