This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

6a34

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of 5-methylthioribose 1-phosphate isomerase from Pyrococcus horikoshii OT3 - Form I

Structural highlights

6a34 is a 2 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 2.3Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MTNA_PYRHO Catalyzes the interconversion of methylthioribose-1-phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P).[HAMAP-Rule:MF_01678]

Publication Abstract from PubMed

5-Methylthioribose 1-phosphate isomerase (M1Pi) is a crucial enzyme involved in the universally conserved methionine salvage pathway (MSP) where it is known to catalyze the conversion of 5-methylthioribose 1-phosphate (MTR-1-P) to 5-methylthioribulose 1-phosphate (MTRu-1-P) via a mechanism which remains unspecified till date. Furthermore, although M1Pi has a discrete function, it surprisingly shares high structural similarity with two functionally non-related proteins such as ribose-1,5-bisphosphate isomerase (R15Pi) and the regulatory subunits of eukaryotic translation initiation factor 2B (eIF2B). To identify the distinct structural features that lead to divergent functional obligations of M1Pi as well as to understand the mechanism of enzyme catalysis, the crystal structure of M1Pi from a hyperthermophilic archaeon Pyrococcus horikoshii OT3 was determined. A meticulous structural investigation of the dimeric M1Pi revealed the presence of an N-terminal extension and a hydrophobic patch absent in R15Pi and the regulatory alpha-subunit of eIF2B. Furthermore, unlike R15Pi in which a kink formation is observed in one of the helices, the domain movement of M1Pi is distinguished by a forward shift in a loop covering the active-site pocket. All these structural attributes contribute towards a hydrophobic microenvironment in the vicinity of the active site of the enzyme making it favorable for the reaction mechanism to commence. Thus, a hydrophobic active-site microenvironment in addition to the availability of optimal amino-acid residues surrounding the catalytic residues in M1Pi led us to propose its probable reaction mechanism via a cis-phosphoenolate intermediate formation.

Structural insights into the catalytic mechanism of 5-methylthioribose 1-phosphate isomerase.,Gogoi P, Mordina P, Kanaujia SP J Struct Biol. 2018 Nov 22. pii: S1047-8477(18)30290-9. doi:, 10.1016/j.jsb.2018.11.007. PMID:30471343^[1]

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

References

↑ Gogoi P, Mordina P, Kanaujia SP. Structural insights into the catalytic mechanism of 5-methylthioribose 1-phosphate isomerase. J Struct Biol. 2018 Nov 22. pii: S1047-8477(18)30290-9. doi:, 10.1016/j.jsb.2018.11.007. PMID:30471343 doi:http://dx.doi.org/10.1016/j.jsb.2018.11.007

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/6a34"

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

@@ Line 1: / Line 1: @@
 ==Crystal structure of 5-methylthioribose 1-phosphate isomerase from Pyrococcus horikoshii OT3 - Form I==
-<StructureSection load='6a34' size='340' side='right' caption='[[6a34]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='6a34' size='340' side='right'caption='[[6a34]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6a34]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A34 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A34 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6a34]] is a 2 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=6A34 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6A34 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEZ:HEXANE-1,6-DIOL'>HEZ</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]] 2.3&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/S-methyl-5-thioribose-1-phosphate_isomerase S-methyl-5-thioribose-1-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.23 5.3.1.23] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEZ:HEXANE-1,6-DIOL'>HEZ</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=6a34 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a34 OCA], [http://pdbe.org/6a34 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a34 RCSB], [http://www.ebi.ac.uk/pdbsum/6a34 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a34 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=6a34 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a34 OCA], [https://pdbe.org/6a34 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6a34 RCSB], [https://www.ebi.ac.uk/pdbsum/6a34 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6a34 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/MTNA_PYRHO MTNA_PYRHO]] Catalyzes the interconversion of methylthioribose-1-phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P).[HAMAP-Rule:MF_01678]
+[https://www.uniprot.org/uniprot/MTNA_PYRHO MTNA_PYRHO] Catalyzes the interconversion of methylthioribose-1-phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P).[HAMAP-Rule:MF_01678]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: S-methyl-5-thioribose-1-phosphate isomerase]]
+[[Category: Large Structures]]
-[[Category: Gogoi, P]]
+[[Category: Pyrococcus horikoshii OT3]]
-[[Category: Kanaujia, S P]]
+[[Category: Gogoi P]]
-[[Category: Mordina, P]]
+[[Category: Kanaujia SP]]
-[[Category: Cis-phosphoenolate intermediate]]
+[[Category: Mordina P]]
-[[Category: Hydride transfer]]
-[[Category: Isomerase]]
-[[Category: Methionine salvage pathway]]
-[[Category: Ph0702]]

6a34

From Proteopedia

Current revision

Crystal structure of 5-methylthioribose 1-phosphate isomerase from Pyrococcus horikoshii OT3 - Form I

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox