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6k5f

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Crystal structure of the CLC-ec1 deltaNC in presence of 200 mM NaBr

Structural highlights

6k5f is a 6 chain structure with sequence from Escherichia coli and Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.203Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CLCA_ECOLI Proton-coupled chloride transporter. Functions as antiport system and exchanges two chloride ions for 1 proton. Probably acts as an electrical shunt for an outwardly-directed proton pump that is linked to amino acid decarboxylation, as part of the extreme acid resistance (XAR) response.^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

The CLC family of proteins are involved in a variety of physiological processes to control cellular chloride concentration. Two distinct classes of CLC proteins, Cl(-) channels and Cl(-)/H(+) antiporters, have been functionally and structurally investigated over the last several decades. Previous studies have suggested that the conformational heterogeneity of the critical glutamate residue, Gluex, could explain the transport cycle of CLC-type Cl(-)/H(+) antiporters. However, the presence of multiple conformations (Up, Middle, and Down) of the Gluex has been suggested from combined structural snapshots of 2 different CLC antiporters: CLC-ec1 from Escherichia coli and cmCLC from a thermophilic red alga, Cyanidioschyzon merolae Thus, we aimed to investigate further the heterogeneity of Gluex-conformations in CLC-ec1, the most deeply studied CLC antiporter, at both functional and structural levels. Here, we show that the crystal structures of the Gluex mutant E148D and wild-type CLC-ec1 with varying anion concentrations suggest a structural intermediate, the "Midlow" conformation. We also found that an extra anion can be located above the external Cl(-)-binding site in the E148D mutant when the anion concentration is high. Moreover, we observed that a carboxylate in solution can occupy either the external or central Cl(-)-binding site in the ungated E148A mutant using an anomalously detectable short carboxylic acid, bromoacetate. These results lend credibility to the idea that the Gluex can take at least 3 distinct conformational states during the transport cycle of a single CLC antiporter.

Mutation of external glutamate residue reveals a new intermediate transport state and anion binding site in a CLC Cl(-)/H(+) antiporter.,Park K, Lee BC, Lim HH Proc Natl Acad Sci U S A. 2019 Aug 13. pii: 1901822116. doi:, 10.1073/pnas.1901822116. PMID:31409705^[6]

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

References

↑ Iyer R, Iverson TM, Accardi A, Miller C. A biological role for prokaryotic ClC chloride channels. Nature. 2002 Oct 17;419(6908):715-8. PMID:12384697 doi:10.1038/nature01000
↑ Accardi A, Miller C. Secondary active transport mediated by a prokaryotic homologue of ClC Cl- channels. Nature. 2004 Feb 26;427(6977):803-7. PMID:14985752 doi:10.1038/nature02314
↑ Lobet S, Dutzler R. Ion-binding properties of the ClC chloride selectivity filter. EMBO J. 2006 Jan 11;25(1):24-33. Epub 2005 Dec 8. PMID:16341087
↑ Nguitragool W, Miller C. Uncoupling of a CLC Cl-/H+ exchange transporter by polyatomic anions. J Mol Biol. 2006 Sep 29;362(4):682-90. Epub 2006 Aug 14. PMID:16905147 doi:10.1016/j.jmb.2006.07.006
↑ Jayaram H, Accardi A, Wu F, Williams C, Miller C. Ion permeation through a Cl--selective channel designed from a CLC Cl-/H+ exchanger. Proc Natl Acad Sci U S A. 2008 Aug 12;105(32):11194-9. Epub 2008 Aug 4. PMID:18678918
↑ Park K, Lee BC, Lim HH. Mutation of external glutamate residue reveals a new intermediate transport state and anion binding site in a CLC Cl(-)/H(+) antiporter. Proc Natl Acad Sci U S A. 2019 Aug 13. pii: 1901822116. doi:, 10.1073/pnas.1901822116. PMID:31409705 doi:http://dx.doi.org/10.1073/pnas.1901822116

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6k5f"

