3d2o: Difference between revisions

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[[Image:3d2o.png|left|200px]]


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==Crystal Structure of Manganese-metallated GTP Cyclohydrolase Type IB==
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<StructureSection load='3d2o' size='340' side='right'caption='[[3d2o]], [[Resolution|resolution]] 2.04&Aring;' scene=''>
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== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[3d2o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Neisseria_gonorrhoeae Neisseria gonorrhoeae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D2O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D2O FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.04&#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=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=LI:LITHIUM+ION'>LI</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
{{STRUCTURE_3d2o|  PDB=3d2o  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3d2o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d2o OCA], [https://pdbe.org/3d2o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d2o RCSB], [https://www.ebi.ac.uk/pdbsum/3d2o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d2o ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/GCH4_NEIG1 GCH4_NEIG1] Converts GTP to 7,8-dihydroneopterin triphosphate.<ref>PMID:17032654</ref>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
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    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d2/3d2o_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=3d2o ConSurf].
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== Publication Abstract from PubMed ==
GTP cyclohydrolase I (GCYH-I) is an essential Zn(2+)-dependent enzyme that catalyzes the first step of the de novo folate biosynthetic pathway in bacteria and plants, the 7-deazapurine biosynthetic pathway in Bacteria and Archaea, and the biopterin pathway in mammals. We recently reported the discovery of a new prokaryotic-specific GCYH-I (GCYH-IB) that displays no sequence identity to the canonical enzyme and is present in approximately 25% of bacteria, the majority of which lack the canonical GCYH-I (renamed GCYH-IA). Genomic and genetic analyses indicate that in those organisms possessing both enzymes, e.g., Bacillus subtilis, GCYH-IA and -IB are functionally redundant, but differentially expressed. Whereas GCYH-IA is constitutively expressed, GCYH-IB is expressed only under Zn(2+)-limiting conditions. These observations are consistent with the hypothesis that GCYH-IB functions to allow folate biosynthesis during Zn(2+) starvation. Here, we present biochemical and structural data showing that bacterial GCYH-IB, like GCYH-IA, belongs to the tunneling-fold (T-fold) superfamily. However, the GCYH-IA and -IB enzymes exhibit significant differences in global structure and active-site architecture. While GCYH-IA is a unimodular, homodecameric, Zn(2+)-dependent enzyme, GCYH-IB is a bimodular, homotetrameric enzyme activated by a variety of divalent cations. The structure of GCYH-IB and the broad metal dependence exhibited by this enzyme further underscore the mechanistic plasticity that is emerging for the T-fold superfamily. Notably, while humans possess the canonical GCYH-IA enzyme, many clinically important human pathogens possess only the GCYH-IB enzyme, suggesting that this enzyme is a potential new molecular target for antibacterial development.


===Crystal Structure of Manganese-metallated GTP Cyclohydrolase Type IB===
Zinc-independent folate biosynthesis: genetic, biochemical, and structural investigations reveal new metal dependence for GTP cyclohydrolase IB.,Sankaran B, Bonnett SA, Shah K, Gabriel S, Reddy R, Schimmel P, Rodionov DA, de Crecy-Lagard V, Helmann JD, Iwata-Reuyl D, Swairjo MA J Bacteriol. 2009 Nov;191(22):6936-49. Epub 2009 Sep 18. PMID:19767425<ref>PMID:19767425</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_19767425}}, adds the Publication Abstract to the page
*[[Cyclohydrolase 3D structures|Cyclohydrolase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 19767425 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_19767425}}
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</StructureSection>
==About this Structure==
[[Category: Large Structures]]
[[3d2o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Neisseria_gonorrhoeae Neisseria gonorrhoeae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D2O OCA].
 
==Reference==
<ref group="xtra">PMID:19767425</ref><ref group="xtra">PMID:17032654</ref><references group="xtra"/>
[[Category: GTP cyclohydrolase I]]
[[Category: Neisseria gonorrhoeae]]
[[Category: Neisseria gonorrhoeae]]
[[Category: Swairjo, M A.]]
[[Category: Swairjo MA]]
[[Category: Bimodular tunnel fold]]
[[Category: Biosynthetic protein]]
[[Category: Folate biosynthesis]]
[[Category: Gtp cyclohydrolase]]
[[Category: Hydrolase]]
[[Category: Manganese]]
[[Category: Metalloenzyme]]
[[Category: Tunneling fold]]

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