2zbf

From Proteopedia

(Difference between revisions)

Revision as of 13:29, 1 November 2023

Calcium pump crystal structure with bound BeF3 and TG in the absence of calcium

Structural highlights

2zbf is a 1 chain structure with sequence from Oryctolagus cuniculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.4Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AT2A1_RABIT This magnesium-dependent enzyme catalyzes the hydrolysis of ATP coupled with the translocation of calcium from the cytosol to the sarcoplasmic reticulum lumen. Contributes to calcium sequestration involved in muscular excitation/contraction (By similarity).

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

Ca(2+)-ATPase of skeletal muscle sarcoplasmic reticulum is the best-studied member of the P-type or E1/E2 type ion transporting ATPases. It has been crystallized in seven different states that cover nearly the entire reaction cycle. Here we describe the structure of this ATPase complexed with phosphate analogs BeF(3)(-) and AlF(4)(-) in the absence of Ca(2+), which correspond to the E2P ground state and E2 approximately P transition state, respectively. The luminal gate is open with BeF(3)(-) and closed with AlF(4)(-). These and the E1 approximately P.ADP analog crystal structures show that a two-step rotation of the cytoplasmic A-domain opens and closes the luminal gate through the movements of the M1-M4 transmembrane helices. There are several conformational switches coupled to the rotation, and the one in the cytoplasmic part of M2 has critical importance. In the second step of rotation, positioning of one water molecule couples the hydrolysis of aspartylphosphate to closing of the gate.

How processing of aspartylphosphate is coupled to lumenal gating of the ion pathway in the calcium pump.,Toyoshima C, Norimatsu Y, Iwasawa S, Tsuda T, Ogawa H Proc Natl Acad Sci U S A. 2007 Dec 11;104(50):19831-6. Epub 2007 Dec 5. PMID:18077416^[1]

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

References

↑ Toyoshima C, Norimatsu Y, Iwasawa S, Tsuda T, Ogawa H. How processing of aspartylphosphate is coupled to lumenal gating of the ion pathway in the calcium pump. Proc Natl Acad Sci U S A. 2007 Dec 11;104(50):19831-6. Epub 2007 Dec 5. PMID:18077416

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/2zbf"

Categories: Large Structures | Oryctolagus cuniculus | Norimatsu Y | Ogawa H | Toyoshima C

@@ Line 3: / Line 3: @@
 <StructureSection load='2zbf' size='340' side='right'caption='[[2zbf]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2zbf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZBF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2ZBF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2zbf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZBF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZBF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TG1:OCTANOIC+ACID+[3S-[3ALPHA,+3ABETA,+4ALPHA,+6BETA,+6ABETA,+7BETA,+8ALPHA(Z),+9BALPHA]]-6-(ACETYLOXY)-2,3,-3A,4,5,6,6A,7,8,9B-DECAHYDRO-3,3A-DIHYDROXY-3,6,9-TRIMETHYL-8-[(2-METHYL-1-OXO-2-BUTENYL)OXY]-2-OXO-4-(1-OXOBUTOXY)-AZULENO[4,5-B]FURAN-7-YL+ESTER'>TG1</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]] 2.4&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TG1:OCTANOIC+ACID+[3S-[3ALPHA,+3ABETA,+4ALPHA,+6BETA,+6ABETA,+7BETA,+8ALPHA(Z),+9BALPHA]]-6-(ACETYLOXY)-2,3,-3A,4,5,6,6A,7,8,9B-DECAHYDRO-3,3A-DIHYDROXY-3,6,9-TRIMETHYL-8-[(2-METHYL-1-OXO-2-BUTENYL)OX+Y]-2-OXO-4-(1-OXOBUTOXY)-AZULENO[4,5-B]FURAN-7-YL+ESTER'>TG1</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1su4|1su4]], [[1iwo|1iwo]], [[1vfp|1vfp]], [[2zbd|2zbd]], [[1wpg|1wpg]], [[2agv|2agv]], [[2dqs|2dqs]], [[2ear|2ear]], [[2eas|2eas]], [[2eat|2eat]], [[2eau|2eau]], [[2zbe|2zbe]], [[2zbg|2zbg]]</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=2zbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zbf OCA], [https://pdbe.org/2zbf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zbf RCSB], [https://www.ebi.ac.uk/pdbsum/2zbf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zbf ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Calcium-transporting_ATPase Calcium-transporting ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.8 3.6.3.8] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2zbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zbf OCA], [http://pdbe.org/2zbf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zbf RCSB], [http://www.ebi.ac.uk/pdbsum/2zbf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zbf ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/AT2A1_RABIT AT2A1_RABIT]] This magnesium-dependent enzyme catalyzes the hydrolysis of ATP coupled with the translocation of calcium from the cytosol to the sarcoplasmic reticulum lumen. Contributes to calcium sequestration involved in muscular excitation/contraction (By similarity).
+[https://www.uniprot.org/uniprot/AT2A1_RABIT AT2A1_RABIT] This magnesium-dependent enzyme catalyzes the hydrolysis of ATP coupled with the translocation of calcium from the cytosol to the sarcoplasmic reticulum lumen. Contributes to calcium sequestration involved in muscular excitation/contraction (By similarity).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 38: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Calcium-transporting ATPase]]
 [[Category: Large Structures]]
 [[Category: Oryctolagus cuniculus]]
-[[Category: Norimatsu, Y]]
+[[Category: Norimatsu Y]]
-[[Category: Ogawa, H]]
+[[Category: Ogawa H]]
-[[Category: Toyoshima, C]]
+[[Category: Toyoshima C]]
-[[Category: Atp-binding]]
-[[Category: Calcium transport]]
-[[Category: Endoplasmic reticulum]]
-[[Category: Had fold]]
-[[Category: Hydrolase]]
-[[Category: Ion transport]]
-[[Category: Magnesium]]
-[[Category: Membrane protein]]
-[[Category: Metal-binding]]
-[[Category: Nucleotide-binding]]
-[[Category: P-type atpase]]
-[[Category: Phosphorylation]]
-[[Category: Sarcoplasmic reticulum]]
-[[Category: Transmembrane]]
-[[Category: Transport]]

2zbf

From Proteopedia

Revision as of 13:29, 1 November 2023

Calcium pump crystal structure with bound BeF3 and TG in the absence of calcium

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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