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PDBsum entry 2fee
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protein Protein-protein interface(s) links
Proton transport,membrane protein PDB id
2fee

 

 

 

 

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Contents
Protein chains
444 a.a. *
221 a.a. *
211 a.a. *
* Residue conservation analysis
PDB id:
2fee
Name: Proton transport,membrane protein
Title: Structure of the cl-/h+ exchanger clc-ec1 from e.Coli in nabr
Structure: H(+)/cl(-) exchange transporter clca. Chain: a, b. Synonym: clc-ec1. Engineered: yes. Fab fragment, heavy chain. Chain: j, i. Fragment: heavy chain. Engineered: yes. Fab fragment, light chain.
Source: Escherichia coli. Organism_taxid: 562. Gene: clca, eric. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Homo sapiens. Human. Organism_taxid: 9606. Expressed in: mus musculus.
Biol. unit: Hexamer (from PQS)
Resolution:
3.20Å     R-factor:   0.254     R-free:   0.293
Authors: A.Accardi,M.P.Walden,W.Nguitragool,H.Jayaram,C.Williams,C.Miller
Key ref: A.Accardi et al. (2005). Separate ion pathways in a Cl-/H+ exchanger. J Gen Physiol, 126, 563-570. PubMed id: 16316975
Date:
15-Dec-05     Release date:   03-Jan-06    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P37019  (CLCA_ECOLI) -  H(+)/Cl(-) exchange transporter ClcA from Escherichia coli (strain K12)
Seq:
Struc: 		473 a.a.
444 a.a.
Protein chains
No UniProt id for this chain
Struc: 221 a.a.
Protein chains
No UniProt id for this chain
Struc: 211 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
J Gen Physiol 126:563-570 (2005)
PubMed id: 16316975  
 
 
Separate ion pathways in a Cl-/H+ exchanger.
A.Accardi, M.Walden, W.Nguitragool, H.Jayaram, C.Williams, C.Miller.
 
