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2dh6

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Revision as of 10:31, 8 December 2021

Crystal structure of E. coli Apo-TrpB

Structural highlights

2dh6 is a 1 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	2dh5
Activity:	Tryptophan synthase, with EC number 4.2.1.20
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

[TRPB_ECOLI] The beta subunit is responsible for the synthesis of L-tryptophan from indole and L-serine.[HAMAP-Rule:MF_00133]

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

To understand the basis for the lower activity of the tryptophan synthase beta(2) subunit in comparison to the alpha(2)beta(2) complex, we determined the crystal structures of apo-beta(2) and holo-beta(2) from Escherichia coli at 3.0 and 2.9 A resolutions, respectively. To our knowledge, this is the first report of both beta(2) subunit structures with and without pyridoxal-5'-phosphate. The apo-type molecule retained a dimeric form in solution, as in the case of the holo-beta(2) subunit. The subunit structures of both the apo-beta(2) and the holo-beta(2) forms consisted of two domains, namely the N domain and the C domain. Although there were significant structural differences between the apo- and holo-structures, they could be easily superimposed with a 22 degrees rigid body rotation of the C domain. The pyridoxal-5'-phosphate-bound holo-form had multiple interactions between the two domains and a long loop (residues 260-310), which were missing in the apo-form. Comparison of the structures of holo-Ecbeta(2) and Stbeta(2) in the alpha(2)beta(2) complex from Salmonella typhimurium (Stalpha(2)beta(2)) identified the cause of the lower enzymatic activity of holo-Ecbeta(2) in comparison with Stalpha(2)beta(2). The substrate (indole) gate residues, Tyr279 and Phe280, block entry of the substrate into the beta(2) subunit, although the indole can directly access the active site as a result of a wider cleft between the N and C domains in the holo-Ecbeta(2) subunit. In addition, the structure around betaAsp305 of the holo-Ecbeta(2) subunit was similar to the open state of Stalpha(2)beta(2) with low activity, resulting in lower activity of holo-Ecbeta(2).

Large conformational changes in the Escherichia coli tryptophan synthase beta(2) subunit upon pyridoxal 5'-phosphate binding.,Nishio K, Ogasahara K, Morimoto Y, Tsukihara T, Lee SJ, Yutani K FEBS J. 2010 May;277(9):2157-70. Epub 2010 Mar 27. PMID:20370823^[1]

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

References

↑ Nishio K, Ogasahara K, Morimoto Y, Tsukihara T, Lee SJ, Yutani K. Large conformational changes in the Escherichia coli tryptophan synthase beta(2) subunit upon pyridoxal 5'-phosphate binding. FEBS J. 2010 May;277(9):2157-70. Epub 2010 Mar 27. PMID:20370823 doi:10.1111/j.1742-4658.2010.07631.x

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/2dh6"

@@ Line 3: / Line 3: @@
 <StructureSection load='2dh6' size='340' side='right'caption='[[2dh6]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2dh6]] is a 1 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=2DH6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DH6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2dh6]] is a 1 chain structure with sequence from [https://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=2DH6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DH6 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2dh5|2dh5]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2dh5|2dh5]]</div></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tryptophan_synthase Tryptophan synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.20 4.2.1.20] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Tryptophan_synthase Tryptophan synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.20 4.2.1.20] </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=2dh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dh6 OCA], [http://pdbe.org/2dh6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dh6 RCSB], [http://www.ebi.ac.uk/pdbsum/2dh6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dh6 ProSAT], [http://www.topsan.org/Proteins/RSGI/2dh6 TOPSAN]</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=2dh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dh6 OCA], [https://pdbe.org/2dh6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dh6 RCSB], [https://www.ebi.ac.uk/pdbsum/2dh6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dh6 ProSAT], [https://www.topsan.org/Proteins/RSGI/2dh6 TOPSAN]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TRPB_ECOLI TRPB_ECOLI]] The beta subunit is responsible for the synthesis of L-tryptophan from indole and L-serine.[HAMAP-Rule:MF_00133]
+[[https://www.uniprot.org/uniprot/TRPB_ECOLI TRPB_ECOLI]] The beta subunit is responsible for the synthesis of L-tryptophan from indole and L-serine.[HAMAP-Rule:MF_00133]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 32: @@
 ==See Also==
-*[[Tryptophan synthase|Tryptophan synthase]]
+*[[Tryptophan synthase 3D structures|Tryptophan synthase 3D structures]]
 == References ==
 <references/>

2dh6

From Proteopedia

Revision as of 10:31, 8 December 2021

Crystal structure of E. coli Apo-TrpB

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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