1s4e: Difference between revisions

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[[Image:1s4e.png|left|200px]]


{{STRUCTURE_1s4e| PDB=1s4e | SCENE= }}
==Pyrococcus furiosus galactokinase in complex with galactose, ADP and magnesium==
<StructureSection load='1s4e' size='340' side='right'caption='[[1s4e]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1s4e]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S4E FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=1s4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s4e OCA], [https://pdbe.org/1s4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s4e RCSB], [https://www.ebi.ac.uk/pdbsum/1s4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s4e ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/GAL1_PYRFU GAL1_PYRFU] Catalyzes the transfer of the gamma-phosphate of ATP to D-galactose to form alpha-D-galactose-1-phosphate (Gal-1-P). Is very specific for its substrate, since it is not able to use D-glucose, D-fructose, D-mannose, 2-deoxy-D-glucose, and D-glucosamine as substrates.<ref>PMID:11978175</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/s4/1s4e_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/main_output.php?pdb_ID=1s4e ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Galactokinase (GalK) catalyses the first step of the Leloir pathway of galactose metabolism, the ATP-dependent phosphorylation of galactose to galactose-1-phosphate. In man, defects in galactose metabolism can result in disorders with severe clinical consequences, and deficiencies in galactokinase have been linked with the development of cataracts within the first few months of life. The crystal structure of GalK from Pyrococcus furiosus in complex with MgADP and galactose has been determined to 2.9 A resolution to provide insights into the substrate specificity and catalytic mechanism of the enzyme. The structure consists of two domains with the active site in a cleft at the domain interface. Inspection of the substrate binding pocket identifies the amino acid residues involved in galactose and nucleotide binding and points to both structural and mechanistic similarities with other enzymes of the GHMP kinase superfamily to which GalK belongs. Comparison of the sequence of the Gal3p inducer protein, which is related to GalK and which forms part of the transcriptional activation of the GAL gene cluster in the yeast Saccharomyces cerevisiae, has led to an understanding of the molecular basis of galactose and nucleotide recognition. Finally, the structure has enabled us to further our understanding on the functional consequences of mutations in human GalK which cause galactosemia.


===Pyrococcus furiosus galactokinase in complex with galactose, ADP and magnesium===
Substrate specificity and mechanism from the structure of Pyrococcus furiosus galactokinase.,Hartley A, Glynn SE, Barynin V, Baker PJ, Sedelnikova SE, Verhees C, de Geus D, van der Oost J, Timson DJ, Reece RJ, Rice DW J Mol Biol. 2004 Mar 19;337(2):387-98. PMID:15003454<ref>PMID:15003454</ref>


{{ABSTRACT_PUBMED_15003454}}
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1s4e" style="background-color:#fffaf0;"></div>


==About this Structure==
==See Also==
[[1s4e]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S4E OCA].
*[[Galactokinase|Galactokinase]]
 
== References ==
==Reference==
<references/>
<ref group="xtra">PMID:015003454</ref><references group="xtra"/>
__TOC__
[[Category: Galactokinase]]
</StructureSection>
[[Category: Large Structures]]
[[Category: Pyrococcus furiosus]]
[[Category: Pyrococcus furiosus]]
[[Category: Baker, P J.]]
[[Category: Baker PJ]]
[[Category: Barynin, V.]]
[[Category: Barynin V]]
[[Category: Geus, D de.]]
[[Category: Glynn SE]]
[[Category: Glynn, S E.]]
[[Category: Hartley A]]
[[Category: Hartley, A.]]
[[Category: Reece RJ]]
[[Category: Oost, J van der.]]
[[Category: Rice DW]]
[[Category: Reece, R J.]]
[[Category: Sedelnikova SE]]
[[Category: Rice, D W.]]
[[Category: Timson DJ]]
[[Category: Sedelnikova, S E.]]
[[Category: Verhees C]]
[[Category: Timson, D J.]]
[[Category: De Geus D]]
[[Category: Verhees, C.]]
[[Category: Van der Oost J]]
[[Category: Ghmp kinase superfamily]]
[[Category: P-loop]]
[[Category: Transferase]]

Latest revision as of 12:41, 25 December 2024

Pyrococcus furiosus galactokinase in complex with galactose, ADP and magnesiumPyrococcus furiosus galactokinase in complex with galactose, ADP and magnesium

Structural highlights

1s4e is a 9 chain structure with sequence from Pyrococcus furiosus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.9Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GAL1_PYRFU Catalyzes the transfer of the gamma-phosphate of ATP to D-galactose to form alpha-D-galactose-1-phosphate (Gal-1-P). Is very specific for its substrate, since it is not able to use D-glucose, D-fructose, D-mannose, 2-deoxy-D-glucose, and D-glucosamine as substrates.[1]

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

Galactokinase (GalK) catalyses the first step of the Leloir pathway of galactose metabolism, the ATP-dependent phosphorylation of galactose to galactose-1-phosphate. In man, defects in galactose metabolism can result in disorders with severe clinical consequences, and deficiencies in galactokinase have been linked with the development of cataracts within the first few months of life. The crystal structure of GalK from Pyrococcus furiosus in complex with MgADP and galactose has been determined to 2.9 A resolution to provide insights into the substrate specificity and catalytic mechanism of the enzyme. The structure consists of two domains with the active site in a cleft at the domain interface. Inspection of the substrate binding pocket identifies the amino acid residues involved in galactose and nucleotide binding and points to both structural and mechanistic similarities with other enzymes of the GHMP kinase superfamily to which GalK belongs. Comparison of the sequence of the Gal3p inducer protein, which is related to GalK and which forms part of the transcriptional activation of the GAL gene cluster in the yeast Saccharomyces cerevisiae, has led to an understanding of the molecular basis of galactose and nucleotide recognition. Finally, the structure has enabled us to further our understanding on the functional consequences of mutations in human GalK which cause galactosemia.

Substrate specificity and mechanism from the structure of Pyrococcus furiosus galactokinase.,Hartley A, Glynn SE, Barynin V, Baker PJ, Sedelnikova SE, Verhees C, de Geus D, van der Oost J, Timson DJ, Reece RJ, Rice DW J Mol Biol. 2004 Mar 19;337(2):387-98. PMID:15003454[2]

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

See Also

References

  1. Verhees CH, Koot DG, Ettema TJ, Dijkema C, de Vos WM, van der Oost J. Biochemical adaptations of two sugar kinases from the hyperthermophilic archaeon Pyrococcus furiosus. Biochem J. 2002 Aug 15;366(Pt 1):121-7. PMID:11978175 doi:http://dx.doi.org/10.1042/BJ20011597
  2. Hartley A, Glynn SE, Barynin V, Baker PJ, Sedelnikova SE, Verhees C, de Geus D, van der Oost J, Timson DJ, Reece RJ, Rice DW. Substrate specificity and mechanism from the structure of Pyrococcus furiosus galactokinase. J Mol Biol. 2004 Mar 19;337(2):387-98. PMID:15003454 doi:10.1016/j.jmb.2004.01.043

1s4e, resolution 2.90Å

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