3hdq

From Proteopedia

(Difference between revisions)

Revision as of 12:45, 23 March 2022

Crystal structure of UDP-galactopyranose mutase (oxidized form) in complex with substrate

Structural highlights

3hdq is a 10 chain structure with sequence from "micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Gene:	DR_A0367, DR_AO367 ("Micrococcus radiodurans" Raj et al. 1960)
Activity:	UDP-galactopyranose mutase, with EC number 5.4.99.9
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

D-Galactofuranose (Galf) residues are found in the cell walls of pathogenic microbes such as Mycobacterium tuberculosis, and are essential for viability. UDP-galactopyranose mutase (UGM) is a unique flavo-enzyme that catalyzes the reversible conversion of UDP-galactopyranose (UDP-Galp) and UDP-galactofuranose (UDP-Galf). UDP-Galf is the active precursor of Galf residues found in cell walls. Despite the wealth of biochemical/mechanistic data generated for UGM, the structural basis of substrate binding is still lacking. Here, we report the crystal structures of UGM from Deinococcus radiodurans (drUGM) in complex with its natural substrate (UDP-Galp) and UDP. Crystal structures of drUGM:UDP-Galp complexes with oxidized and reduced FAD were determined at 2.36 A and 2.50 A resolution, respectively. The substrate is buried in the active site in an unusual folded conformation and the anomeric carbon of the galactose is at a favorable distance (2.8 A) from N5 of FAD to form an FAD-galactose adduct. The mobile loops in the substrate complex structure exist in a closed conformation. The drUGM-UDP complex structure was determined at 2.55 A resolution and its overall structure is identical with that of the oxidized and reduced complexes, including the conformation of the mobile loops. Comparison with the recently reported UGM:UDP-glucose complex structure reveals key differences and the structures reported here are likely to represent the productive/active conformation of UGM. These structures provide valuable insights into substrate recognition and a basis for understanding the mechanism. These complex structures may serve as a platform for structure-guided design of inhibitors of UGM.

Structural basis of substrate binding to UDP-galactopyranose mutase: crystal structures in the reduced and oxidized state complexed with UDP-galactopyranose and UDP.,Partha SK, van Straaten KE, Sanders DA J Mol Biol. 2009 Dec 18;394(5):864-77. Epub 2009 Oct 21. PMID:19836401^[1]

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

References

↑ Partha SK, van Straaten KE, Sanders DA. Structural basis of substrate binding to UDP-galactopyranose mutase: crystal structures in the reduced and oxidized state complexed with UDP-galactopyranose and UDP. J Mol Biol. 2009 Dec 18;394(5):864-77. Epub 2009 Oct 21. PMID:19836401 doi:10.1016/j.jmb.2009.10.013

1 Structural highlights
2 Evolutionary Conservation
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/3hdq"

@@ Line 1: / Line 1: @@
 ==Crystal structure of UDP-galactopyranose mutase (oxidized form) in complex with substrate==
-<StructureSection load='3hdq' size='340' side='right' caption='[[3hdq]], [[Resolution|resolution]] 2.36&Aring;' scene=''>
+<StructureSection load='3hdq' size='340' side='right'caption='[[3hdq]], [[Resolution|resolution]] 2.36&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3hdq]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HDQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HDQ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3hdq]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HDQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HDQ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GDU:GALACTOSE-URIDINE-5-DIPHOSPHATE'>GDU</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GDU:GALACTOSE-URIDINE-5-DIPHOSPHATE'>GDU</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DR_A0367, DR_AO367 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 "Micrococcus radiodurans" Raj et al. 1960])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DR_A0367, DR_AO367 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 "Micrococcus radiodurans" Raj et al. 1960])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-galactopyranose_mutase UDP-galactopyranose mutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.99.9 5.4.99.9] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/UDP-galactopyranose_mutase UDP-galactopyranose mutase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.99.9 5.4.99.9] </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=3hdq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hdq OCA], [http://pdbe.org/3hdq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hdq RCSB], [http://www.ebi.ac.uk/pdbsum/3hdq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3hdq 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=3hdq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hdq OCA], [https://pdbe.org/3hdq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hdq RCSB], [https://www.ebi.ac.uk/pdbsum/3hdq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hdq ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 30: / Line 30: @@
 ==See Also==
-*[[UDP-galactopyranose mutase|UDP-galactopyranose mutase]]
+*[[UDP-galactopyranose mutase 3D structures|UDP-galactopyranose mutase 3D structures]]
 == References ==
 <references/>
@@ Line 36: / Line 36: @@
 </StructureSection>
 [[Category: Micrococcus radiodurans raj et al. 1960]]
+[[Category: Large Structures]]
 [[Category: UDP-galactopyranose mutase]]
 [[Category: Partha, S K]]

3hdq

From Proteopedia

Revision as of 12:45, 23 March 2022

Crystal structure of UDP-galactopyranose mutase (oxidized form) in complex with substrate

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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