Protein/PDB/Reference

Orientation

Endophilin-A1 BAR domain

PDB:1zww

Journal of Molecular Biology Volume 351, Issue 3 , 19 August 2005, Pages 653-661 Crystal Structure of the Endophilin-A1 BAR Domain Winfried Weissenhorn Link

Concave side of the BAR domain interacts with membranes, thus either inducing or sensing curvature. The distance between the distal ends of the endo-BAR dimer is 114 Ang (between residue 173A and 173B) and the concave surface could fit a curved membrane with a diameter of 300Ang if the disordered part of the additional domain extends towards the side of the endo-BAR domain. The endophilin-A1 BAR domain contains a conserved N-terminal region, which is mostly disordered in the crystal structure and its N-terminal ends at residue 27 point in the direction of the distal ends of the dimer.

Amphiphysin bar domain from drosophila

PDB:1uru

B.J.Peter, H.M.Kent, I.G.Mills, Y.Vallis, P.J.Butler, P.R.Evans, H.T.McMahon. (2004). BAR domains as sensors of membrane curvature: the amphiphysin BAR structure. Science, 303, 495-499. Link

Lys161 + Lys163 on the disordered loop between helices 2 and 3 and Lys137 + Arg140 on the concave face have been shown to reduce the binding to liposomes and inhibit the tubulation of liposomes.

endophilin bar domain

PDB:1x03

m.masuda, s.takeda, m.sone, t.ohki, h.mori, y.kamioka, n.mochizuki. (2006). Endophilin BAR domain drives membrane curvature by two newly identified structure-based mechanisms EMBO J, 25, 2889-2897.Link

The helix 0 of endophilin BAR domain is disordered in the wild type and has been suggested to be helical only when the domain binds to liposomes. The helix 0 displays the hydrophobic branch of T14, V17 and V21 on one side, while K12, K16 and E19 on the other side. The helix 0 is connecting with the Helix I by a flexible linker G23-G24-A25. Truncation of the helix 0 results in loss of liposome binding activity and consequently abolishes the tubulation. In contrast, all the helix 0-containing mutants, including the A66D, showed intact liposome binding activity irrespective of their tubulation or vesiculation activities indicating that the helix 0 in the endA1-BAR is critical for liposome binding.

Protein/PDB/Reference

Orientation

Remarks

Cys2 activator-binding domain of protein kinase C-delta

PDB:1ptq          1ptr

Gongyi Zhang, Marcelo G. Kazanietz, Peter M. Blumberg and James H. Hurley Volume 81, Issue 6 , 16 June 1995, Pages 917-924 Link

Orientation from OPM database

Three residues involved in binding phorbol ester are Gly-253, Leu-251 and Thr 242. Phorbol ester accepts a hydrogen bond from the main-chain amide of Gly-253 and also donates a hydrogen-bond to the main-chain carbonyl of Gly-253. It also accepts a hydrogen bond from the main-chain amide of Thr-242 and donates a bifurcated hydrogen bond to the main-chain carbonyls of Thr-242 and Leu-251, acting as an interstrand bridge.

protein kinasE C-g phorbol-binding domain

PDB:1tbn

Biochemistry, 36 (35), 10709 -10717, 1997 Robert X. Xu, Tadeucz Pawelczyk, Tai-He Xia, and Stephen C. Brown Link

Orientation from OPM database

Residues S111, T113, F114, L122, Y123, and G124 are involved in phorbol binding where as residues around the phorbol-binding site (106-111, 113-116, L121, 124-127, 130) interact with lipid micelles.

Protein/PDB/Reference

Orientation

Remarks

C2 domain from novel protein kinase C epsilon

PDB:1gmi

W.F.Ochoa, J.Garcia-Garcia, I.Fita, S.Corbalan-Garcia, N.Verdaguer, J.C.Gomez-Fernandez. (2001). Structure of the C2 domain from novel protein kinase Cepsilon. A membrane binding model for Ca(2+)-independent C2 domains. J Mol Biol, 311, 837-849. Link

Orientation from OPM database

For C2 domain of PKC-epsilon, loop 1 remains mostly on the surface of the membrane while loop 3, with Ile89 and Tyr91 fully exposed at the apex of the loop, inserts into the membrane. Interactions of loop 1 is contributed by positively charged residues, in particular Arg26 and Arg32, and by the bulky side-chains, in particular Trp23, penetrating to the inner core of the membrane. The side-chain of His85, inside the pocket defined by loops 1 and 3, is situated in the vicinity of the membrane- charged groups. Asp86 and Asp92, require the presence of divalent ions for their interaction with negatively charged membrane groups. Other residues, like Arg50 in the connection between strands ?3-?4, also participate in electrostatic interactions.

Phosphoinositide-specific phospholipasE C-delta1 from rat complexed with lanthanum

PDB:1djg

L.O.Essen et al. (1997). A ternary metal binding site in the C2 domain of phosphoinositide-specific phospholipase C-delta1.. Biochemistry, 36, 2753-2762. Link

In PKC-delta1, basic residues nearby, Lys 646 and Lys 648 on CBR1 and Lys 712 on CBR3, assist the binding of negatively charged phospholipids in the calcium binding region. Beta-strand beta-3 of the PLC-delta1 C2 domain runs almost parallel to the membrane and might employ Arg 665 and Arg 670 for interaction with phospholipid head groups. Other basic regions on the membrane-facing part of the PLC-delta1 C2 domain that might affect interaction with the phospholipid membrane are formed by Lys 646, Lys 648, Lys 655, Lys 712, and Lys 738.

Protein/PDB/Reference

Orientation

Remarks

Epsin enth bound to ins(1,4,5)p3

PDB:1h0a

M.G.Ford, I.G.Mills, B.J.Peter, Y.Vallis, G.J.Praefcke, P.R.Evans, H.T.McMahon. (2002). Curvature of clathrin-coated pits driven by epsin. Nature, 419, 361-366.Link

Orientation from OPM database

Amphipathic helix 0 of the ENTH domain binds Ins(1,4,5)P3. Mutants of residue L6 to E, Q, H and W shows less binding to liposomes, implying a role for helix 0 in membrane interactions. L6Q with its hydrophobic and polar component binds to liposomes but does not tubulate them. L6H tubulates liposomes, whereas L6W with its larger hydrophobic surface leads to extensive tubulation and vesiculation. The hydrophobic outer surface of helix 0 is crucial for the induction of membrane curvature.

Protein/PDB/Reference

Orientation

Remarks

radixin ferm domain complexed with inositol-(1,4,5)-triphosphate

PDB:1gc6

Structural basis of the membrane-targeting and unmasking mechanisms of the radixin FERM domain Keisuke Hamada1, Toshiyuki Shimizu1, Takeshi Matsui2, 3, Shoichiro Tsukita2, Sachiko Tsukita2, 4 and Toshio Hakoshima1 The EMBO Journal (2000) 19, 4449–4462.Link

Orientation from OPM database

Three lysines (Lys60 and Lys63 from subdomain A and Lys278 from subdomain C) and one asparagine (Asn62 from subdomain A) contact the three phosphate groups of IP3. These contacts suggest stereochemically cooperative interactions that enhance specificity. In the orientation of the bound IP3 molecule, the 1-phosphate group is exposed to solvent, which enables PIP2 to reach the binding site from the membrane surface. The proposed orientation of the radixin FERM domain associated with the membrane enables the positively charged molecular surface between subdomains A and C to interact with the negatively charged membrane surface. This relatively flat molecular surface seems to maximize the interactions with the membrane surface.

Protein/PDB/Reference

Orientation

Remarks

vhs and fyve tandem domains of hrs, a protein involved in membrane trafficking and signal transduction

PDB:1dvp

Y.Mao, A.Nickitenko, X.Duan, T.E.Lloyd, M.N.Wu, H.Bellen, F.A.Quiocho. (2000). Crystal structure of the VHS and FYVE tandem domains of Hrs, a protein involved in membrane trafficking and signal transduction. Cell, 100, 447-456. Link

Orientation from OPM database

In PI(3)P-binding mode of FYVE domain of hrs, a large portion of the PI(3)P is buried. The mode of PI(3)P binding places the 3-phosphate close to His-179 and the 1-phosphate close to His-178 and Arg-208. The sidechain of Arg-176 is juxtaposed between the 1- and 3-phosphates. Arg-181 and its symmetry-related counterpart may be involved in interacting with the inositol hydroxyl groups. Thus, the phosphate and hydroxyl groups of PI(3)P are assumed to be extensively involved in charge-coupling and hydrogen-bonding interactions with the conserved basic residues.

