5gpb

From Proteopedia

(Difference between revisions)

Revision as of 06:49, 13 May 2020

COMPARISON OF THE BINDING OF GLUCOSE AND GLUCOSE-1-PHOSPHATE DERIVATIVES TO T-STATE GLYCOGEN PHOSPHORYLASE B

Structural highlights

5gpb is a 1 chain structure with sequence from European rabbit. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Activity:	Phosphorylase, with EC number 2.4.1.1
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[PYGM_RABIT] Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties.

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 binding of T-state- and R-state-stabilizing ligands to the catalytic C site of T-state glycogen phosphorylase b has been investigated by crystallographic methods to study the interactions made and the conformational changes that occur at the C site. The compounds studied were alpha-D-glucose, 1, a T-state-stabilizing inhibitor of the enzyme, and the R-state-stabilizing phosphorylated ligands alpha-D-glucose 1-phosphate (2), 2-deoxy-2-fluoro-alpha-D-glucose 1-phosphate (3), and alpha-D-glucose 1-methylenephosphonate (4). The complexes have been refined, giving crystallographic R factors of less than 19%, for data between 8 and 2.3 A. Analysis of the refined structures shows that the glucosyl portions of the phosphorylated ligands bind in the same orientation as glucose and retain most of the interactions formed between glucose and the enzyme. However, the phosphates of the phosphorylated ligands adopt different conformations in each case; the stability of these conformations have been studied by using computational methods to rationalize the different binding modes. Binding of the phosphorylated ligands is accompanied by movement of C-site residues, most notably a shift of a loop out of the C site and toward the exterior of the protein. The C-site alterations do not include movement of Arg569, which has been observed in both the refined complex with 1-deoxy-D-gluco-heptulose 2-phosphate (5) [Johnson, L. N., et al (1990) J. Mol. Biol. 211, 645-661] and in the R-state enzyme [Barford, D. & Johnson, L. N. (1989) Nature 340, 609-616]. Refinement of the ligand complexes has also led to the observation of additional electron density for residues 10-19 at the N-terminus which had not previously been localized in the native structure. The conformation of this stretch of residues is different from that observed in glycogen phosphorylase a.

Comparison of the binding of glucose and glucose 1-phosphate derivatives to T-state glycogen phosphorylase b.,Martin JL, Johnson LN, Withers SG Biochemistry. 1990 Dec 4;29(48):10745-57. PMID:2125493^[1]

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

References

↑ Martin JL, Johnson LN, Withers SG. Comparison of the binding of glucose and glucose 1-phosphate derivatives to T-state glycogen phosphorylase b. Biochemistry. 1990 Dec 4;29(48):10745-57. PMID:2125493

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/5gpb"

@@ Line 1: / Line 1: @@
 ==COMPARISON OF THE BINDING OF GLUCOSE AND GLUCOSE-1-PHOSPHATE DERIVATIVES TO T-STATE GLYCOGEN PHOSPHORYLASE B==
-<StructureSection load='5gpb' size='340' side='right' caption='[[5gpb]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='5gpb' size='340' side='right'caption='[[5gpb]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5gpb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/European_rabbit European rabbit]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GPB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GPB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5gpb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/European_rabbit European rabbit]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GPB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5GPB FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GPM:GLUCOPYRANOSYL-1-METHYL-PHOSPHONIC+ACID'>GPM</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GPM:GLUCOPYRANOSYL-1-METHYL-PHOSPHONIC+ACID'>GPM</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphorylase Phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.1 2.4.1.1] </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=5gpb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gpb OCA], [http://pdbe.org/5gpb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gpb RCSB], [http://www.ebi.ac.uk/pdbsum/5gpb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gpb ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5gpb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gpb OCA], [http://pdbe.org/5gpb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gpb RCSB], [http://www.ebi.ac.uk/pdbsum/5gpb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gpb ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 14: / Line 14: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gp/5gpb_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gp/5gpb_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 29: / Line 29: @@
 </div>
 <div class="pdbe-citations 5gpb" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Glycogen phosphorylase 3D structures|Glycogen phosphorylase 3D structures]]
 == References ==
 <references/>
@@ Line 34: / Line 37: @@
 </StructureSection>
 [[Category: European rabbit]]
+[[Category: Large Structures]]
 [[Category: Phosphorylase]]
 [[Category: Johnson, L N]]
 [[Category: Martin, J L]]
 [[Category: Glycogen phosphorylase]]

5gpb

From Proteopedia

Revision as of 06:49, 13 May 2020

COMPARISON OF THE BINDING OF GLUCOSE AND GLUCOSE-1-PHOSPHATE DERIVATIVES TO T-STATE GLYCOGEN PHOSPHORYLASE B

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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