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PDBsum entry 1cii
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Transmembrane protein
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PDB id
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1cii
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Contents |
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* Residue conservation analysis
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Nature
385:461-464
(1997)
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PubMed id:
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Crystal structure of colicin Ia.
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M.Wiener,
D.Freymann,
P.Ghosh,
R.M.Stroud.
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ABSTRACT
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The ion-channel forming colicins A, B, E1, Ia, Ib and N all kill bacterial cells
selectively by co-opting bacterial active-transport pathways and forming
voltage-gated ion conducting channels across the plasma membrane of the target
bacterium. The crystal structure of colicin Ia reveals a molecule 210 A long
with three distinct functional domains arranged along a backbone of two
extraordinarily long alpha-helices. A central domain at the bend of the
hairpin-like structure mediates specific recognition and binding to an
outer-membrane receptor. A second domain mediates translocation across the outer
membrane via the TonB transport pathway; the TonB-box recognition element of
colicin Ia is on one side of three 80 A-long helices arranged as a helical
sheet. A third domain is made up of 10 alpha-helices which form a
voltage-activated and voltage-gated ion conducting channel across the plasma
membrane of the target cell. The two 160 A-long alpha-helices that link the
receptor-binding domain to the other domains enable the colicin Ia molecule to
span the periplasmic space and contact both the outer and plasma membranes
simultaneously during function.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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K.D.Krewulak,
and
H.J.Vogel
(2011).
TonB or not TonB: is that the question?
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Biochem Cell Biol,
89,
87-97.
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L.Prieto,
and
T.Lazaridis
(2011).
Computational studies of colicin insertion into membranes: the closed state.
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Proteins,
79,
126-141.
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C.Kleanthous
(2010).
Translocator hunt comes full Cir-Col.
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Mol Microbiol,
75,
529-533.
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C.Kleanthous
(2010).
Swimming against the tide: progress and challenges in our understanding of colicin translocation.
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Nat Rev Microbiol,
8,
843-848.
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K.S.Jakes,
and
A.Finkelstein
(2010).
The colicin Ia receptor, Cir, is also the translocator for colicin Ia.
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Mol Microbiol,
75,
567-578.
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N.Noinaj,
M.Guillier,
T.J.Barnard,
and
S.K.Buchanan
(2010).
TonB-dependent transporters: regulation, structure, and function.
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Annu Rev Microbiol,
64,
43-60.
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S.L.Greig,
M.Radjainia,
and
A.K.Mitra
(2009).
Oligomeric structure of colicin ia channel in lipid bilayer membranes.
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J Biol Chem,
284,
16126-16134.
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T.Arnold,
K.Zeth,
and
D.Linke
(2009).
Structure and Function of Colicin S4, a Colicin with a Duplicated Receptor-binding Domain.
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J Biol Chem,
284,
6403-6413.
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PDB code:
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A.C.Doxey,
M.D.Lynch,
K.M.Müller,
E.M.Meiering,
and
B.J.McConkey
(2008).
Insights into the evolutionary origins of clostridial neurotoxins from analysis of the Clostridium botulinum strain A neurotoxin gene cluster.
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BMC Evol Biol,
8,
316.
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A.Valeva,
I.Siegel,
M.Wylenzek,
T.M.Wassenaar,
S.Weis,
N.Heinz,
R.Schmitt,
C.Fischer,
R.Reinartz,
S.Bhakdi,
and
I.Walev
(2008).
Putative identification of an amphipathic alpha-helical sequence in hemolysin of Escherichia coli (HlyA) involved in transmembrane pore formation.
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Biol Chem,
389,
1201-1207.
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G.Anderluh,
and
J.H.Lakey
(2008).
Disparate proteins use similar architectures to damage membranes.
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Trends Biochem Sci,
33,
482-490.
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J.Hullmann,
S.I.Patzer,
C.Römer,
K.Hantke,
and
V.Braun
(2008).
Periplasmic chaperone FkpA is essential for imported colicin M toxicity.
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Mol Microbiol,
69,
926-937.
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K.Zeth,
C.Römer,
S.I.Patzer,
and
V.Braun
(2008).
Crystal structure of colicin M, a novel phosphatase specifically imported by Escherichia coli.
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J Biol Chem,
283,
25324-25331.
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PDB codes:
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P.K.Kienker,
K.S.Jakes,
and
A.Finkelstein
(2008).
Identification of channel-lining amino acid residues in the hydrophobic segment of colicin Ia.
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J Gen Physiol,
132,
693-707.
