3i7u

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of AP4A hydrolase (aq_158) from Aquifex aeolicus VF5

Structural highlights

3i7u is a 4 chain structure with sequence from Aquifex aeolicus VF5. This structure supersedes the now removed PDB entry 2pbt. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

O66548_AQUAE

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

Asymmetric diadenosine tetraphosphate (Ap(4)A) hydrolases degrade the metabolite Ap(4)A back into ATP and AMP. The three-dimensional crystal structure of Ap(4)A hydrolase (16 kDa) from Aquifex aeolicus has been determined in free and ATP-bound forms at 1.8 and 1.95 A resolution, respectively. The overall three-dimensional crystal structure of the enzyme shows an alphabetaalpha-sandwich architecture with a characteristic loop adjacent to the catalytic site of the protein molecule. The ATP molecule is bound in the primary active site and the adenine moiety of the nucleotide binds in a ring-stacking arrangement equivalent to that observed in the X-ray structure of Ap(4)A hydrolase from Caenorhabditis elegans. Binding of ATP in the active site induces local conformational changes which may have important implications in the mechanism of substrate recognition in this class of enzymes. Furthermore, two invariant water molecules have been identified and their possible structural and/or functional roles are discussed. In addition, modelling of the substrate molecule at the primary active site of the enzyme suggests a possible path for entry and/or exit of the substrate and/or product molecule.

Free and ATP-bound structures of Ap4A hydrolase from Aquifex aeolicus V5.,Jeyakanthan J, Kanaujia SP, Nishida Y, Nakagawa N, Praveen S, Shinkai A, Kuramitsu S, Yokoyama S, Sekar K Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):116-24. Epub 2010, Jan 22. PMID:20124691^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Jeyakanthan J, Kanaujia SP, Nishida Y, Nakagawa N, Praveen S, Shinkai A, Kuramitsu S, Yokoyama S, Sekar K. Free and ATP-bound structures of Ap4A hydrolase from Aquifex aeolicus V5. Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):116-24. Epub 2010, Jan 22. PMID:20124691 doi:10.1107/S0907444909047064

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3i7u"

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:3i7u.png|left|200px]]
-<!--
+==Crystal structure of AP4A hydrolase (aq_158) from Aquifex aeolicus VF5==
-The line below this paragraph, containing "STRUCTURE_3i7u", creates the "Structure Box" on the page.
+<StructureSection load='3i7u' size='340' side='right'caption='[[3i7u]], [[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'>[[3i7u]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus_VF5 Aquifex aeolicus VF5]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2pbt 2pbt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I7U 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>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-{{STRUCTURE_3i7u|  PDB=3i7u  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3i7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7u OCA], [https://pdbe.org/3i7u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i7u RCSB], [https://www.ebi.ac.uk/pdbsum/3i7u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i7u ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/O66548_AQUAE O66548_AQUAE]
+== 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/i7/3i7u_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=3i7u ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Asymmetric diadenosine tetraphosphate (Ap(4)A) hydrolases degrade the metabolite Ap(4)A back into ATP and AMP. The three-dimensional crystal structure of Ap(4)A hydrolase (16 kDa) from Aquifex aeolicus has been determined in free and ATP-bound forms at 1.8 and 1.95 A resolution, respectively. The overall three-dimensional crystal structure of the enzyme shows an alphabetaalpha-sandwich architecture with a characteristic loop adjacent to the catalytic site of the protein molecule. The ATP molecule is bound in the primary active site and the adenine moiety of the nucleotide binds in a ring-stacking arrangement equivalent to that observed in the X-ray structure of Ap(4)A hydrolase from Caenorhabditis elegans. Binding of ATP in the active site induces local conformational changes which may have important implications in the mechanism of substrate recognition in this class of enzymes. Furthermore, two invariant water molecules have been identified and their possible structural and/or functional roles are discussed. In addition, modelling of the substrate molecule at the primary active site of the enzyme suggests a possible path for entry and/or exit of the substrate and/or product molecule.
-===Crystal structure of AP4A hydrolase (aq_158) from Aquifex aeolicus VF5===
+Free and ATP-bound structures of Ap4A hydrolase from Aquifex aeolicus V5.,Jeyakanthan J, Kanaujia SP, Nishida Y, Nakagawa N, Praveen S, Shinkai A, Kuramitsu S, Yokoyama S, Sekar K Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):116-24. Epub 2010, Jan 22. PMID:20124691<ref>PMID:20124691</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_20124691}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3i7u" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 20124691 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20124691}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Aquifex aeolicus VF5]]
-I7U is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Aquifex_aeolicus_vf5 Aquifex aeolicus vf5]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2pbt 2pbt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7U OCA].
+[[Category: Large Structures]]
+[[Category: Jeyakanthan J]]
-==Reference==
+[[Category: Kanaujia SP]]
-<ref group="xtra">PMID:20124691</ref><references group="xtra"/>
+[[Category: Kuramitsu S]]
-[[Category: Aquifex aeolicus vf5]]
+[[Category: Nakagawa N]]
-[[Category: Jeyakanthan, J.]]
+[[Category: Sekar K]]
-[[Category: Kanaujia, S P.]]
+[[Category: Shinkai A]]
-[[Category: Kuramitsu, S.]]
+[[Category: Yokoyama S]]
-[[Category: Nakagawa, N.]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
-[[Category: Sekar, K.]]
-[[Category: Shinkai, A.]]
-[[Category: Yokoyama, S.]]
-[[Category: Ap4a]]
-[[Category: Diadenosine polyphosphate]]
-[[Category: Hydrolase]]
-[[Category: National project on protein structural and functional analyse]]
-[[Category: Nppsfa]]
-[[Category: Nudix protein]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rsgi]]
-[[Category: Structural genomic]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 17 10:02:51 2010''

3i7u

From Proteopedia

Current revision

Crystal structure of AP4A hydrolase (aq_158) from Aquifex aeolicus VF5

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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