  ABSTRACT  
 
CLC-ec1 is a prokaryotic CLC-type Cl(-)/H+ exchange transporter. Little is known about the mechanism of H+ coupling to Cl-. A critical glutamate residue, E148, was previously shown to be required for Cl(-)/H+ exchange by mediating proton transfer between the protein and the extracellular solution. To test whether an analogous H+ acceptor exists near the intracellular side of the protein, we performed a mutagenesis scan of inward-facing carboxyl-bearing residues and identified E203 as the unique residue whose neutralization abolishes H+ coupling to Cl- transport. Glutamate at this position is strictly conserved in all known CLCs of the transporter subclass, while valine is always found here in CLC channels. The x-ray crystal structure of the E203Q mutant is similar to that of the wild-type protein. Cl- transport rate in E203Q is inhibited at neutral pH, and the double mutant, E148A/E203Q, shows maximal Cl- transport, independent of pH, as does the single mutant E148A. The results argue that substrate exchange by CLC-ec1 involves two separate but partially overlapping permeation pathways, one for Cl- and one for H+. These pathways are congruent from the protein's extracellular surface to E148, and they diverge beyond this point toward the intracellular side. This picture demands a transport mechanism fundamentally different from familiar alternating-access schemes.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22484316 A.Picollo, Y.Xu, N.Johner, S.Bernèche, and A.Accardi (2012).
Synergistic substrate binding determines the stoichiometry of transport of a prokaryotic H(+)/Cl(-) exchanger.
  Nat Struct Mol Biol, 19, 525.  
  21282402 E.Ohana, N.Shcheynikov, D.Yang, I.So, and S.Muallem (2011).
Determinants of coupled transport and uncoupled current by the electrogenic SLC26 transporters.
  J Gen Physiol, 137, 239-251.  
21275645 H.Barbier-Brygoo, A.De Angeli, S.Filleur, J.M.Frachisse, F.Gambale, S.Thomine, and S.Wege (2011).
Anion channels/transporters in plants: from molecular bases to regulatory networks.
  Annu Rev Plant Biol, 62, 25-51.  
20421284 A.J.Smith, and J.D.Lippiat (2010).
Direct endosomal acidification by the outwardly rectifying CLC-5 Cl(-)/H(+) exchanger.
  J Physiol, 588, 2033-2045.  
20501796 A.J.Smith, and J.D.Lippiat (2010).
Voltage-dependent charge movement associated with activation of the CLC-5 2Cl-/1H+ exchanger.
  FASEB J, 24, 3696-3705.  
  20513761 A.Picollo, M.Malvezzi, and A.Accardi (2010).
Proton block of the CLC-5 Cl-/H+ exchanger.
  J Gen Physiol, 135, 653-659.  
19827947 C.Duran, C.H.Thompson, Q.Xiao, and H.C.Hartzell (2010).
Chloride channels: often enigmatic, rarely predictable.
  Annu Rev Physiol, 72, 95.  
20303857 G.V.Miloshevsky, A.Hassanein, and P.C.Jordan (2010).
Antiport mechanism for Cl(-)/H(+) in ClC-ec1 from normal-mode analysis.
  Biophys J, 98, 999.  
19132363 G.Zifarelli, and M.Pusch (2010).
The role of protons in fast and slow gating of the Torpedo chloride channel ClC-0.
  Eur Biophys J, 39, 869-875.  
19926787 J.J.Matsuda, M.S.Filali, M.M.Collins, K.A.Volk, and F.S.Lamb (2010).
The ClC-3 Cl-/H+ antiporter becomes uncoupled at low extracellular pH.
  J Biol Chem, 285, 2569-2579.  
20929736 L.Feng, E.B.Campbell, Y.Hsiung, and R.MacKinnon (2010).
Structure of a eukaryotic CLC transporter defines an intermediate state in the transport cycle.
  Science, 330, 635-641.
PDB code: 3org
20049483 L.Wellhauser, C.D'Antonio, and C.E.Bear (2010).
ClC transporters: discoveries and challenges in defining the mechanisms underlying function and regulation of ClC-5.
  Pflugers Arch, 460, 543-557.  
20530571 N.A.Braun, B.Morgan, T.P.Dick, and B.Schwappach (2010).
The yeast CLC protein counteracts vesicular acidification during iron starvation.
  J Cell Sci, 123, 2342-2350.  
20204338 R.J.Naftalin (2010).
Reassessment of models of facilitated transport and cotransport.
  J Membr Biol, 234, 75.  
18957376 A.De Angeli, D.Monachello, G.Ephritikhine, J.M.Frachisse, S.Thomine, F.Gambale, and H.Barbier-Brygoo (2009).
Review. CLC-mediated anion transport in plant cells.
  Philos Trans R Soc Lond B Biol Sci, 364, 195-201.  
19019917 A.J.Smith, A.A.Reed, N.Y.Loh, R.V.Thakker, and J.D.Lippiat (2009).
Characterization of Dent's disease mutations of CLC-5 reveals a correlation between functional and cell biological consequences and protein structure.
  Am J Physiol Renal Physiol, 296, F390-F397.  
  19364886 A.K.Alekov, and C.Fahlke (2009).
Channel-like slippage modes in the human anion/proton exchanger ClC-4.
  J Gen Physiol, 133, 485-496.  
19898476 A.Picollo, M.Malvezzi, J.C.Houtman, and A.Accardi (2009).
