1dnl: Difference between revisions

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{{Seed}}
[[Image:1dnl.png|left|200px]]


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==X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-PHOSPHATE OXIDASE COMPLEXED WITH FMN AT 1.8 ANGSTROM RESOLUTION==
The line below this paragraph, containing "STRUCTURE_1dnl", creates the "Structure Box" on the page.
<StructureSection load='1dnl' size='340' side='right'caption='[[1dnl]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1dnl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DNL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DNL FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
{{STRUCTURE_1dnl|  PDB=1dnl  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dnl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dnl OCA], [https://pdbe.org/1dnl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dnl RCSB], [https://www.ebi.ac.uk/pdbsum/1dnl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dnl ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PDXH_ECOLI PDXH_ECOLI] Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP).[HAMAP-Rule:MF_01629]
== 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/dn/1dnl_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1dnl ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
BACKGROUND: Escherichia coli pyridoxine 5'-phosphate oxidase (PNPOx) catalyzes the terminal step in the biosynthesis of pyridoxal 5'-phosphate (PLP), a cofactor used by many enzymes involved in amino acid metabolism. The enzyme oxidizes either the 4'-hydroxyl group of pyridoxine 5'-phosphate (PNP) or the 4'-primary amine of pyridoxamine 5'-phosphate (PMP) to an aldehyde. PNPOx is a homodimeric enzyme with one flavin mononucleotide (FMN) molecule non-covalently bound to each subunit. A high degree of sequence homology among the 15 known members of the PNPOx family suggests that all members of this group have similar three-dimensional folds. RESULTS: The crystal structure of PNPOx from E. coli has been determined to 1.8 A resolution. The monomeric subunit folds into an eight-stranded beta sheet surrounded by five alpha-helical structures. Two monomers related by a twofold axis interact extensively along one-half of each monomer to form the dimer. There are two clefts at the dimer interface that are symmetry-related and extend from the top to the bottom of the dimer. An FMN cofactor that makes interactions with both subunits is located in each of these two clefts. CONCLUSIONS: The structure is quite similar to the recently deposited 2.7 A structure of Saccharomyces cerevisiae PNPOx and also, remarkably, shares a common structural fold with the FMN-binding protein from Desulfovibrio vulgaris and a domain of chymotrypsin. This high-resolution E. coli PNPOx structure permits predictions to be made about residues involved in substrate binding and catalysis. These predictions provide testable hypotheses, which can be answered by making site-directed mutants.


===X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-PHOSPHATE OXIDASE COMPLEXED WITH FMN AT 1.8 ANGSTROM RESOLUTION===
X-ray structure of Escherichia coli pyridoxine 5'-phosphate oxidase complexed with FMN at 1.8 A resolution.,Safo MK, Mathews I, Musayev FN, di Salvo ML, Thiel DJ, Abraham DJ, Schirch V Structure. 2000 Jul 15;8(7):751-62. PMID:10903950<ref>PMID:10903950</ref>


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


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_10903950}}, adds the Publication Abstract to the page
*[[Pyridoxine 5'-phosphate oxidase|Pyridoxine 5'-phosphate oxidase]]
(as it appears on PubMed at http://www.pubmed.gov), where 10903950 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_10903950}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Escherichia coli K-12]]
1DNL is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DNL OCA].
[[Category: Large Structures]]
 
[[Category: Abraham DJ]]
==Reference==
[[Category: Mathews I]]
X-ray structure of Escherichia coli pyridoxine 5'-phosphate oxidase complexed with FMN at 1.8 A resolution., Safo MK, Mathews I, Musayev FN, di Salvo ML, Thiel DJ, Abraham DJ, Schirch V, Structure. 2000 Jul 15;8(7):751-62. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10903950 10903950]
[[Category: Musayev FN]]
[[Category: Escherichia coli]]
[[Category: Safo MK]]
[[Category: Pyridoxal 5'-phosphate synthase]]
[[Category: Schirch V]]
[[Category: Single protein]]
[[Category: Thiel DJ]]
[[Category: Abraham, D J.]]
[[Category: Di Salvo ML]]
[[Category: Mathews, I.]]
[[Category: Musayev, F N.]]
[[Category: Safo, M K.]]
[[Category: Salvo, M L.di.]]
[[Category: Schirch, V.]]
[[Category: Thiel, D J.]]
[[Category: Beta barrel]]
[[Category: Oxidoreductase]]
[[Category: Protein-fmn complex]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 23:20:26 2008''

Latest revision as of 07:13, 9 October 2024

X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-PHOSPHATE OXIDASE COMPLEXED WITH FMN AT 1.8 ANGSTROM RESOLUTION

1dnl, resolution 1.80Å

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