1rft: Difference between revisions

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[[Image:1rft.png|left|200px]]
==Crystal structure of pyridoxal kinase complexed with AMP-PCP and pyridoxamine==
<StructureSection load='1rft' size='340' side='right' caption='[[1rft]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1rft]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ovis_aries Ovis aries]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RFT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RFT FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PXM:4-(AMINOMETHYL)-5-(HYDROXYMETHYL)-2-METHYLPYRIDIN-3-OL'>PXM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1lhp|1lhp]], [[1lhr|1lhr]], [[1rfu|1rfu]], [[1rfv|1rfv]]</td></tr>
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyridoxal_kinase Pyridoxal kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.35 2.7.1.35] </span></td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rft FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rft OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rft RCSB], [http://www.ebi.ac.uk/pdbsum/1rft PDBsum]</span></td></tr>
<table>
== 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/rf/1rft_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/chain_selection.php?pdb_ID=2ata ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
To understand the processes involved in the catalytic mechanism of pyridoxal kinase (PLK),1 we determined the crystal structures of PLK.AMP-PCP-pyridoxamine, PLK.ADP.PLP, and PLK.ADP complexes. Comparisons of these structures have revealed that PLK exhibits different conformations during its catalytic process. After the binding of AMP-PCP (an analogue that replaced ATP) and pyridoxamine to PLK, this enzyme retains a conformation similar to that of the PLK.ATP complex. The distance between the reacting groups of the two substrates is 5.8 A apart, indicating that the position of ATP is not favorable to spontaneous transfer of its phosphate group. However, the structure of PLK.ADP.PLP complex exhibited significant changes in both the conformation of the enzyme and the location of the ligands at the active site. Therefore, it appears that after binding of both substrates, the enzyme-substrate complex requires changes in the protein structure to enable the transfer of the phosphate group from ATP to vitamin B(6). Furthermore, a conformation of the enzyme-substrate complex before the transition state of the enzymatic reaction was also hypothesized.


{{STRUCTURE_1rft|  PDB=1rft  |  SCENE=  }}
Conformational changes in the reaction of pyridoxal kinase.,Li MH, Kwok F, Chang WR, Liu SQ, Lo SC, Zhang JP, Jiang T, Liang DC J Biol Chem. 2004 Apr 23;279(17):17459-65. Epub 2004 Jan 13. PMID:14722069<ref>PMID:14722069</ref>


===Crystal structure of pyridoxal kinase complexed with AMP-PCP and pyridoxamine===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


{{ABSTRACT_PUBMED_14722069}}
==See Also==
 
*[[Pyridoxal kinase|Pyridoxal kinase]]
==About this Structure==
== References ==
[[1rft]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ovis_aries Ovis aries]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RFT OCA].
<references/>
 
__TOC__
==Reference==
</StructureSection>
<ref group="xtra">PMID:014722069</ref><ref group="xtra">PMID:012235162</ref><ref group="xtra">PMID:012198308</ref><references group="xtra"/>
[[Category: Ovis aries]]
[[Category: Ovis aries]]
[[Category: Pyridoxal kinase]]
[[Category: Pyridoxal kinase]]

Revision as of 19:38, 29 September 2014

Crystal structure of pyridoxal kinase complexed with AMP-PCP and pyridoxamineCrystal structure of pyridoxal kinase complexed with AMP-PCP and pyridoxamine

Structural highlights

1rft is a 1 chain structure with sequence from Ovis aries. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, , ,
Related:1lhp, 1lhr, 1rfu, 1rfv
Activity:Pyridoxal kinase, with EC number 2.7.1.35
Resources:FirstGlance, OCA, RCSB, PDBsum

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 processes involved in the catalytic mechanism of pyridoxal kinase (PLK),1 we determined the crystal structures of PLK.AMP-PCP-pyridoxamine, PLK.ADP.PLP, and PLK.ADP complexes. Comparisons of these structures have revealed that PLK exhibits different conformations during its catalytic process. After the binding of AMP-PCP (an analogue that replaced ATP) and pyridoxamine to PLK, this enzyme retains a conformation similar to that of the PLK.ATP complex. The distance between the reacting groups of the two substrates is 5.8 A apart, indicating that the position of ATP is not favorable to spontaneous transfer of its phosphate group. However, the structure of PLK.ADP.PLP complex exhibited significant changes in both the conformation of the enzyme and the location of the ligands at the active site. Therefore, it appears that after binding of both substrates, the enzyme-substrate complex requires changes in the protein structure to enable the transfer of the phosphate group from ATP to vitamin B(6). Furthermore, a conformation of the enzyme-substrate complex before the transition state of the enzymatic reaction was also hypothesized.

Conformational changes in the reaction of pyridoxal kinase.,Li MH, Kwok F, Chang WR, Liu SQ, Lo SC, Zhang JP, Jiang T, Liang DC J Biol Chem. 2004 Apr 23;279(17):17459-65. Epub 2004 Jan 13. PMID:14722069[1]

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

See Also

References

  1. ↑ Li MH, Kwok F, Chang WR, Liu SQ, Lo SC, Zhang JP, Jiang T, Liang DC. Conformational changes in the reaction of pyridoxal kinase. J Biol Chem. 2004 Apr 23;279(17):17459-65. Epub 2004 Jan 13. PMID:14722069 doi:http://dx.doi.org/10.1074/jbc.M312380200

1rft, resolution 2.80Å

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