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4hfq

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Revision as of 08:14, 3 November 2022

Crystal structure of UDP-X diphosphatase

Structural highlights

4hfq is a 2 chain structure with sequence from Streptococcus pneumoniae TIGR4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A0A0H2URA0_STRPN

Publication Abstract from PubMed

The gene for a Nudix enzyme (SP_1669) was found to code for a UDP-X diphosphatase. The SP_1669 gene is localized among genes encoding proteins that participate in cell division in Streptococcus pneumoniae. One of these genes, MurF, encodes an enzyme that catalyzes the last step of the Mur pathway of peptidoglycan biosynthesis. Mur pathway substrates are all derived from UDP-glucosamine and all are potential Nudix substrates. We showed that UDP-X diphosphatase can hydrolyze the Mur pathway substrates UDP-N-acetylmuramic acid and UDP-N-acetylmuramoyl-L-alanine. The 1.39 A resolution crystal structure of this enzyme shows that it folds as an asymmetric homodimer with two distinct active sites, each containing elements of the conserved Nudix box sequence. In addition to its Nudix catalytic activity, the enzyme has a 3'5' RNA exonuclease activity. We propose that the structural asymmetry in UDP-X diphosphatase facilitates the recognition of these two distinct classes of substrates, Nudix substrates and RNA. UDP-X diphosphatase is a prototype of a new family of Nudix enzymes with unique structural characteristics: two monomers, each consisting of an N-terminal helix bundle domain and a C-terminal Nudix domain, form an asymmetric dimer with two distinct active sites. These enzymes function to hydrolyze bacterial cell wall precursors and degrade RNA.

A UDP-X diphosphatase from Streptococcus pneumoniae hydrolyzes precursors of peptidoglycan biosynthesis.,Duong-Ly KC, Woo HN, Dunn CA, Xu W, Babic A, Bessman MJ, Amzel LM, Gabelli SB PLoS One. 2013 May 15;8(5):e64241. doi: 10.1371/journal.pone.0064241. Print 2013. PMID:23691178^[1]

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

References

↑ Duong-Ly KC, Woo HN, Dunn CA, Xu W, Babic A, Bessman MJ, Amzel LM, Gabelli SB. A UDP-X diphosphatase from Streptococcus pneumoniae hydrolyzes precursors of peptidoglycan biosynthesis. PLoS One. 2013 May 15;8(5):e64241. doi: 10.1371/journal.pone.0064241. Print 2013. PMID:23691178 doi:10.1371/journal.pone.0064241

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/4hfq"

Categories: Large Structures | Streptococcus pneumoniae TIGR4 | Amzel LM | Duong-Ly KC | Gabelli SB

@@ Line 1: / Line 1: @@
 ==Crystal structure of UDP-X diphosphatase==
-<StructureSection load='4hfq' size='340' side='right' caption='[[4hfq]], [[Resolution|resolution]] 1.39&Aring;' scene=''>
+<StructureSection load='4hfq' size='340' side='right'caption='[[4hfq]], [[Resolution|resolution]] 1.39&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4hfq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Strpn Strpn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HFQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HFQ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4hfq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_TIGR4 Streptococcus pneumoniae TIGR4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HFQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HFQ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SP1669, SP_1669 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=170187 STRPN])</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=4hfq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hfq OCA], [https://pdbe.org/4hfq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hfq RCSB], [https://www.ebi.ac.uk/pdbsum/4hfq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hfq 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=4hfq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hfq OCA], [http://pdbe.org/4hfq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4hfq RCSB], [http://www.ebi.ac.uk/pdbsum/4hfq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4hfq ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/A0A0H2URA0_STRPN A0A0H2URA0_STRPN]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Strpn]]
+[[Category: Large Structures]]
-[[Category: Amzel, L M]]
+[[Category: Streptococcus pneumoniae TIGR4]]
-[[Category: Duong-Ly, K C]]
+[[Category: Amzel LM]]
-[[Category: Gabelli, S B]]
+[[Category: Duong-Ly KC]]
-[[Category: Hydrolase]]
+[[Category: Gabelli SB]]
-[[Category: Mur pathway]]
-[[Category: Nudix]]
-[[Category: Pyrophosphatase]]
-[[Category: Rna exonuclease]]
-[[Category: Udp-sugar diphosphatase]]

4hfq

From Proteopedia

Revision as of 08:14, 3 November 2022

Crystal structure of UDP-X diphosphatase

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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