Basis of substrate binding and conservation of selectivity in the CLC family of channels and transporters.
  Nat Struct Mol Biol, 16, 1294-1301.  
18977737 C.Miller, and W.Nguitragool (2009).
A provisional transport mechanism for a chloride channel-type Cl-/H+ exchanger.
  Philos Trans R Soc Lond B Biol Sci, 364, 175-180.  
19339978 D.C.Gadsby (2009).
Ion channels versus ion pumps: the principal difference, in principle.
  Nat Rev Mol Cell Biol, 10, 344-352.  
19580750 D.Wang, and G.A.Voth (2009).
Proton transport pathway in the ClC Cl-/H+ antiporter.
  Biophys J, 97, 121-131.  
19261613 E.Y.Bergsdorf, A.A.Zdebik, and T.J.Jentsch (2009).
Residues important for nitrate/proton coupling in plant and mammalian CLC transporters.
  J Biol Chem, 284, 11184-11193.  
19207039 F.S.Lamb, J.G.Moreland, and F.J.Miller (2009).
Electrophysiology of reactive oxygen production in signaling endosomes.
  Antioxid Redox Signal, 11, 1335-1347.  
  19139174 H.H.Lim, and C.Miller (2009).
Intracellular proton-transfer mutants in a CLC Cl-/H+ exchanger.
  J Gen Physiol, 133, 131-138.
PDB codes: 3ejy 3ejz
18957380 J.Lísal, and M.Maduke (2009).
Review. Proton-coupled gating in chloride channels.
  Philos Trans R Soc Lond B Biol Sci, 364, 181-187.  
19745816 S.M.Elvington, C.W.Liu, and M.C.Maduke (2009).
Substrate-driven conformational changes in ClC-ec1 observed by fluorine NMR.
  EMBO J, 28, 3090-3102.  
18853181 V.Plans, G.Rickheit, and T.J.Jentsch (2009).
Physiological roles of CLC Cl(-)/H (+) exchangers in renal proximal tubules.
  Pflugers Arch, 458, 23-37.  
  18591423 G.Zifarelli, A.R.Murgia, P.Soliani, and M.Pusch (2008).
Intracellular proton regulation of ClC-0.
  J Gen Physiol, 132, 185-198.  
18678918 H.Jayaram, A.Accardi, F.Wu, C.Williams, and C.Miller (2008).
Ion permeation through a Cl--selective channel designed from a CLC Cl-/H+ exchanger.
  Proc Natl Acad Sci U S A, 105, 11194-11199.
PDB code: 3det
18641661 J.Lísal, and M.Maduke (2008).
The ClC-0 chloride channel is a 'broken' Cl-/H+ antiporter.
  Nat Struct Mol Biol, 15, 805-810.  
  18378800 M.L.Jennings, and J.Cui (2008).
Chloride homeostasis in Saccharomyces cerevisiae: high affinity influx, V-ATPase-dependent sequestration, and identification of a candidate Cl- sensor.
  J Gen Physiol, 131, 379-391.  
18058905 Z.Kuang, A.Liu, and T.L.Beck (2008).
TransPath: a computational method for locating ion transit pathways through membrane proteins.
  Proteins, 71, 1349-1359.  
17376158 J.von der Fecht-Bartenbach, M.Bogner, M.Krebs, Y.D.Stierhof, K.Schumacher, and U.Ludewig (2007).
Function of the anion transporter AtCLC-d in the trans-Golgi network.
  Plant J, 50, 466-474.  
  17389248 M.Walden, A.Accardi, F.Wu, C.Xu, C.Williams, and C.Miller (2007).
Uncoupling and turnover in a Cl-/H+ exchange transporter.
  J Gen Physiol, 129, 317-329.  
17534424 S.Ignoul, J.Simaels, D.Hermans, W.Annaert, and J.Eggermont (2007).
Human ClC-6 is a late endosomal glycoprotein that associates with detergent-resistant lipid domains.
  PLoS ONE, 2, e474.  
18093952 W.Nguitragool, and C.Miller (2007).
Inaugural Article: CLC Cl /H+ transporters constrained by covalent cross-linking.
  Proc Natl Acad Sci U S A, 104, 20659-20665.  
17410581 Z.Kuang, U.Mahankali, and T.L.Beck (2007).
Proton pathways and H+/Cl- stoichiometry in bacterial chloride transporters.
  Proteins, 68, 26-33.  
16878138 A.De Angeli, D.Monachello, G.Ephritikhine, J.M.Frachisse, S.Thomine, F.Gambale, and H.Barbier-Brygoo (2006).
The nitrate/proton antiporter AtCLCa mediates nitrate accumulation in plant vacuoles.
  Nature, 442, 939-942.  
16554809 C.Miller (2006).
ClC chloride channels viewed through a transporter lens.
  Nature, 440, 484-489.  
17115052 E.A.Bykova, X.D.Zhang, T.Y.Chen, and J.Zheng (2006).
Large movement in the C terminus of CLC-0 chloride channel during slow gating.
  Nat Struct Mol Biol, 13, 1115-1119.  
16878141 J.I.Schroeder (2006).
Physiology: nitrate at the ion exchange.
  Nature, 442, 877-878.  
16814540 R.Dutzler (2006).
The ClC family of chloride channels and transporters.
  Curr Opin Struct Biol, 16, 439-446.  
16914964 S.Sile, C.G.Vanoye, and A.L.George (2006).
Molecular physiology of renal ClC chloride channels/transporters.
  Curr Opin Nephrol Hypertens, 15, 511-516.  
  16567465 X.D.Zhang, Y.Li, W.P.Yu, and T.Y.Chen (2006).
Roles of K149, G352, and H401 in the channel functions of ClC-0: testing the predictions from theoretical calculations.
  J Gen Physiol, 127, 435-447.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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