4j6e: Difference between revisions

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<StructureSection load='4j6e' size='340' side='right'caption='[[4j6e]], [[Resolution|resolution]] 2.52&Aring;' scene=''>
<StructureSection load='4j6e' size='340' side='right'caption='[[4j6e]], [[Resolution|resolution]] 2.52&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4j6e]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cauvn Cauvn]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4ggi 4ggi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J6E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4J6E FirstGlance]. <br>
<table><tr><td colspan='2'>[[4j6e]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Caulobacter_vibrioides_NA1000 Caulobacter vibrioides NA1000]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4ggi 4ggi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J6E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4J6E FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UDG:(2R,3R,4R,5S,6R)-2-{[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-5-HYDROXY-6-(HYDROXYMETHYL)-3-{[(3R)-3-HYDROXYTETRADECANOYL]AMINO}TETRAHYDRO-2H-PYRAN-4-YL+(3R)-3-HYDROXYTETRADECANOATE'>UDG</scene></td></tr>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UDG:(2R,3R,4R,5S,6R)-2-{[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-5-HYDROXY-6-(HYDROXYMETHYL)-3-{[(3R)-3-HYDROXYTETRADECANOYL]AMINO}TETRAHYDRO-2H-PYRAN-4-YL+(3R)-3-HYDROXYTETRADECANOATE'>UDG</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ggm|4ggm]]</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=4j6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j6e OCA], [https://pdbe.org/4j6e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4j6e RCSB], [https://www.ebi.ac.uk/pdbsum/4j6e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4j6e ProSAT]</span></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">77330127, CCNA_01987, CC_1910, lpxI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=565050 CAUVN])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-2,3-diacylglucosamine_diphosphatase UDP-2,3-diacylglucosamine diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.54 3.6.1.54] </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=4j6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j6e OCA], [http://pdbe.org/4j6e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4j6e RCSB], [http://www.ebi.ac.uk/pdbsum/4j6e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4j6e ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/A0A0H3C8Q1_CAUVN A0A0H3C8Q1_CAUVN]
<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: Cauvn]]
[[Category: Caulobacter vibrioides NA1000]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: UDP-2,3-diacylglucosamine diphosphatase]]
[[Category: Finer-Moore JS]]
[[Category: CSMP, Center for Structures of Membrane Proteins]]
[[Category: Lee JK]]
[[Category: Finer-Moore, J S]]
[[Category: Metzger IV LE]]
[[Category: IV, L E.Metzger]]
[[Category: Raetz CRH]]
[[Category: Lee, J K]]
[[Category: Stroud RM]]
[[Category: Raetz, C R.H]]
[[Category: Stroud, R M]]
[[Category: Center for structures of membrane protein]]
[[Category: Csmp]]
[[Category: Hydrolase]]
[[Category: Lipid binding]]
[[Category: Psi-biology]]
[[Category: Structural genomic]]

Revision as of 13:55, 24 November 2022

Structure of LPXI D225A MutantStructure of LPXI D225A Mutant

Structural highlights

4j6e is a 1 chain structure with sequence from Caulobacter vibrioides NA1000. This structure supersedes the now removed PDB entry 4ggi. 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

A0A0H3C8Q1_CAUVN

Publication Abstract from PubMed

Enzymes in lipid metabolism acquire and deliver hydrophobic substrates and products from within lipid bilayers. The structure at 2.55 A of one isozyme of a constitutive enzyme in lipid A biosynthesis, LpxI from Caulobacter crescentus, has a novel fold. Two domains close around a completely sequestered substrate, UDP-2,3-diacylglucosamine, and open to release products either to the neighboring enzyme in a putative multienzyme complex or to the bilayer. Mutation analysis identifies Asp225 as key to Mg(2+)-catalyzed diphosphate hydrolysis. These structures provide snapshots of the enzymatic synthesis of a critical lipid A precursor.

LpxI structures reveal how a lipid A precursor is synthesized.,Metzger LE 4th, Lee JK, Finer-Moore JS, Raetz CR, Stroud RM Nat Struct Mol Biol. 2012 Nov;19(11):1132-8. doi: 10.1038/nsmb.2393. Epub 2012, Oct 7. PMID:23042606[1]

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

References

  1. ↑ Metzger LE 4th, Lee JK, Finer-Moore JS, Raetz CR, Stroud RM. LpxI structures reveal how a lipid A precursor is synthesized. Nat Struct Mol Biol. 2012 Nov;19(11):1132-8. doi: 10.1038/nsmb.2393. Epub 2012, Oct 7. PMID:23042606 doi:http://dx.doi.org/10.1038/nsmb.2393

4j6e, resolution 2.52Å

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