1n4g: Difference between revisions

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[[Image:1n4g.gif|left|200px]]


{{Structure
==Structure of CYP121, a Mycobacterial P450, in Complex with Iodopyrazole==
|PDB= 1n4g |SIZE=350|CAPTION= <scene name='initialview01'>1n4g</scene>, resolution 1.80&Aring;
<StructureSection load='1n4g' size='340' side='right'caption='[[1n4g]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PYZ:4-IODOPYRAZOLE'>PYZ</scene>
<table><tr><td colspan='2'>[[1n4g]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N4G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N4G FirstGlance]. <br>
|ACTIVITY=
</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>
|GENE= CYP121 OR RV2276 OR MT2336 OR MTCY339.34C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])
<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=PYZ:4-IODOPYRAZOLE'>PYZ</scene></td></tr>
|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG2124 CypX]</span>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1n4g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n4g OCA], [https://pdbe.org/1n4g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n4g RCSB], [https://www.ebi.ac.uk/pdbsum/1n4g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n4g ProSAT]</span></td></tr>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1n4g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n4g OCA], [http://www.ebi.ac.uk/pdbsum/1n4g PDBsum], [http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1kfv JenaLib], [http://www.rcsb.org/pdb/explore.do?structureId=1n4g RCSB]</span>
</table>
}}
== Function ==
[https://www.uniprot.org/uniprot/CP121_MYCTU CP121_MYCTU]
== 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/n4/1n4g_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=1n4g ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The first structure of a P450 to an atomic resolution of 1.06 A has been solved for CYP121 from Mycobacterium tuberculosis. A comparison with P450 EryF (CYP107A1) reveals a remarkable overall similarity in fold with major differences residing in active site structural elements. The high resolution obtained allows visualization of several unusual aspects. The heme cofactor is bound in two distinct conformations while being notably kinked in one pyrrole group due to close interaction with the proline residue (Pro(346)) immediately following the heme iron-ligating cysteine (Cys(345)). The active site is remarkably rigid in comparison with the remainder of the structure, notwithstanding the large cavity volume of 1350 A(3). The region immediately surrounding the distal water ligand is remarkable in several aspects. Unlike other bacterial P450s, the I helix shows no deformation, similar to mammalian CYP2C5. In addition, the positively charged Arg(386) is located immediately above the heme plane, dominating the local structure. Putative proton relay pathways from protein surface to heme (converging at Ser(279)) are identified. Most interestingly, the electron density indicates weak binding of a dioxygen molecule to the P450. This structure provides a basis for rational design of putative antimycobacterial agents.


'''Structure of CYP121, a Mycobacterial P450, in Complex with Iodopyrazole'''
Atomic structure of Mycobacterium tuberculosis CYP121 to 1.06 A reveals novel features of cytochrome P450.,Leys D, Mowat CG, McLean KJ, Richmond A, Chapman SK, Walkinshaw MD, Munro AW J Biol Chem. 2003 Feb 14;278(7):5141-7. Epub 2002 Nov 14. PMID:12435731<ref>PMID:12435731</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1n4g" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
The first structure of a P450 to an atomic resolution of 1.06 A has been solved for CYP121 from Mycobacterium tuberculosis. A comparison with P450 EryF (CYP107A1) reveals a remarkable overall similarity in fold with major differences residing in active site structural elements. The high resolution obtained allows visualization of several unusual aspects. The heme cofactor is bound in two distinct conformations while being notably kinked in one pyrrole group due to close interaction with the proline residue (Pro(346)) immediately following the heme iron-ligating cysteine (Cys(345)). The active site is remarkably rigid in comparison with the remainder of the structure, notwithstanding the large cavity volume of 1350 A(3). The region immediately surrounding the distal water ligand is remarkable in several aspects. Unlike other bacterial P450s, the I helix shows no deformation, similar to mammalian CYP2C5. In addition, the positively charged Arg(386) is located immediately above the heme plane, dominating the local structure. Putative proton relay pathways from protein surface to heme (converging at Ser(279)) are identified. Most interestingly, the electron density indicates weak binding of a dioxygen molecule to the P450. This structure provides a basis for rational design of putative antimycobacterial agents.
*[[Cytochrome P450 3D structures|Cytochrome P450 3D structures]]
 
== References ==
==About this Structure==
<references/>
1N4G is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N4G OCA].
__TOC__
 
</StructureSection>
==Reference==
[[Category: Large Structures]]
Atomic structure of Mycobacterium tuberculosis CYP121 to 1.06 A reveals novel features of cytochrome P450., Leys D, Mowat CG, McLean KJ, Richmond A, Chapman SK, Walkinshaw MD, Munro AW, J Biol Chem. 2003 Feb 14;278(7):5141-7. Epub 2002 Nov 14. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12435731 12435731]
[[Category: Mycobacterium tuberculosis]]
[[Category: Mycobacterium tuberculosis]]
[[Category: Single protein]]
[[Category: Chapman SK]]
[[Category: Chapman, S K.]]
[[Category: Leys D]]
[[Category: Leys, D.]]
[[Category: McLean KJ]]
[[Category: McLean, K J.]]
[[Category: Mowat CG]]
[[Category: Mowat, C G.]]
[[Category: Munro AW]]
[[Category: Munro, A W.]]
[[Category: Richmond A]]
[[Category: Richmond, A.]]
[[Category: Walkinshaw MD]]
[[Category: TBSGC, TB Structural Genomics Consortium.]]
[[Category: Walkinshaw, M D.]]
[[Category: heme binding]]
[[Category: iodopyrazole complex]]
[[Category: p450 fold]]
[[Category: protein structure initiative]]
[[Category: psi]]
[[Category: structural genomic]]
[[Category: tb structural genomics consortium]]
[[Category: tbsgc]]
 
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