2i5b: Difference between revisions

Revision as of 10:06, 30 August 2023

The crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parralel emergence of enzyme activity during evolution

Structural highlights

2i5b is a 5 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.8Å
Ligands:	ADP
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PDXK_BACSU Phosphorylates B6 vitamers; functions in a salvage pathway. Uses pyridoxal, pyridoxine, and pyridoxamine as substrates. Can also use hydroxymethylpyrimidine (HMP) as substrate.^[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

Pyridoxal kinase catalyses the phosphorylation of pyridoxal, pyridoxine and pyridoxamine to their 5' phosphates and plays an important role in the pyridoxal 5' phosphate salvage pathway. The crystal structure of a dimeric pyridoxal kinase from Bacillus subtilis has been solved in complex with ADP to 2.8 A resolution. Analysis of the structure suggests that binding of the nucleotide induces the ordering of two loops, which operate independently to close a flap on the active site. Comparisons with other ribokinase superfamily members reveal that B. subtilis pyridoxal kinase is more closely related in both sequence and structure to the family of HMPP kinases than to other pyridoxal kinases, suggesting that this structure represents the first for a novel family of "HMPP kinase-like" pyridoxal kinases. Moreover this further suggests that this enzyme activity has evolved independently on multiple occasions from within the ribokinase superfamily.

The crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parallel emergence of enzyme activity during evolution.,Newman JA, Das SK, Sedelnikova SE, Rice DW J Mol Biol. 2006 Oct 20;363(2):520-30. Epub 2006 Aug 12. PMID:16978644^[2]

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

References

↑ Park JH, Burns K, Kinsland C, Begley TP. Characterization of two kinases involved in thiamine pyrophosphate and pyridoxal phosphate biosynthesis in Bacillus subtilis: 4-amino-5-hydroxymethyl-2methylpyrimidine kinase and pyridoxal kinase. J Bacteriol. 2004 Mar;186(5):1571-3. PMID:14973012 doi:10.1128/JB.186.5.1571-1573.2004
↑ Newman JA, Das SK, Sedelnikova SE, Rice DW. The crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parallel emergence of enzyme activity during evolution. J Mol Biol. 2006 Oct 20;363(2):520-30. Epub 2006 Aug 12. PMID:16978644 doi:10.1016/j.jmb.2006.08.013

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OCA

[1] Park JH, Burns K, Kinsland C, Begley TP. Characterization of two kinases involved in thiamine pyrophosphate and pyridoxal phosphate biosynthesis in Bacillus subtilis: 4-amino-5-hydroxymethyl-2methylpyrimidine kinase and pyridoxal kinase. J Bacteriol. 2004 Mar;186(5):1571-3. PMID:14973012 doi:10.1128/JB.186.5.1571-1573.2004

[2] Newman JA, Das SK, Sedelnikova SE, Rice DW. The crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parallel emergence of enzyme activity during evolution. J Mol Biol. 2006 Oct 20;363(2):520-30. Epub 2006 Aug 12. PMID:16978644 doi:10.1016/j.jmb.2006.08.013

[1]

[2]

@@ Line 3: / Line 3: @@
 <StructureSection load='2i5b' size='340' side='right'caption='[[2i5b]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2i5b]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I5B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I5B FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2i5b]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I5B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I5B FirstGlance]. <br>
-</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></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]] 2.8&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">thiD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</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></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Phosphomethylpyrimidine_kinase Phosphomethylpyrimidine kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.7 2.7.4.7] </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=2i5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i5b OCA], [https://pdbe.org/2i5b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i5b RCSB], [https://www.ebi.ac.uk/pdbsum/2i5b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i5b ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/THID_BACSU THID_BACSU]] Catalyzes the phosphorylation of hydroxymethylpyrimidine phosphate (HMP-P) to HMP-PP, and of HMP to HMP-P. Shows no activity with pyridoxal, pyridoxamine or pyridoxine.
+[https://www.uniprot.org/uniprot/PDXK_BACSU PDXK_BACSU] Phosphorylates B6 vitamers; functions in a salvage pathway. Uses pyridoxal, pyridoxine, and pyridoxamine as substrates. Can also use hydroxymethylpyrimidine (HMP) as substrate.<ref>PMID:14973012</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 37: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus globigii migula 1900]]
+[[Category: Bacillus subtilis]]
 [[Category: Large Structures]]
-[[Category: Phosphomethylpyrimidine kinase]]
+[[Category: Das SK]]
-[[Category: Das, S K]]
+[[Category: Newman JA]]
-[[Category: Newman, J A]]
+[[Category: Rice DW]]
-[[Category: Rice, D W]]
+[[Category: Sedelnikova SE]]
-[[Category: Sedelnikova, S E]]
-[[Category: Adp complex]]
-[[Category: Pdxk]]
-[[Category: Ribokinase superfamily]]
-[[Category: Thid]]
-[[Category: Transferase]]

2i5b: Difference between revisions

Revision as of 10:06, 30 August 2023

The crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parralel emergence of enzyme activity during evolution

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

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