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Y.Zhang,
M.N.Vankemmelbeke,
L.E.Holland,
D.C.Walker,
R.James,
and
C.N.Penfold
(2008).
Investigating early events in receptor binding and translocation of colicin E9 using synchronized cell killing and proteolytic cleavage.
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J Bacteriol,
190,
4342-4350.
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D.Duché
(2007).
Colicin E2 is still in contact with its receptor and import machinery when its nuclease domain enters the cytoplasm.
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J Bacteriol,
189,
4217-4222.
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D.Walker,
K.Mosbahi,
M.Vankemmelbeke,
R.James,
and
C.Kleanthous
(2007).
The role of electrostatics in colicin nuclease domain translocation into bacterial cells.
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J Biol Chem,
282,
31389-31397.
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E.Cascales,
S.K.Buchanan,
D.Duché,
C.Kleanthous,
R.Lloubès,
K.Postle,
M.Riley,
S.Slatin,
and
D.Cavard
(2007).
Colicin biology.
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Microbiol Mol Biol Rev,
71,
158-229.
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M.Masi,
P.Vuong,
M.Humbard,
K.Malone,
and
R.Misra
(2007).
Initial steps of colicin E1 import across the outer membrane of Escherichia coli.
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J Bacteriol,
189,
2667-2676.
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O.Sharma,
E.Yamashita,
M.V.Zhalnina,
S.D.Zakharov,
K.A.Datsenko,
B.L.Wanner,
and
W.A.Cramer
(2007).
Structure of the complex of the colicin E2 R-domain and its BtuB receptor. The outer membrane colicin translocon.
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J Biol Chem,
282,
23163-23170.
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PDB code:
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O.Sharma,
and
W.A.Cramer
(2007).
Minimum length requirement of the flexible N-terminal translocation subdomain of colicin E3.
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J Bacteriol,
189,
363-368.
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S.K.Buchanan,
P.Lukacik,
S.Grizot,
R.Ghirlando,
M.M.Ali,
T.J.Barnard,
K.S.Jakes,
P.K.Kienker,
and
L.Esser
(2007).
Structure of colicin I receptor bound to the R-domain of colicin Ia: implications for protein import.
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EMBO J,
26,
2594-2604.
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PDB codes:
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T.C.Pham,
R.W.Kriwacki,
and
A.L.Parrill
(2007).
Peptide design and structural characterization of a GPCR loop mimetic.
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Biopolymers,
86,
298-310.
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PDB code:
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D.Duché,
A.Frenkian,
V.Prima,
and
R.Lloubès
(2006).
Release of immunity protein requires functional endonuclease colicin import machinery.
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J Bacteriol,
188,
8593-8600.
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D.White,
A.A.Musse,
J.Wang,
E.London,
and
A.R.Merrill
(2006).
Toward elucidating the membrane topology of helix two of the colicin E1 channel domain.
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J Biol Chem,
281,
32375-32384.
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S.J.Tilley,
and
H.R.Saibil
(2006).
The mechanism of pore formation by bacterial toxins.
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Curr Opin Struct Biol,
16,
230-236.
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T.H.Davis,
and
R.M.Stroud
(2006).
Profile of Robert M. Stroud.
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Proc Natl Acad Sci U S A,
103,
5256-5258.
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Z.Wu,
K.S.Jakes,
B.S.Samelson-Jones,
B.Lai,
G.Zhao,
E.London,
and
A.Finkelstein
(2006).
Protein translocation by bacterial toxin channels: a comparison of diphtheria toxin and colicin Ia.
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Biophys J,
91,
3249-3256.
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C.Q.Morales,
J.Posada,
E.Macneale,
D.Franklin,
I.Rivas,
M.Bravo,
J.Minsavage,
R.E.Stall,
and
M.C.Whalen
(2005).
Functional analysis of the early chlorosis factor gene.
|
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Mol Plant Microbe Interact,
18,
477-486.
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K.Möbius,
A.Savitsky,
C.Wegener,
M.Plato,
M.Fuchs,
A.Schnegg,
A.A.Dubinskii,
Y.A.Grishin,
I.A.Grigor'ev,
M.Kühn,
D.Duché,
H.Zimmermann,
and
H.J.Steinhoff
(2005).
Combining high-field EPR with site-directed spin labeling reveals unique information on proteins in action.
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Magn Reson Chem,
43,
S4.
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N.G.Housden,
S.R.Loftus,
G.R.Moore,
R.James,
and
C.Kleanthous
(2005).
Cell entry mechanism of enzymatic bacterial colicins: porin recruitment and the thermodynamics of receptor binding.
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Proc Natl Acad Sci U S A,
102,
13849-13854.
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N.Umadevi,
S.Kumar,
and
N.Narayana
(2005).
Crystallization and preliminary X-ray diffraction studies of the WW4 domain of the Nedd4-2 ubiquitin-protein ligase.
|
| |
Acta Crystallogr Sect F Struct Biol Cryst Commun,
61,
1084-1086.
|
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S.L.Hands,
L.E.Holland,
M.Vankemmelbeke,
L.Fraser,
C.J.Macdonald,
G.R.Moore,
R.James,
and
C.N.Penfold
(2005).
Interactions of TolB with the translocation domain of colicin E9 require an extended TolB box.
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J Bacteriol,
187,
6733-6741.
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Z.Shi,
K.F.Chak,
and
H.S.Yuan
(2005).
Identification of an essential cleavage site in ColE7 required for import and killing of cells.
|
| |
J Biol Chem,
280,
24663-24668.
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G.Anderluh,
I.Gökçe,
and
J.H.Lakey
(2004).
A natively unfolded toxin domain uses its receptor as a folding template.
|
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J Biol Chem,
279,
22002-22009.
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J.L.Hilsenbeck,
H.Park,
G.Chen,
B.Youn,
K.Postle,
and
C.Kang
(2004).
Crystal structure of the cytotoxic bacterial protein colicin B at 2.5 A resolution.
|
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Mol Microbiol,
51,
711-720.
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PDB code:
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S.D.Zakharov,
V.Y.Eroukova,
T.I.Rokitskaya,
M.V.Zhalnina,
O.Sharma,
P.J.Loll,
H.I.Zgurskaya,
Y.N.Antonenko,
and
W.A.Cramer
(2004).
Colicin occlusion of OmpF and TolC channels: outer membrane translocons for colicin import.
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Biophys J,
87,
3901-3911.
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S.L.Slatin,
D.Duché,
P.K.Kienker,
and
D.Baty
(2004).
Gating movements of colicin A and colicin Ia are different.
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J Membr Biol,
202,
73-83.
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A.A.Musse,
and
A.R.Merrill
(2003).
The molecular basis for the pH-activation mechanism in the channel-forming bacterial colicin E1.
|
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J Biol Chem,
278,
24491-24499.
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A.K.Mohanty,
C.M.Bishop,
T.C.Bishop,
W.C.Wimley,
and
M.C.Wiener
(2003).
Enzymatic E-colicins bind to their target receptor BtuB by presentation of a small binding epitope on a coiled-coil scaffold.
|
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J Biol Chem,
278,
40953-40958.
|
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G.Anderluh,
Q.Hong,
R.Boetzel,
C.MacDonald,
G.R.Moore,
R.Virden,
and
J.H.Lakey
(2003).
Concerted folding and binding of a flexible colicin domain to its periplasmic receptor TolA.
|
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J Biol Chem,
278,
21860-21868.
|
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G.Kurisu,
S.D.Zakharov,
M.V.Zhalnina,
S.Bano,
V.Y.Eroukova,
T.I.Rokitskaya,
Y.N.Antonenko,
M.C.Wiener,
and
W.A.Cramer
(2003).
The structure of BtuB with bound colicin E3 R-domain implies a translocon.
|
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Nat Struct Biol,
10,
948-954.
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PDB code:
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P.K.Kienker,
K.S.Jakes,
R.O.Blaustein,
C.Miller,
and
A.Finkelstein
(2003).
Sizing the protein translocation pathway of colicin Ia channels.
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J Gen Physiol,
122,
161-176.
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D.Cavard
(2002).
Assembly of colicin A in the outer membrane of producing Escherichia coli cells requires both phospholipase A and one porin, but phospholipase A is sufficient for secretion.
|
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J Bacteriol,
184,
3723-3733.
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M.D.Purdy,
P.Ge,
J.Chen,
P.R.Selvin,
and
M.C.Wiener
(2002).
Thiol-reactive lanthanide chelates for phasing protein X-ray diffraction data.
|
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Acta Crystallogr D Biol Crystallogr,
58,
1111-1117.
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S.D.Zakharov,
T.I.Rokitskaya,
V.L.Shapovalov,
Y.N.Antonenko,
and
W.A.Cramer
(2002).
Tuning the membrane surface potential for efficient toxin import.
|
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Proc Natl Acad Sci U S A,
99,
8654-8659.
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S.L.Slatin,
A.Nardi,
K.S.Jakes,
D.Baty,
and
D.Duché
(2002).
Translocation of a functional protein by a voltage-dependent ion channel.
|
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Proc Natl Acad Sci U S A,
99,
1286-1291.
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C.Kleanthous,
and
D.Walker
(2001).
Immunity proteins: enzyme inhibitors that avoid the active site.
|
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Trends Biochem Sci,
26,
624-631.
|
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J.Walshaw,
and
D.N.Woolfson
(2001).
Open-and-shut cases in coiled-coil assembly: alpha-sheets and alpha-cylinders.
|
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Protein Sci,
10,
668-673.
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K.C.Usher,
E.Ozkan,
K.H.Gardner,
and
J.Deisenhofer
(2001).
The plug domain of FepA, a TonB-dependent transport protein from Escherichia coli, binds its siderophore in the absence of the transmembrane barrel domain.
|
| |
Proc Natl Acad Sci U S A,
98,
10676-10681.
|
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K.S.Jakes
(2001).
The importance of being cleaved: an essential step in killing by enzymatic colicins.
|
| |
Mol Cell,
8,
4-6.
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L.Journet,
E.Bouveret,
A.Rigal,
R.Lloubes,
C.Lazdunski,
and
H.Bénédetti
(2001).
Import of colicins across the outer membrane of Escherichia coli involves multiple protein interactions in the periplasm.
|
| |
Mol Microbiol,
42,
331-344.
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M.Lindeberg,
and
W.A.Cramer
(2001).
Identification of specific residues in colicin E1 involved in immunity protein recognition.
|
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J Bacteriol,
183,
2132-2136.
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O.Carugo
(2001).
Detection of breaking points in helices linking separate domains.
|
| |
Proteins,
42,
390-398.
|
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O.I.Loseva,
E.I.Tiktopulo,
V.D.Vasiliev,
A.D.Nikulin,
A.P.Dobritsa,
and
S.A.Potekhin
(2001).
Structure of Cry3A delta-endotoxin within phospholipid membranes.
|
| |
Biochemistry,
40,
14143-14151.
|
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S.Soelaiman,
K.Jakes,
N.Wu,
C.Li,
and
M.Shoham
(2001).
Crystal structure of colicin E3: implications for cell entry and ribosome inactivation.
|
| |
Mol Cell,
8,
1053-1062.
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PDB code:
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A.J.Wallace,
T.J.Stillman,
A.Atkins,
S.J.Jamieson,
P.A.Bullough,
J.Green,
and
P.J.Artymiuk
(2000).
E. coli hemolysin E (HlyE, ClyA, SheA): X-ray crystal structure of the toxin and observation of membrane pores by electron microscopy.
|
| |
Cell,
100,
265-276.
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PDB code:
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L.G.Dover,
L.J.Evans,
S.L.Fridd,
G.Bainbridge,
E.M.Raggett,
and
J.H.Lakey
(2000).
Colicin pore-forming domains bind to Escherichia coli trimeric porins.
|
| |
Biochemistry,
39,
8632-8637.
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M.C.Wiener
(2000).
Bacterial export takes its Tol.
|
| |
Structure,
8,
R171-R175.
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P.K.Kienker,
K.S.Jakes,
and
A.Finkelstein
(2000).
Protein translocation across planar bilayers by the colicin Ia channel-forming domain: where will it end?
|
| |
J Gen Physiol,
116,
587-598.
|
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S.Carr,
D.Walker,
R.James,
C.Kleanthous,
and
A.M.Hemmings
(2000).
Crystallization of the cytotoxic domain of a ribosome-inactivating colicin in complex with its immunity protein.
|
| |
Acta Crystallogr D Biol Crystallogr,
56,
1630-1633.
|
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A.J.Pommer,
U.C.Kühlmann,
A.Cooper,
A.M.Hemmings,
G.R.Moore,
R.James,
and
C.Kleanthous
(1999).
Homing in on the role of transition metals in the HNH motif of colicin endonucleases.
|
| |
J Biol Chem,
274,
27153-27160.
|
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H.Zhang,
and
N.V.Grishin
(1999).
The alpha-subunit of protein prenyltransferases is a member of the tetratricopeptide repeat family.
|
| |
Protein Sci,
8,
1658-1667.
|
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Filamentous phage infection: crystal structure of g3p in complex with its coreceptor, the C-terminal domain of TolA.
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| |
Structure,
7,
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PDB code:
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K.J.Oh,
L.Senzel,
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Translocation of the catalytic domain of diphtheria toxin across planar phospholipid bilayers by its own T domain.
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Proc Natl Acad Sci U S A,
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Structure in the channel forming domain of colicin E1 bound to membranes: the 402-424 sequence.
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Adventures in membrane protein topology. A study of the membrane-bound state of colicin E1.
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J Biol Chem,
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T.P.Ko,
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The crystal structure of the DNase domain of colicin E7 in complex with its inhibitor Im7 protein.
|
| |
Structure,
7,
91.
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|
PDB code:
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U.C.Kühlmann,
C.Kleanthous,
R.James,
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Preliminary X-ray crystallographic analysis of the complex between the DNAase domain of colicin E9 and its cognate immunity protein.
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Acta Crystallogr D Biol Crystallogr,
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C.J.Lazdunski,
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Colicin import into Escherichia coli cells.
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J Bacteriol,
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C.Kleanthous,
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Immunity proteins and their specificity for endonuclease colicins: telling right from wrong in protein-protein recognition.
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Mol Microbiol,
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D.B.Lacy,
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Curr Opin Struct Biol,
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and
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(1998).
Crystal structure of botulinum neurotoxin type A and implications for toxicity.
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| |
Nat Struct Biol,
5,
898-902.
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PDB code:
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|
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E.Bouveret,
A.Rigal,
C.Lazdunski,
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Distinct regions of the colicin A translocation domain are involved in the interaction with TolA and TolB proteins upon import into Escherichia coli.
|
| |
Mol Microbiol,
27,
143-157.
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L.J.Evans,
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Discovery of critical Tol A-binding residues in the bactericidal toxin colicin N: a biophysical approach.
|
| |
Mol Microbiol,
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H.Pilsl,
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(1998).
The tip of the hydrophobic hairpin of colicin U is dispensable for colicin U activity but is important for interaction with the immunity protein.
|
| |
J Bacteriol,
180,
4111-4115.
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I.R.Vetter,
M.W.Parker,
A.D.Tucker,
J.H.Lakey,
F.Pattus,
and
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(1998).
Crystal structure of a colicin N fragment suggests a model for toxicity.
|
| |
Structure,
6,
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PDB code:
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J.A.Mindell
(1998).
Swimming through the hydrophobic sea: new insights in protein translocation.
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| |
Proc Natl Acad Sci U S A,
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K.F.Chak,
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(1998).
Change of thermal stability of colicin E7 triggered by acidic pH suggests the existence of unfolded intermediate during the membrane-translocation phase.
|
| |
Proteins,
32,
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K.S.Jakes,
P.K.Kienker,
S.L.Slatin,
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Translocation of inserted foreign epitopes by a channel-forming protein.
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Proc Natl Acad Sci U S A,
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M.A.Riley
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Molecular mechanisms of bacteriocin evolution.
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K.Reiling,
M.Wiener,
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Ion-channel-forming colicins.
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Curr Opin Struct Biol,
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Membrane-bound state of the colicin E1 channel domain as an extended two-dimensional helical array.
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Proc Natl Acad Sci U S A,
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Membrane insertion: The strategies of toxins (review).
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Mol Membr Biol,
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D.Smajs,
H.Pilsl,
and
V.Braun
(1997).
Colicin U, a novel colicin produced by Shigella boydii.
|
| |
J Bacteriol,
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E.Gouaux
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Channel-forming toxins: tales of transformation.
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The long and short of colicin action: the molecular basis for the biological activity of channel-forming colicins.
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| |
Structure,
5,
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L.Riechmann,
and
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(1997).
The C-terminal domain of TolA is the coreceptor for filamentous phage infection of E. coli.
|
| |
Cell,
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M.A.Payne,
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Z.Cao,
S.B.Foster,
S.M.Newton,
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(1997).
Biphasic binding kinetics between FepA and its ligands.
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| |
J Biol Chem,
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M.W.Parker
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More than one way to make a hole.
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Nat Struct Biol,
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W.A.Cramer,
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(1997).
A mechanism for toxin insertion into membranes is suggested by the crystal structure of the channel-forming domain of colicin E1.
|
| |
Structure,
5,
443-458.
|
|
|
PDB code:
|
|
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|
|
|
|
|
P.K.Kienker,
X.Qiu,
S.L.Slatin,
A.Finkelstein,
and
K.S.Jakes
(1997).
Transmembrane insertion of the colicin Ia hydrophobic hairpin.
|
| |
J Membr Biol,
157,
27-37.
|
|
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|
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from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
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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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|
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