2cgk

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of L-rhamnulose kinase from Escherichia coli in an open uncomplexed conformation.

Structural highlights

2cgk is a 2 chain structure with sequence from Escherichia coli BL21(DE3). Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.46Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RHAB_ECOLI Involved in the catabolism of L-rhamnose (6-deoxy-L-mannose). It could also play a role in the metabolism of some rare sugars such as L-fructose. Catalyzes the transfer of the gamma-phosphate group from ATP to the 1-hydroxyl group of L-rhamnulose to yield L-rhamnulose 1-phosphate. Uridine triphosphate (UTP), cytidine 5-triphosphate (CTP), guanosine 5-triphosphate (GTP), and thymidine triphosphate (TTP) also can act as phosphoryl donors. It can also phosphorylate L-fuculose and L-xylulose.[HAMAP-Rule:MF_01535]^[1] ^[2] ^[3]

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

Bacterial L-rhamnulose kinase participates in the degradation of L-rhamnose, which is ubiquitous and particularly abundant in some plants. The enzyme catalyzes the transfer of the gamma-phosphate group from ATP to the 1-hydroxyl group of L-rhamnulose. We determined the crystal structures of the substrate-free kinase and of a complex between the enzyme, ADP and L-fructose, which besides rhamnulose is also processed. According to its chainfold, the kinase belongs to the hexokinase-hsp70-actin superfamily. The closest structurally known homologue is glycerol kinase. The reported structures reveal a large conformational change on substrate binding as well as the key residues involved in catalysis. The substrates ADP and beta-L-fructose are in an ideal position to define a direct in-line phosphoryl transfer through a bipyramidal pentavalent intermediate. The enzyme contains one disulfide bridge at a position where two homologous glycerol kinases are regulated by phosphorylation and effector binding, respectively, and it has two more pairs of cysteine residues near the surface that are poised for bridging. However, identical catalytic rates were observed for the enzyme in reducing and oxidizing environments, suggesting that regulation by disulfide formation is unlikely.

Structure and reaction mechanism of L-rhamnulose kinase from Escherichia coli.,Grueninger D, Schulz GE J Mol Biol. 2006 Jun 9;359(3):787-97. Epub 2006 Apr 25. PMID:16674975^[4]

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

References

↑ CHIU TH, FEINGOLD DS. THE PURIFICATION AND PROPERTIES OF L-RHAMNULOKINASE. Biochim Biophys Acta. 1964 Dec 23;92:489-97. PMID:14264882 doi:10.1016/0926-6569(64)90009-4
↑ Grueninger D, Schulz GE. Structure and reaction mechanism of L-rhamnulose kinase from Escherichia coli. J Mol Biol. 2006 Jun 9;359(3):787-97. Epub 2006 Apr 25. PMID:16674975 doi:10.1016/j.jmb.2006.04.013
↑ Power J. The L-rhamnose genetic system in Escherichia coli K-12. Genetics. 1967 Mar;55(3):557-68. PMID:5341476 doi:10.1093/genetics/55.3.557
↑ Grueninger D, Schulz GE. Structure and reaction mechanism of L-rhamnulose kinase from Escherichia coli. J Mol Biol. 2006 Jun 9;359(3):787-97. Epub 2006 Apr 25. PMID:16674975 doi:10.1016/j.jmb.2006.04.013

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/2cgk"

Categories: Large Structures | Grueninger D | Schulz GE

@@ Line 3: / Line 3: @@
 <StructureSection load='2cgk' size='340' side='right'caption='[[2cgk]], [[Resolution|resolution]] 2.46&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2cgk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CGK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2CGK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2cgk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CGK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CGK FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2cgj|2cgj]], [[2cgl|2cgl]]</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]] 2.46&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Rhamnulokinase Rhamnulokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.5 2.7.1.5] </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=2cgk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cgk OCA], [https://pdbe.org/2cgk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cgk RCSB], [https://www.ebi.ac.uk/pdbsum/2cgk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cgk 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=2cgk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cgk OCA], [http://pdbe.org/2cgk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2cgk RCSB], [http://www.ebi.ac.uk/pdbsum/2cgk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2cgk ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RHAB_ECO57 RHAB_ECO57]] Involved in the catabolism of L-rhamnose (6-deoxy-L-mannose). Catalyzes the transfer of the gamma-phosphate group from ATP to the 1-hydroxyl group of L-rhamnulose to yield L-rhamnulose 1-phosphate.
+[https://www.uniprot.org/uniprot/RHAB_ECOLI RHAB_ECOLI] Involved in the catabolism of L-rhamnose (6-deoxy-L-mannose). It could also play a role in the metabolism of some rare sugars such as L-fructose. Catalyzes the transfer of the gamma-phosphate group from ATP to the 1-hydroxyl group of L-rhamnulose to yield L-rhamnulose 1-phosphate. Uridine triphosphate (UTP), cytidine 5-triphosphate (CTP), guanosine 5-triphosphate (GTP), and thymidine triphosphate (TTP) also can act as phosphoryl donors. It can also phosphorylate L-fuculose and L-xylulose.[HAMAP-Rule:MF_01535]<ref>PMID:14264882</ref> <ref>PMID:16674975</ref> <ref>PMID:5341476</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 15: / Line 14: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cg/2cgk_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 33: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
 [[Category: Large Structures]]
-[[Category: Rhamnulokinase]]
+[[Category: Grueninger D]]
-[[Category: Grueninger, D]]
+[[Category: Schulz GE]]
-[[Category: Schulz, G E]]
-[[Category: Hexokinase-hsp70- actin superfamily]]
-[[Category: In-line phosphoryl transfer]]
-[[Category: Induced fit]]
-[[Category: Kinase]]
-[[Category: L-rhamnulose kinase]]
-[[Category: Rhamnose degradation]]
-[[Category: Rhamnose metabolism]]
-[[Category: Transferase]]

2cgk

From Proteopedia

Current revision

Crystal Structure of L-rhamnulose kinase from Escherichia coli in an open uncomplexed conformation.

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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