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3i72

From Proteopedia

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Structural characterization for the nucleotide binding ability of subunit A with SO4 of the A1AO ATP synthase

Structural highlights

3i72 is a 1 chain structure with sequence from Pyrococcus horikoshii OT3. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.47Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

VATA_PYRHO Produces ATP from ADP in the presence of a proton gradient across the membrane. The archaeal alpha chain is a catalytic subunit.

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

The crystal structures of the nucleotide-empty (A(E)), 5'-adenylyl-beta,gamma-imidodiphosphate (A(PNP))-bound, and ADP (A(DP))-bound forms of the catalytic A subunit of the energy producer A(1)A(O) ATP synthase from Pyrococcus horikoshii OT3 have been solved at 2.47 A and 2.4 A resolutions. The structures provide novel features of nucleotide binding and depict the residues involved in the catalysis of the A subunit. In the A(E) form, the phosphate analog SO(4)(2-) binds, via a water molecule, to the phosphate binding loop (P-loop) residue Ser238, which is also involved in the phosphate binding of ADP and 5'-adenylyl-beta,gamma-imidodiphosphate. Together with amino acids Gly234 and Phe236, the serine residue stabilizes the arched P-loop conformation of subunit A, as shown by the 2.4-A structure of the mutant protein S238A in which the P-loop flips into a relaxed state, comparable to the one in catalytic beta subunits of F(1)F(O) ATP synthases. Superposition of the existing P-loop structures of ATPases emphasizes the unique P-loop in subunit A, which is also discussed in the light of an evolutionary P-loop switch in related A(1)A(O) ATP synthases, F(1)F(O) ATP synthases, and vacuolar ATPases and implicates diverse catalytic mechanisms inside these biological motors.

Nucleotide binding states of subunit A of the A-ATP synthase and the implication of P-loop switch in evolution.,Kumar A, Manimekalai MS, Balakrishna AM, Jeyakanthan J, Gruber G J Mol Biol. 2010 Feb 19;396(2):301-20. Epub 2009 Nov 26. PMID:19944110^[1]

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

References

↑ Kumar A, Manimekalai MS, Balakrishna AM, Jeyakanthan J, Gruber G. Nucleotide binding states of subunit A of the A-ATP synthase and the implication of P-loop switch in evolution. J Mol Biol. 2010 Feb 19;396(2):301-20. Epub 2009 Nov 26. PMID:19944110 doi:10.1016/j.jmb.2009.11.046

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3i72"

@@ Line 3: / Line 3: @@
 <StructureSection load='3i72' size='340' side='right'caption='[[3i72]], [[Resolution|resolution]] 2.47&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3i72]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I72 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I72 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3i72]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I72 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I72 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 2.47&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3i4l|3i4l]], [[1vdz|1vdz]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">atpA, PH1975 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/H(+)-transporting_two-sector_ATPase H(+)-transporting two-sector ATPase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.14 3.6.3.14] </span></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=3i72 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i72 OCA], [https://pdbe.org/3i72 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i72 RCSB], [https://www.ebi.ac.uk/pdbsum/3i72 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i72 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/VATA_PYRHO VATA_PYRHO]] Produces ATP from ADP in the presence of a proton gradient across the membrane. The archaeal alpha chain is a catalytic subunit.
+[https://www.uniprot.org/uniprot/VATA_PYRHO VATA_PYRHO] Produces ATP from ADP in the presence of a proton gradient across the membrane. The archaeal alpha chain is a catalytic subunit.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 39: / Line 37: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Pyrococcus horikoshii]]
+[[Category: Pyrococcus horikoshii OT3]]
-[[Category: Balakrishna, A M]]
+[[Category: Balakrishna AM]]
-[[Category: Gruber, G]]
+[[Category: Gruber G]]
-[[Category: Kumar, A]]
+[[Category: Kumar A]]
-[[Category: Manimekalai, S M.S]]
+[[Category: Manimekalai SMS]]
-[[Category: Atp synthesis]]
-[[Category: Atp-binding]]
-[[Category: Autocatalytic cleavage]]
-[[Category: Hydrogen ion transport]]
-[[Category: Hydrolase]]
-[[Category: Intron homing]]
-[[Category: Ion transport]]
-[[Category: Nuclease]]
-[[Category: Nucleotide-binding]]
-[[Category: Transport]]

3i72

From Proteopedia

Current revision

Structural characterization for the nucleotide binding ability of subunit A with SO4 of the A1AO ATP synthase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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