| SRP-nucleotide/magnesium interactions | ||||||
| Escherichia coli (+2 from T. aquaticus) | Thermus aquaticus | Acidianus ambivalens | H p21 Ras | |||
| HYPOTHESIZED | ||||||
| Ffh | FtsY | 4.5 S RNA | Ffh | Ffh | ||
| ALLEADV | 37-43 | 234-240 | 37-43 | 35-44 | ||
| G1 | 101-116 | 294-309 | 100-115 | 100-115 | 5-20 | |
| G2 | 137-143 | 330-340 | 135-145 | 135-145 | 32-40 | |
| G3 | 186-195 | 378-387 | 183-192 | 183-192 | 53-62 | |
| G4 | 244-251 | 441-449 | 240-248 | 242-250 | 112-119 | |
| G5 "closing loop" | 274-280 | 472-478 | 271-279 | 273-279 | 144-146 | |
| P-loop | 107-114 | 299-306 | 105-112 | 105-112 | 10-17 | |
| Conserved P-loop residues | GKTT308…D382…NK447…D449 | GKTT113…D187…NK246…D248 | GKSA18…D57…NK117…D119 | |||
| DARRG loop | Gly249-Gly253 | |||||
| NG domain | 197-497 | |||||
| N domain | 197-280 | |||||
| GTPase domain | 291-495 | |||||
| M domain | A39 contacts with M domain: stacks with Arg398, H-bonds Arg401; C62 recognized by M domain; Ala377 contacts G48; Asn380 contacts A47; protein contacts also with G48 + G49 | 337-355 (signal sequence binding), 378-401 (arginine rich segment) | ||||
| Switch I (switch regions are involved in the protein-protein interactions)(adjacent to G2) | 135,137 | |||||
| Switch II (linked via a5 to N-domain) | Arg191,194,197 | 59,60,61,75 | ||||
| a-b-a I-box insertion | 333-377 | Thr136 stabilzes the I-box | ||||
| Bind RNA | Arg384, Arg387, Lys390, also Gly391, Gly393 | |||||
| Mg2+ | Asp189, Thr114 | Asp330, Thr331 stabilizes interaction in I-box | (hypoth.) Asp187, (in Mg/GDP) Thr112 | (hypoth.) Tyr137 or Asp135 | b+g phopshates of GTP, Thr35, Ser16 | |
| GTP-binding (hypoth.) | Gln108/Gly109, Thr114, Asp250 | Asp449, Thr446, Gly385, Arg333, Asp330, Phe332 | in GMPPNP, Gln107, Thr112, Asp248 bind | |||
| GTP:a+b or b+g (?) phosphates | Gln144 (as hypoth.) + Asp187 interact with a + b phosphates, Lys111 | Lys16 e amino group | ||||
| GTP:g phosphate | Arg140, Arg193, Gln108/Gly109, Gly192 | Arg386 | (hypoth.) Arg138 stabilize this leaving group; Arg191 potentially stabilizes nucleopilic water molecule- "peptide-flip" or arginine finger, Gln107 of P-loop hypoth. open to contact this, Gly190 (hypoth.) H-bonds | Thr35 mc NH | ||
| GTP: g phosphate | Gly60 mc NH | |||||
| GTP: NH of C1 and NH2 of C2 of guanine | Asp119 side chain COO- | |||||
| GTP: O off C6 of guanine | Ala146 mc NH | |||||
| GTP: 2'-OH of ribose ring | Val29 mc O | |||||
| GTP: a phosphate | Ala18 mc NH | |||||
| GTP: b phosphate | Lys112/Thr113 | (hypoth.) Lys111 | ||||
| guanine base contact | (hypoth.) Asp248, (Mg/GDP) Ser273, Glu274, Lys246, (GDP) Thr114, Lys117, Lys246, Asp248 | |||||
| SR/SRP interface possible contacts | H-bonding Distance when overlayed on 1N2C: Val138, Tyr139, Arg140, Gln165, His195, Val196, Lys248; Other possible: Leu107, Gly108, Gly109, Gln153, Gly192, Arg193, Leu194, Asp197, Glu198, Met223, Thr224, Asp227, Arg254 | H-bonding Distance when overlayed on 1N2C: Arg333, Ala335, Gln339, Leu387, Gln388, Ser422; Other possible: Lys205, Glu208, Asn302, Gly303, Thr307, Thr308, Ala334, Ala336, Glu338, Trp343, Arg386, Thr 423, Asn426, Lys447, Gly450, Lys453, Glu475, Arg476 | ||||
| Other: | Mutations at Thr446Asn and Asp449Ala reduce GTP binding ability | Arg398 and Arg401 form a salt bridge with Glu386; the RNA binds on the salt bridge surface | Leu322, Ile365, Met369, Phe406 form part of hydrophobic core of M domain | AA Asp135 oriented to active site (like Asp330 EC FtsY) and no salt link with Arg191 | Gln61 involved in GTP hydrolysis | |
| P-loop stabilized by Asn302 H-bond with Gly385, Lys306 interacts with Asp382 + Thr383, Thr331 H-bonds mc O Ala358, mc O Ala358 H-bonds mc NH Gly357 | C62G is required for the protein/RNA interface | Leu320, Phe325, Leu326, Met329, Leu362, Phe402, Met409 contribute to hydrophobic groove | T112A mutant cannot hydrolyze GTP, the loss of the polar OH of Thr abolishes interaction with Asp187 sc and H-bond formed by Gln107 + Arg138 | G2 region interacts with GAP | ||
| Asp330 EC FtsY forms no salt link with Arg386 EC | Asp135-Arg191 form salt bridge, in apo Gly190 H-bonds Arg191 but in GDP structures orients to active site | Tyr137 stacks with Arg191 guanidinium moiety | GTP binding changes relative orientations of G2 and b3 | |||
| Leu106 and Leu192 may contribute to protein interaction surface | polar interactions of mainchains of Gly275, Glu280, Leu278, + Lys117 sc stabilize closing b-hairpin loop | Ser17 rotates away after GTP hydrolysis | ||||
| Leu106, Gln107, Leu192 or P-loop restrict its opening | Arg138 and Arg191 may be arginine fingers |