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1cd5

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GLUCOSAMINE-6-PHOSPHATE DEAMINASE FROM E.COLI, T CONFORMER

Structural highlights

1cd5 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 2.3Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NAGB_ECOLI Catalyzes the reversible isomerization-deamination of glucosamine 6-phosphate (GlcN6P) to form fructose 6-phosphate (Fru6P) and ammonium ion.[HAMAP-Rule:MF_01241]

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

BACKGROUND: The allosteric hexameric enzyme glucosamine-6-phosphate deaminase from Escherichia coli catalyses the regulatory step of N-acetylglucosamine catabolism, which consists of the isomerisation and deamination of glucosamine 6-phosphate (GlcN6P) to form fructose 6-phosphate (Fru6P) and ammonia. The reversibility of the catalysis and its rapid-equilibrium random kinetic mechanism, among other properties, make this enzyme a good model for studying allosteric processes. RESULTS: Here we present the structure of P6(3)22 crystals, obtained in sodium acetate, of GlcN6P deaminase in its ligand-free T state. These crystals are very sensitive to X-ray radiation and have a high (78%) solvent content. The activesite lid (residues 162-185) is highly disordered in the T conformer; this may contribute significantly to the free-energy change of the whole allosteric transition. Comparison of the structure with the crystallographic coordinates of the R conformer (Brookhaven Protein Data Bank entry 1 dea) allows us to describe the geometrical changes associated with the allosteric transition as the movement of two rigid entities within each monomer. The active site, located in a deep cleft between these two rigid entities, presents a more open geometry in the T conformer than in the R conformer. CONCLUSIONS: The differences in active-site geometry are related to alterations in the substrate-binding properties associated with the allosteric transition. The rigid nature of the two mobile structural units of each monomer seems to be essential in order to explain the observed kinetics of the deaminase hexamer. The triggers for both the homotropic and heterotropic allosteric transitions are discussed and particular residues are assigned to these functions. A structural basis for an entropic term in the allosteric transition is an interesting new feature that emerges from this study.

The allosteric transition of glucosamine-6-phosphate deaminase: the structure of the T state at 2.3 A resolution.,Horjales E, Altamirano MM, Calcagno ML, Garratt RC, Oliva G Structure. 1999 May;7(5):527-37. PMID:10378272^[1]

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

References

↑ Horjales E, Altamirano MM, Calcagno ML, Garratt RC, Oliva G. The allosteric transition of glucosamine-6-phosphate deaminase: the structure of the T state at 2.3 A resolution. Structure. 1999 May;7(5):527-37. PMID:10378272

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1cd5"

@@ Line 1: / Line 1: @@
 ==GLUCOSAMINE-6-PHOSPHATE DEAMINASE FROM E.COLI, T CONFORMER==
-<StructureSection load='1cd5' size='340' side='right' caption='[[1cd5]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='1cd5' size='340' side='right'caption='[[1cd5]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1cd5]] 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=1CD5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CD5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1cd5]] 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=1CD5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CD5 FirstGlance]. <br>
-</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucosamine-6-phosphate_deaminase Glucosamine-6-phosphate deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.99.6 3.5.99.6] </span></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]] 2.3&#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=1cd5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cd5 OCA], [http://pdbe.org/1cd5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1cd5 RCSB], [http://www.ebi.ac.uk/pdbsum/1cd5 PDBsum]</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=1cd5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cd5 OCA], [https://pdbe.org/1cd5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cd5 RCSB], [https://www.ebi.ac.uk/pdbsum/1cd5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cd5 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NAGB_ECOLI NAGB_ECOLI]] Catalyzes the reversible isomerization-deamination of glucosamine 6-phosphate (GlcN6P) to form fructose 6-phosphate (Fru6P) and ammonium ion.[HAMAP-Rule:MF_01241]
+[https://www.uniprot.org/uniprot/NAGB_ECOLI NAGB_ECOLI] Catalyzes the reversible isomerization-deamination of glucosamine 6-phosphate (GlcN6P) to form fructose 6-phosphate (Fru6P) and ammonium ion.[HAMAP-Rule:MF_01241]
 == 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/cd/1cd5_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cd/1cd5_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 29: / Line 30: @@
 ==See Also==
-*[[Deaminase|Deaminase]]
+*[[Deaminase 3D structures|Deaminase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Ecoli]]
+[[Category: Escherichia coli K-12]]
-[[Category: Glucosamine-6-phosphate deaminase]]
+[[Category: Large Structures]]
-[[Category: Altamirano, M M]]
+[[Category: Altamirano MM]]
-[[Category: Calcagno, M L]]
+[[Category: Calcagno ML]]
-[[Category: Garratt, R C]]
+[[Category: Garratt RC]]
-[[Category: Horjales, E]]
+[[Category: Horjales E]]
-[[Category: Oliva, G]]
+[[Category: Oliva G]]
-[[Category: Aldose-ketose isomerase]]
-[[Category: Allosteric enzyme]]
-[[Category: Entropic effect]]
-[[Category: Isomerase]]

1cd5

From Proteopedia

Current revision

GLUCOSAMINE-6-PHOSPHATE DEAMINASE FROM E.COLI, T CONFORMER

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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