1kwk: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,332,843 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,332,843 edits
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1kwk.jpg|left|200px]]


{{Structure
==Crystal structure of Thermus thermophilus A4 beta-galactosidase in complex with galactose==
|PDB= 1kwk |SIZE=350|CAPTION= <scene name='initialview01'>1kwk</scene>, resolution 2.20&Aring;
<StructureSection load='1kwk' size='340' side='right'caption='[[1kwk]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
<table><tr><td colspan='2'>[[1kwk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KWK FirstGlance]. <br>
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-galactosidase Beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </span>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
|GENE=
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kwk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kwk OCA], [https://pdbe.org/1kwk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kwk RCSB], [https://www.ebi.ac.uk/pdbsum/1kwk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kwk ProSAT]</span></td></tr>
|RELATEDENTRY=[[1kwg|1KWG]]
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kwk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kwk OCA], [http://www.ebi.ac.uk/pdbsum/1kwk PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1kwk RCSB]</span>
== Function ==
}}
[https://www.uniprot.org/uniprot/BGAL_THETH BGAL_THETH]
== 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/kw/1kwk_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/main_output.php?pdb_ID=1kwk ConSurf].
<div style="clear:both"></div>


'''Crystal structure of Thermus thermophilus A4 beta-galactosidase in complex with galactose'''
==See Also==
 
*[[Galactosidase 3D structures|Galactosidase 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
The beta-galactosidase from an extreme thermophile, Thermus thermophilus A4 (A4-beta-Gal), is thermostable and belongs to the glycoside hydrolase family 42 (GH-42). As the first known structures of a GH-42 enzyme, we determined the crystal structures of free and galactose-bound A4-beta-Gal at 1.6A and 2.2A resolution, respectively. A4-beta-Gal forms a homotrimeric structure resembling a flowerpot. Each monomer has an active site located inside a large central tunnel. The N-terminal domain of A4-beta-Gal has a TIM barrel fold, as predicted from hydrophobic cluster analysis. The putative catalytic residues of A4-beta-Gal (Glu141 and Glu312) superimpose well with the catalytic residues of Escherichia coli beta-galactosidase. The environment around the catalytic nucleophile (Glu312) is similar to that in the case of E.coli beta-galactosidase, but the recognition mechanism for a substrate is different. Trp182 of the next subunit of the trimer constitutes a part of the active-site pocket, indicating that the trimeric structure is essential for the enzyme activity. Structural comparison with other glycoside hydrolases revealed that many features of the 4/7 superfamily are conserved in the A4-beta-Gal structure. On the basis of the results of 1H NMR spectroscopy, A4-beta-Gal was determined to be a "retaining" enzyme. Interestingly, the active site was similar with those of retaining enzymes, but the overall fold of the TIM barrel domain was very similar to that of an inverting enzyme, beta-amylase.
[[Category: Large Structures]]
 
==About this Structure==
1KWK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWK OCA].
 
==Reference==
Trimeric crystal structure of the glycoside hydrolase family 42 beta-galactosidase from Thermus thermophilus A4 and the structure of its complex with galactose., Hidaka M, Fushinobu S, Ohtsu N, Motoshima H, Matsuzawa H, Shoun H, Wakagi T, J Mol Biol. 2002 Sep 6;322(1):79-91. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12215416 12215416]
[[Category: Beta-galactosidase]]
[[Category: Single protein]]
[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]
[[Category: Fushinobu, S.]]
[[Category: Fushinobu S]]
[[Category: Hidaka, M.]]
[[Category: Hidaka M]]
[[Category: Matsuzawa, H.]]
[[Category: Matsuzawa H]]
[[Category: Motoshima, H.]]
[[Category: Motoshima H]]
[[Category: Ohtsu, N.]]
[[Category: Ohtsu N]]
[[Category: Shoun, H.]]
[[Category: Shoun H]]
[[Category: Wakagi, T.]]
[[Category: Wakagi T]]
[[Category: galactose complex]]
[[Category: glycoside hydrolase family 42]]
[[Category: tim barrel]]
[[Category: trimer]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:54:37 2008''
Retrieved from "https://proteopedia.org/1kwk"