3nc7: Difference between revisions

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==CYP134A1 2-phenylimidazole bound structure==
==CYP134A1 2-phenylimidazole bound structure==
<StructureSection load='3nc7' size='340' side='right' caption='[[3nc7]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
<StructureSection load='3nc7' size='340' side='right'caption='[[3nc7]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3nc7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NC7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NC7 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3nc7]] is a 2 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=3NC7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NC7 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PIY:2-PHENYL-1H-IMIDAZOLE'>PIY</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]] 3.3&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3nc3|3nc3]], [[3nc5|3nc5]], [[3nc6|3nc6]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PIY:2-PHENYL-1H-IMIDAZOLE'>PIY</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BSU35060, cyp134, cypB, cypX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</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=3nc7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nc7 OCA], [https://pdbe.org/3nc7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nc7 RCSB], [https://www.ebi.ac.uk/pdbsum/3nc7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nc7 ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3nc7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nc7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3nc7 RCSB], [http://www.ebi.ac.uk/pdbsum/3nc7 PDBsum]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/CYPX_BACSU CYPX_BACSU]] Involved in the biosynthesis of pulcherrimin, a red extracellular pigment. Catalyzes the oxidation of cyclo(L-Leu-L-Leu) (cLL) to yield pulcherriminic acid which forms pulcherrimin via a nonenzymic reaction with Fe(3+). Substrates with small alkyl groups (cAA, cLG, cLP) exhibit weaker binding to CYP134A1, but substrates with larger hydrophobic side chains bind in a similar regime to cLL.<ref>PMID:20690619</ref>
[https://www.uniprot.org/uniprot/CYPX_BACSU CYPX_BACSU] Involved in the biosynthesis of pulcherrimin, a red extracellular pigment. Catalyzes the oxidation of cyclo(L-Leu-L-Leu) (cLL) to yield pulcherriminic acid which forms pulcherrimin via a nonenzymic reaction with Fe(3+). Substrates with small alkyl groups (cAA, cLG, cLP) exhibit weaker binding to CYP134A1, but substrates with larger hydrophobic side chains bind in a similar regime to cLL.<ref>PMID:20690619</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nc/3nc7_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nc/3nc7_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </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].
</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=3nc7 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Cytochrome P450 CypX (CYP134A1), isolated from Bacillus subtilis, has previously been implicated in the three-step oxidative transformation of the diketopiperazine cyclo-l-leucyl-l-leucyl into pulcherriminic acid, a precursor of the extracellular iron chelate pulcherrimin. In this study, we present the first experimental data relating to CYP134A1, where we show that CYP134A1 binds cyclo-l-leucyl-l-leucyl with an affinity of 24.5 +/- 0.5 muM. Structurally related diketopiperazines sharing similar alkyl side chains to cyclo-l-leucyl-l-leucyl also bind to CYP134A1 with comparable affinity. CYP134A1 is capable of catalyzing the in vitro oxidation of diketopiperazine substrates when supported with several alternate electron transfer partner systems. Products containing one additional oxygen atom and which are intermediate products of the expected pulcherriminic acid were identified by GCMS. The oxidation of related diketopiperazines reveals that different oxidative pathways exist for CYP134A1-catalyzed diketopiperazine oxidation. The crystal structure of CYP134A1 has been determined to 2.7 A resolution in the absence of substrate and in the presence of bound phenylimidazole ligands to 3.1 and 3.2 A resolution. The active site is dominated by hydrophobic residues and contains an unusual proline residue in place of the normally conserved alcohol residue that typically plays an important role in oxygen activation. The B-B(2) substrate recognition loop, which forms part of the active site, shows considerable flexibility and was found in both open and closed conformations in different structures. These results represent the first insights into the structural and biochemical basis underlying the multistep oxidation catalyzed by CYP134A1.
Structural and biochemical characterization of the cytochrome P450 CypX (CYP134A1) from Bacillus subtilis: a cyclo-L-leucyl-L-leucyl dipeptide oxidase.,Cryle MJ, Bell SG, Schlichting I Biochemistry. 2010 Aug 31;49(34):7282-96. PMID:20690619<ref>PMID:20690619</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[Cytochrome P450|Cytochrome P450]]
*[[Cytochrome P450 3D structures|Cytochrome P450 3D structures]]
== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
[[Category: Cryle, M J]]
[[Category: Large Structures]]
[[Category: Schlichting, I]]
[[Category: Cryle MJ]]
[[Category: Cytochrome p450 oxidase]]
[[Category: Schlichting I]]
[[Category: Haem protein]]
[[Category: Oxidoreductase]]

Latest revision as of 13:29, 21 February 2024

CYP134A1 2-phenylimidazole bound structureCYP134A1 2-phenylimidazole bound structure

Structural highlights

3nc7 is a 2 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 3.3Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CYPX_BACSU Involved in the biosynthesis of pulcherrimin, a red extracellular pigment. Catalyzes the oxidation of cyclo(L-Leu-L-Leu) (cLL) to yield pulcherriminic acid which forms pulcherrimin via a nonenzymic reaction with Fe(3+). Substrates with small alkyl groups (cAA, cLG, cLP) exhibit weaker binding to CYP134A1, but substrates with larger hydrophobic side chains bind in a similar regime to cLL.[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Cryle MJ, Bell SG, Schlichting I. Structural and biochemical characterization of the cytochrome P450 CypX (CYP134A1) from Bacillus subtilis: a cyclo-L-leucyl-L-leucyl dipeptide oxidase. Biochemistry. 2010 Aug 31;49(34):7282-96. PMID:20690619 doi:10.1021/bi100910y

3nc7, resolution 3.30Å

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