Protein/PDB/Reference

Orientation

Remarks

Ph domain from bruton's tyrosine kinase in complex with inositol 1,3,4,5-tetrakisphosphate

PDB:1b55

E.Baraldi, K.D.Carugo, M.Hyvönen, P.L.Surdo, A.M.Riley, B.V.Potter, R.O'Brien, J.E.Ladbury, M.Saraste. (1999). Structure of the PH domain from Bruton's tyrosine kinase in complex with inositol 1,3,4,5-tetrakisphosphate. Structure, 7, 449-460.Link

The amino acids involved in the interaction with Ins(1,3,4,5)P4 are located in the b1-b2 and b3-b4 loops. The ligand interacts with the PH domain directly, forming many hydrogen bonds. Key residues coordinating the ligand are K12 and R28, which interact with the 3- and 4-phosphates, and the residues on the b1-b2 loop, which are involved in the interaction with the 5-phosphate. K12 contacts both 3- and 4-phosphates with two and one hydrogen bonds, respectively. The side-chain of R28 contacts the 3-phosphate with two hydrogen bonds. In addition, the 4-phosphate directly interacts with the side-chain of Y39 and the backbone NH group of Q15, and with the backbone carbonyl group of K53 and the side-chain of K17. The 3-phosphate contacts the sidechain of K53 of strand b4 via a water molecule.

pleckstrin homology domain from phospholipasE C delta in complex with inositol trisphosphate

PDB:1mai

K.M.Ferguson et al. (1995). Structure of the high affinity complex of inositol trisphosphate with a phospholipase C pleckstrin homology domain.. Cell, 83, 1037-1046. Link

Orientation from OPM database

The amino acids that interact with Ins(1 ,4,5)P3 are mostly in the b1/b2 and b3/b4 loops of PLC-delta-PH. Direct hydrogen bonds are seen between the bound Ins(l,4,5)P3 and seven amino acids. Two lysine side chains, K30 and K57, clamp the 4- and 5-phosphate groups of Ins(1 ,4,5)P3 in the binding pocket, each hydrogen bonding with both phosphates. Through additional interactions with the side chains of R40, S55, and the backbone NH of R56, plus a water-mediated hydrogen bond with the backbone carbony1 of E54, the 5-phosphate of Ins(1 ,4,5)P3 is completely buried. The 4-phosphate forms hydrogen bonds directly to the side chains of K30, K32, and K57, and via a water molecule to the backbone carbonyl of T107.

Crystal structure of the dh/ph fragment of murine dbs in complex with the placental isoform of human cdc42

PDB:1kz7               1kzg

K.L.Rossman et al. (2002). A crystallographic view of interactions between Dbs and Cdc42: PH domain-assisted guanine nucleotide exchange.. EMBO J, 21, 1315-1326. Link

Residues that appear necessary for binding to lipid head groups include Arg861 (at the base of beta-2), Lys874 (within beta-3), Lys892 and Gln893 (within beta-4), and Tyr924 (within beta-7). Similar to other PH domains, residues within the beta-1/beta-2 loop are also expected to be required for binding phospholipids; however, this region is disordered within Dbs and Cdc42.

Protein/PDB/Reference

Orientation

Remarks

vam7p px domain

PDB:1kmd

Solution Structure of the Vam7p PX Domain Jun Lu, Jesus Garcia, Irina Dulubova, Thomas C. Südhof, and Josep Rizo Biochemistry; 2002; 41(19) pp 5956 - 5962Link

Orientation from OPM database

Five basic side chains (R41, K47, K67, R77, and R88) point toward the ligand. The Vam7p R41 and R88 side chains are conserved in many PX domains, and are involved in coordinating the 3-phosphate and the 4- and 5-hydroxyl groups of PtdIns(3)P, respectively. K47 and K67 side chains of Vam7p interact with the 1-phosphate group of PtdIns(3)P. In addition to R41, the highly conserved K40R41Y42 sequence contains an aromatic residue that is shown to be critical for PtdIns(3)P binding to the Vam7p PX domain.

Crystal structure of cisk-px domain

PDB:1xtn               1xte

Y.Xing, D.Liu, R.Zhang, A.Joachimiak, Z.Songyang, W.Xu. (2004). Structural basis of membrane targeting by the Phox homology domain of cytokine-independent survival kinase (CISK-PX). J Biol Chem, 279, 30662-30669.Link

Orientation from OPM database

In addition to binding to PIs, CISK-PX may insert a hydrophobic part of the PPII/alpha-2 loop (Ile-77 and Phe-78) into the membrane to assist with the orientation during membrane targeting and to provide additional interactions with the membrane lipid bilayer. The backbone conformation of residues 76-79 in the PPII/ alpha-2 loop is very different upon membrane insertion. Side-chain flipping of the hydrophobic residues in the PPII/ alpha-2 loop seems favored by the binding of PIs and could be a common structural feature coupled to the membrane targeting of the domain.