1rfv: Difference between revisions

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[[Image:1rfv.jpg|left|200px]]


{{Structure
==Crystal structure of pyridoxal kinase complexed with ADP==
|PDB= 1rfv |SIZE=350|CAPTION= <scene name='initialview01'>1rfv</scene>, resolution 2.8&Aring;
<StructureSection load='1rfv' size='340' side='right'caption='[[1rfv]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> and <scene name='pdbligand=ADP:ADENOSINE-5&#39;-DIPHOSPHATE'>ADP</scene>
<table><tr><td colspan='2'>[[1rfv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ovis_aries Ovis aries]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RFV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RFV FirstGlance]. <br>
|ACTIVITY= [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]  
</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>
|GENE=  
<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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=1rfv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rfv OCA], [https://pdbe.org/1rfv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rfv RCSB], [https://www.ebi.ac.uk/pdbsum/1rfv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rfv ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PDXK_SHEEP PDXK_SHEEP] Required for synthesis of pyridoxal-5-phosphate from vitamin B6.
== 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/1rfv_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=1rfv 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.


'''Crystal structure of pyridoxal kinase complexed with ADP'''
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>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1rfv" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
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.
*[[Pyridoxal kinase|Pyridoxal kinase]]
 
== References ==
==About this Structure==
<references/>
1RFV is a [[Single protein]] structure of 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=1RFV OCA].
__TOC__
 
</StructureSection>
==Reference==
[[Category: Large Structures]]
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:[http://www.ncbi.nlm.nih.gov/pubmed/14722069 14722069]
[[Category: Ovis aries]]
[[Category: Ovis aries]]
[[Category: Pyridoxal kinase]]
[[Category: Jiang T]]
[[Category: Single protein]]
[[Category: Li M-H]]
[[Category: Jiang, T.]]
[[Category: Liang D-C]]
[[Category: Li, M H.]]
[[Category: Liang, D C.]]
[[Category: ADP]]
[[Category: ZN]]
[[Category: transferase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 13:28:23 2008''

Latest revision as of 10:24, 25 October 2023

Crystal structure of pyridoxal kinase complexed with ADPCrystal structure of pyridoxal kinase complexed with ADP

Structural highlights

1rfv is a 2 chain structure with sequence from Ovis aries. 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:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PDXK_SHEEP Required for synthesis of pyridoxal-5-phosphate from vitamin B6.

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

1rfv, resolution 2.80Å

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