1z7b: Difference between revisions

Revision as of 09:18, 2 May 2018

Crystal structure of E.coli ArnA dehydrogenase (decarboxylase) domain, R619E mutant

Structural highlights

1z7b is a 1 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	SO4
Related:	1z73, 1z74, 1z75, 1z7e
Gene:	PMRI, YFBG ("Bacillus coli" Migula 1895)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[ARNA_ECOLI] Bifunctional enzyme that catalyzes the oxidative decarboxylation of UDP-glucuronic acid (UDP-GlcUA) to UDP-4-keto-arabinose (UDP-Ara4O) and the addition of a formyl group to UDP-4-amino-4-deoxy-L-arabinose (UDP-L-Ara4N) to form UDP-L-4-formamido-arabinose (UDP-L-Ara4FN). The modified arabinose is attached to lipid A and is required for resistance to polymyxin and cationic antimicrobial peptides.^[1] ^[2]

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

The modification of lipid A with 4-amino-4-deoxy-L-arabinose (Ara4N) allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. ArnA is the first enzyme specific to the lipid A-Ara4N pathway. It contains two functionally and physically separable domains: a dehydrogenase domain (ArnA_DH) catalyzing the NAD+-dependent oxidative decarboxylation of UDP-Glucuronic acid (UDP-GlcA), and a transformylase domain that formylates UDP-Ara4N. Here, we describe the crystal structure of the full-length bifunctional ArnA with UDP-GlcA and ATP bound to the dehydrogenase domain. Binding of UDP-GlcA triggers a 17 A conformational change in ArnA_DH that opens the NAD+ binding site while trapping UDP-GlcA. We propose an ordered mechanism of substrate binding and product release. Mutation of residues R619 and S433 demonstrates their importance in catalysis and suggests that R619 functions as a general acid in catalysis. The proposed mechanism for ArnA_DH has important implications for the design of selective inhibitors.

Structure and mechanism of ArnA: conformational change implies ordered dehydrogenase mechanism in key enzyme for polymyxin resistance.,Gatzeva-Topalova PZ, May AP, Sousa MC Structure. 2005 Jun;13(6):929-42. PMID:15939024^[3]

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

References

↑ Breazeale SD, Ribeiro AA, Raetz CR. Oxidative decarboxylation of UDP-glucuronic acid in extracts of polymyxin-resistant Escherichia coli. Origin of lipid a species modified with 4-amino-4-deoxy-L-arabinose. J Biol Chem. 2002 Jan 25;277(4):2886-96. Epub 2001 Nov 8. PMID:11706007 doi:https://dx.doi.org/10.1074/jbc.M109377200
↑ Breazeale SD, Ribeiro AA, McClerren AL, Raetz CR. A formyltransferase required for polymyxin resistance in Escherichia coli and the modification of lipid A with 4-Amino-4-deoxy-L-arabinose. Identification and function oF UDP-4-deoxy-4-formamido-L-arabinose. J Biol Chem. 2005 Apr 8;280(14):14154-67. Epub 2005 Jan 28. PMID:15695810 doi:https://dx.doi.org/M414265200
↑ Gatzeva-Topalova PZ, May AP, Sousa MC. Structure and mechanism of ArnA: conformational change implies ordered dehydrogenase mechanism in key enzyme for polymyxin resistance. Structure. 2005 Jun;13(6):929-42. PMID:15939024 doi:10.1016/j.str.2005.03.018

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Breazeale SD, Ribeiro AA, Raetz CR. Oxidative decarboxylation of UDP-glucuronic acid in extracts of polymyxin-resistant Escherichia coli. Origin of lipid a species modified with 4-amino-4-deoxy-L-arabinose. J Biol Chem. 2002 Jan 25;277(4):2886-96. Epub 2001 Nov 8. PMID:11706007 doi:https://dx.doi.org/10.1074/jbc.M109377200

[2] Breazeale SD, Ribeiro AA, McClerren AL, Raetz CR. A formyltransferase required for polymyxin resistance in Escherichia coli and the modification of lipid A with 4-Amino-4-deoxy-L-arabinose. Identification and function oF UDP-4-deoxy-4-formamido-L-arabinose. J Biol Chem. 2005 Apr 8;280(14):14154-67. Epub 2005 Jan 28. PMID:15695810 doi:https://dx.doi.org/M414265200

[3] Gatzeva-Topalova PZ, May AP, Sousa MC. Structure and mechanism of ArnA: conformational change implies ordered dehydrogenase mechanism in key enzyme for polymyxin resistance. Structure. 2005 Jun;13(6):929-42. PMID:15939024 doi:10.1016/j.str.2005.03.018

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==Crystal structure of E.coli ArnA dehydrogenase (decarboxylase) domain, R619E mutant==
 <StructureSection load='1z7b' size='340' side='right' caption='[[1z7b]], [[Resolution|resolution]] 2.31&Aring;' scene=''>
@@ Line 6: / Line 7: @@
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1z73|1z73]], [[1z74|1z74]], [[1z75|1z75]], [[1z7e|1z7e]]</td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PMRI, YFBG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1z7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z7b OCA], [http://pdbe.org/1z7b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1z7b RCSB], [http://www.ebi.ac.uk/pdbsum/1z7b PDBsum]</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=1z7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z7b OCA], [http://pdbe.org/1z7b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1z7b RCSB], [http://www.ebi.ac.uk/pdbsum/1z7b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1z7b ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 14: / Line 15: @@
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z7/1z7b_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z7/1z7b_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1z7b ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">

1z7b: Difference between revisions

Revision as of 09:18, 2 May 2018

Crystal structure of E.coli ArnA dehydrogenase (decarboxylase) domain, R619E mutant

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools