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2dxu

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Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horikoshii Complexed with Biotinyl-5'-AMP, Mutation R48A

Structural highlights

2dxu is a 2 chain structure with sequence from Pyrococcus horikoshii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.28Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

O57883_PYRHO

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

Biotin protein ligase (BPL) catalyzes the biotinylation of the biotin carboxyl carrier protein (BCCP) only at a special lysine residue. Here we report the first structure of BPL.BCCP complex crystals, which are prepared using two BPL mutants: R48A and R48A/K111A. From a detailed structural characterization, it is likely that the mutants retain functionality as enzymes but have a reduced activity to produce the reaction intermediate biotinyl-5'-AMP. The observed biotin and partly disordered ATP in the mutant structures may act as a non-reactive analog of the substrates or biotinyl-5'-AMP, thereby providing the complex crystals. The four crystallographically independent BPL.BCCP complexes obtained can be classified structurally into three groups: the formation stages 1 and 2 with apo-BCCP and the product stage with biotinylated holo-BCCP. Residues responsible for the complex formation as well as for the biotinylation reaction have been identified. The C-terminal domain of BPL shows especially large conformational changes to accommodate BCCP, suggesting its functional importance. The formation stage 1 complex shows the closest distance between the carboxyl carbon of biotin and the special lysine of BCCP, suggesting its relevance to the unobserved reaction stage. Interestingly, bound ATP and biotin are also seen in the product stage, indicating that the substrates may be recruited into the product stage complex before the release of holo-BCCP, probably for the next reaction cycle. The existence of formation and product stages before and after the reaction stage would be favorable to ensure both the reaction efficiency and the extreme substrate specificity of the biotinylation reaction.

Protein biotinylation visualized by a complex structure of biotin protein ligase with a substrate.,Bagautdinov B, Matsuura Y, Bagautdinova S, Kunishima N J Biol Chem. 2008 May 23;283(21):14739-50. Epub 2008 Mar 26. PMID:18372281^[1]

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

References

↑ Bagautdinov B, Matsuura Y, Bagautdinova S, Kunishima N. Protein biotinylation visualized by a complex structure of biotin protein ligase with a substrate. J Biol Chem. 2008 May 23;283(21):14739-50. Epub 2008 Mar 26. PMID:18372281 doi:http://dx.doi.org/10.1074/jbc.M709116200

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/2dxu"

@@ Line 3: / Line 3: @@
 <StructureSection load='2dxu' size='340' side='right'caption='[[2dxu]], [[Resolution|resolution]] 1.28&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2dxu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/'pyrococcus_shinkaii' 'pyrococcus shinkaii']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DXU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DXU FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2dxu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DXU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DXU FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BT5:BIOTINYL-5-AMP'>BT5</scene></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]] 1.28&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1wqw|1wqw]], [[2dxt|2dxt]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BT5:BIOTINYL-5-AMP'>BT5</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">birA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 'Pyrococcus shinkaii'])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Biotin--[acetyl-CoA-carboxylase]_ligase Biotin--[acetyl-CoA-carboxylase] ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.4.15 6.3.4.15] </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=2dxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dxu OCA], [https://pdbe.org/2dxu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dxu RCSB], [https://www.ebi.ac.uk/pdbsum/2dxu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dxu ProSAT], [https://www.topsan.org/Proteins/RSGI/2dxu TOPSAN]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/O57883_PYRHO O57883_PYRHO]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 36: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Pyrococcus shinkaii]]
 [[Category: Large Structures]]
-[[Category: Bagautdinov, B]]
+[[Category: Pyrococcus horikoshii]]
-[[Category: Kunishima, N]]
+[[Category: Bagautdinov B]]
-[[Category: Matsuura, Y]]
+[[Category: Kunishima N]]
-[[Category: Structural genomic]]
+[[Category: Matsuura Y]]
-[[Category: Taketa, M]]
+[[Category: Taketa M]]
-[[Category: Biotin biosynthesis]]
-[[Category: Dimer]]
-[[Category: Ligase]]
-[[Category: National project on protein structural and functional analyse]]
-[[Category: Nppsfa]]
-[[Category: Rsgi]]

2dxu

From Proteopedia

Current revision

Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horikoshii Complexed with Biotinyl-5'-AMP, Mutation R48A

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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