3i7v

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of AP4A hydrolase complexed with AP4A (ATP) (aq_158) from Aquifex aeolicus Vf5

Structural highlights

3i7v is a 2 chain structure with sequence from Aquifex aeolicus VF5. This structure supersedes the now removed PDB entry 2pq1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.95Å
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/3i7v"

@@ Line 1: / Line 1: @@
 ==Crystal structure of AP4A hydrolase complexed with AP4A (ATP) (aq_158) from Aquifex aeolicus Vf5==
-<StructureSection load='3i7v' size='340' side='right' caption='[[3i7v]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
+<StructureSection load='3i7v' size='340' side='right'caption='[[3i7v]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3i7v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquae Aquae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2pq1 2pq1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I7V FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3i7v]] is a 2 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=2pq1 2pq1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I7V FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=B4P:BIS(ADENOSINE)-5-TETRAPHOSPHATE'>B4P</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.95&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3i7u|3i7u]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=B4P:BIS(ADENOSINE)-5-TETRAPHOSPHATE'>B4P</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">apfA, aq_158 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 AQUAE])</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=3i7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7v OCA], [https://pdbe.org/3i7v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i7v RCSB], [https://www.ebi.ac.uk/pdbsum/3i7v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i7v 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=3i7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7v OCA], [http://pdbe.org/3i7v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3i7v RCSB], [http://www.ebi.ac.uk/pdbsum/3i7v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3i7v ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/O66548_AQUAE O66548_AQUAE]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Aquae]]
+[[Category: Aquifex aeolicus VF5]]
-[[Category: Jeyakanthan, J]]
+[[Category: Large Structures]]
-[[Category: Kanaujia, S P]]
+[[Category: Jeyakanthan J]]
-[[Category: Kuramitsu, S]]
+[[Category: Kanaujia SP]]
-[[Category: Nakagawa, N]]
+[[Category: Kuramitsu S]]
-[[Category: Structural genomic]]
+[[Category: Nakagawa N]]
-[[Category: Sekar, K]]
+[[Category: Sekar K]]
-[[Category: Shinkai, A]]
+[[Category: Shinkai A]]
-[[Category: Yokoyama, S]]
+[[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: Rsgi]]

3i7v

From Proteopedia

Current revision

Crystal structure of AP4A hydrolase complexed with AP4A (ATP) (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

Personal tools

Navigation

Search

Toolbox