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