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2c4n

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NagD from E.coli K-12 strain

Structural highlights

2c4n is a 1 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NAGD_ECOLI Catalyzes the dephosphorylation of an unusually broad range of substrate including deoxyribo- and ribonucleoside tri-, di-, and monophosphates, as well as polyphosphate and glucose-1-P (Glu1P).^[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 HAD superfamily is a large superfamily of proteins which share a conserved core domain that provides those active site residues responsible for the chemistry common to all family members. The superfamily is further divided into the four subfamilies I, IIA, IIB, and III, based on the topology and insertion site of a cap domain that provides substrate specificity. This structural and functional division implies that members of a given HAD structural subclass may target substrates that have similar structural characteristics. To understand the structure/function relationships in all of the subfamilies, a type IIA subfamily member, NagD from Escherichia coli K-12, was selected (type I, IIB, and III members have been more extensively studied). The structure of the NagD protein was solved to 1.80 A with R(work) = 19.8% and R(free) = 21.8%. Substrate screening and kinetic analysis showed NagD to have high specificity for nucleotide monophosphates with k(cat)/K(m) = 3.12 x 10(4) and 1.28 x 10(4) microM(-)(1) s(-)(1) for UMP and GMP, respectively. This specificity is consistent with the presence of analogues of NagD that exist as fusion proteins with a nucleotide pyrophosphatase from the Nudix family. Docking of the nucleoside substrate in the active site brings it in contact with conserved residues from the cap domain that can act as a substrate specificity loop (NagD residues 144-149) in the type IIA subfamily. NagD and other subfamily IIA and IIB members show the common trait that substrate specificity and catalytic efficiencies (k(cat)/K(m)) are low (1 x 10(4) M(-)(1) s(-)(1)) and the boundaries defining physiological substrates are somewhat overlapping. The ability to catabolize other related secondary metabolites indicates that there is regulation at the genetic level.

Structure and activity analyses of Escherichia coli K-12 NagD provide insight into the evolution of biochemical function in the haloalkanoic acid dehalogenase superfamily.,Tremblay LW, Dunaway-Mariano D, Allen KN Biochemistry. 2006 Jan 31;45(4):1183-93. PMID:16430214^[3]

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

References

↑ Kuznetsova E, Proudfoot M, Gonzalez CF, Brown G, Omelchenko MV, Borozan I, Carmel L, Wolf YI, Mori H, Savchenko AV, Arrowsmith CH, Koonin EV, Edwards AM, Yakunin AF. Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family. J Biol Chem. 2006 Nov 24;281(47):36149-61. Epub 2006 Sep 21. PMID:16990279 doi:10.1074/jbc.M605449200
↑ Tremblay LW, Dunaway-Mariano D, Allen KN. Structure and activity analyses of Escherichia coli K-12 NagD provide insight into the evolution of biochemical function in the haloalkanoic acid dehalogenase superfamily. Biochemistry. 2006 Jan 31;45(4):1183-93. PMID:16430214 doi:http://dx.doi.org/10.1021/bi051842j
↑ Tremblay LW, Dunaway-Mariano D, Allen KN. Structure and activity analyses of Escherichia coli K-12 NagD provide insight into the evolution of biochemical function in the haloalkanoic acid dehalogenase superfamily. Biochemistry. 2006 Jan 31;45(4):1183-93. PMID:16430214 doi:http://dx.doi.org/10.1021/bi051842j

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2c4n"

Categories: Escherichia coli K-12 | Large Structures | Allen K | Dunaway-Mariano D | Tremblay LW

@@ Line 1: / Line 1: @@
-==NAGD FROM E.COLI K-12 STRAIN==
-<StructureSection load='2c4n' size='340' side='right' caption='[[2c4n]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+==NagD from E.coli K-12 strain==
+<StructureSection load='2c4n' size='340' side='right'caption='[[2c4n]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2c4n]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C4N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C4N FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2c4n]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C4N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C4N FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.8&#8491;</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=2c4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c4n OCA], [http://pdbe.org/2c4n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2c4n RCSB], [http://www.ebi.ac.uk/pdbsum/2c4n PDBsum]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=2c4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c4n OCA], [https://pdbe.org/2c4n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c4n RCSB], [https://www.ebi.ac.uk/pdbsum/2c4n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c4n ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NAGD_ECOLI NAGD_ECOLI]] Catalyzes the dephosphorylation of an unusually broad range of substrate including deoxyribo- and ribonucleoside tri-, di-, and monophosphates, as well as polyphosphate and glucose-1-P (Glu1P).<ref>PMID:16990279</ref> <ref>PMID:16430214</ref>
+[https://www.uniprot.org/uniprot/NAGD_ECOLI NAGD_ECOLI] Catalyzes the dephosphorylation of an unusually broad range of substrate including deoxyribo- and ribonucleoside tri-, di-, and monophosphates, as well as polyphosphate and glucose-1-P (Glu1P).<ref>PMID:16990279</ref> <ref>PMID:16430214</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c4/2c4n_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c4/2c4n_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=2c4n ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 31: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Ecoli]]
+[[Category: Escherichia coli K-12]]
-[[Category: Allen, K]]
+[[Category: Large Structures]]
-[[Category: Dunaway-Mariano, D]]
+[[Category: Allen K]]
-[[Category: Tremblay, L W]]
+[[Category: Dunaway-Mariano D]]
-[[Category: Carbohydrate metabolism]]
+[[Category: Tremblay LW]]
-[[Category: Had superfamily]]
-[[Category: Hydrolase]]
-[[Category: Nagd]]
-[[Category: Nucleotide phosphatase]]
-[[Category: Ump phosphatase]]

2c4n

From Proteopedia

Current revision

NagD from E.coli K-12 strain

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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