Categories: Escherichia coli | Large Structures | Mus musculus | Lim HH | Park K

@@ Line 3: / Line 3: @@
 <StructureSection load='6k5f' size='340' side='right'caption='[[6k5f]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6k5f]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K5F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K5F FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6k5f]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K5F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K5F FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</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]] 3.203&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">yadQ, clcA, eriC, A6592_03060, A9819_00720, A9R57_04335, AC067_04570, AC789_1c01550, ACN002_0160, ACN81_28610, ACU57_18640, AM270_18100, AM446_22830, AMK83_01920, AWP75_13405, B1K96_13065, B7C53_01430, B9M99_16180, BANRA_02286, BANRA_02303, BANRA_03326, BB545_20825, BE963_14760, BER14_07860, BFD29_18565, BHF46_07945, BHS81_00575, BHS87_00725, BIQ87_00715, BIU72_13480, BJJ90_21425, BK292_13605, BK373_09530, BK383_20300, BMT53_09575, BMT91_01430, BN17_45791, BVL39_02260, BXT93_20950, BZL31_15015, BZL69_20275, C2M16_10720, C2U48_09685, C3444_11105, C3449_15895, C4J69_03510, C5715_17420, C5P01_08850, C5P43_19885, C7235_20305, C7B02_09235, CG691_14570, CIJ94_20900, COD46_06560, CR538_20715, CRD98_15250, CRM83_15165, CRT46_00820, CV83915_01419, CWM24_04960, CWS33_09545, CXB56_23210, D2184_08665, D2185_20055, D2188_12715, D3821_06135, D3822_17405, D3I61_01530, D3O91_03110, D3Y67_10980, D5618_10265, D5653_16505, D8K42_10345, D9D20_18555, D9D29_16860, D9D31_08820, D9D55_03155, D9D69_06945, D9E22_13175, D9E34_01170, D9F17_00235, D9F57_04830, D9H66_18270, D9H68_13700, D9H94_13970, D9I47_04165, D9I87_01705, D9I88_06500, D9I97_03880, D9J03_00240, D9J11_16750, D9J44_14145, D9J60_02140, DL545_20465, DLW18_08025, DMZ31_06935, DNQ26_06330, DP277_13800, DQF57_05740, DQO13_06325, DS732_05700, DTL43_06000, DTM10_02705, DTM45_12560, DU321_03585, EAI42_18265, EAI44_17040, EAI46_14565, EAI52_10940, EC1094V2_3697, EC3234A_2c01370, Eco118UI_00790, EEP23_00240, EFV01_09785, EFV02_20350, EFV04_15100, EFV08_17265, EFV11_08020, EFV12_18730, EFV14_08750, EFV15_17340, EFV17_09990, EIA10_05995, EL75_3609, EL79_3718, EL80_3665, EOL26_04835, ERS085366_02706, ERS085379_00551, ERS150873_01097, GJ11_00825, HMPREF3040_02596, MJ49_06260, NCTC10082_01396, NCTC10090_02173, NCTC10429_04214, NCTC11126_03619, NCTC12950_04437, NCTC13148_05172, NCTC7922_05796, NCTC7927_04520, NCTC8009_07339, NCTC8179_01364, NCTC8500_04562, NCTC8959_04830, NCTC9036_04037, NCTC9037_04203, NCTC9044_03171, NCTC9050_02039, NCTC9055_00980, NCTC9058_02783, NCTC9062_04200, NCTC9073_03413, NCTC9077_05114, NCTC9111_04278, NCTC9702_04777, NCTC9703_03448, NCTC9706_01351, NCTC9777_00485, PU06_23100, RG28_03970, RK56_028075, RX35_04890, SAMEA3472044_04171, SAMEA3472055_02614, SAMEA3472070_02408, SAMEA3472090_04472, SAMEA3472110_04526, SAMEA3472112_04666, SAMEA3472147_00367, SAMEA3484427_01361, SAMEA3484429_01120, SAMEA3484433_03082, SAMEA3485113_00827, SAMEA3752372_04445, SAMEA3752553_02908, SAMEA3752557_00860, SAMEA3752559_03726, SAMEA3752620_02075, SAMEA3753097_03891, SAMEA3753164_02448, SK85_00155, UC41_07360, UN86_07645, WQ89_09495, WR15_02265, YDC107_3382 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene></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=6k5f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k5f OCA], [http://pdbe.org/6k5f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k5f RCSB], [http://www.ebi.ac.uk/pdbsum/6k5f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k5f ProSAT]</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=6k5f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k5f OCA], [https://pdbe.org/6k5f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k5f RCSB], [https://www.ebi.ac.uk/pdbsum/6k5f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k5f ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/J7Q633_ECOLX J7Q633_ECOLX]] Probably acts as an electrical shunt for an outwardly-directed proton pump that is linked to amino acid decarboxylation, as part of the extreme acid resistance (XAR) response.[SAAS:SAAS00552659]  Proton-coupled chloride transporter. Functions as antiport system and exchanges two chloride ions for 1 proton. Probably acts as an electrical shunt for an outwardly-directed proton pump that is linked to amino acid decarboxylation, as part of the extreme acid resistance (XAR) response.[HAMAP-Rule:MF_01128][SAAS:SAAS00010056]
+[https://www.uniprot.org/uniprot/CLCA_ECOLI CLCA_ECOLI] Proton-coupled chloride transporter. Functions as antiport system and exchanges two chloride ions for 1 proton. Probably acts as an electrical shunt for an outwardly-directed proton pump that is linked to amino acid decarboxylation, as part of the extreme acid resistance (XAR) response.<ref>PMID:12384697</ref> <ref>PMID:14985752</ref> <ref>PMID:16341087</ref> <ref>PMID:16905147</ref> <ref>PMID:18678918</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 6k5f" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Ion channels 3D structures|Ion channels 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Lk3 transgenic mice]]
+[[Category: Mus musculus]]
-[[Category: Lim, H H]]
+[[Category: Lim HH]]
-[[Category: Park, K]]
+[[Category: Park K]]
-[[Category: Cl- / h+ antiporter]]
-[[Category: Clc transporter]]
-[[Category: Membrane protein]]

6k5f

From Proteopedia

Current revision

Crystal structure of the CLC-ec1 deltaNC in presence of 200 mM NaBr

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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