Skip to main content

Table 1 Modular division and FCCRs connecting functional modules for the studied allosteric proteins

From: Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages

Protein (ID) Functional sites Modules Linking FCCRs
Hemoglobin (1bz0 A) ['15,48,49] Hem BS 1,2 65(1)(1-2)
  AB interface 1 66(1)(1-2)
    98(2)(2-1)
    128(1)(1-2)
Glycogen phosphorylase (1e1y A) ['50-53] Cat site 5 84(2)(2-3-4)
  AMP BS 1 93(1)(1-2-5)
  280 loop* 2 138(2)(2-1-4)
  Glycogen BS 2 161(2)(2-1)
  Tower helix* 2 490(1)(1-2-5)
    608(5)(5-2)
    648(5)(5-2-4)
Retinoic acid receptor RXR-alpha (1g5y A) Cat ligand BS 5 305(1)(1-5)
[54-56] AF2 helix* 4 309(5)(5-3-1)
  Coactivator BS 1,4 310(5)(5-1)
  AB interface 5 315(5)(5-1)
    371(1)(1-5)
Catabolite gene activator protein (1g6n A) DNA BS 3 63(2)(2-3)
[57-61] cAMP BS 2,1 64(2)(2-1-4)
    65(2)(2-1-3)
    69(1)(1-2-4)
Glutamate dehydrogenase (1hwz A) [62-64] Cat site 2 110(2) (2-1)
  NAPH BS DomA2 in 2 and DomA3 in 5,1 173(2) (2-5)
  GTP BS 5 211(2) (2-5-1)
  Glutamate BS DomA2 in 2 and DomA3 in 2 252(5) (5-1)
  Antenna* 7 347(1) (1-5)
Rhodopsine (1l9h A) [65-69] Retinal BS
G protein BS
1
2
301(1)(1-3-2)
Pyruvate kinase (1liu A) [70,71] Cat site DomA2 in 5 and DomA3 in 7 163(7)(7-4)
  FBP BS 3 337(6)(6-2-7)
  PEP BS 6,4 342(7)(7-6)
    361(6)(6-2-3)
    482(3)(3-6-2)
    488(3)(3-6-2)
Phosphofructokinase (1pfk A) [72-74] Cat site DomA1 in 2 and DomA2 in 3 126(2)(2-3)
  FBP BS DomA1 in 2 and DomA2 in 3 139(2)(2-3)
  MgADP BS 2,1 169(3)(3-2)
Tyrosine phosphatase 1B (1pty) [28] Cat site 2 81(2)(2-1)
  Phosphotyrosine BS 2,1 109(2)(2-1)
  Inhibitor BS 1 194(1)(1-2)
    199(1)(1-2)
    254(1)(1-2)
    257(2)(2-1)
Beta-trypsin (2ptc E) ['15,74,76-78] Cat site DomA2 in 3 and DomA1 in 3 29(3)(3-1)
  S1 site* 2,1 30(3)(3-1)
  Loop1* 2 138(1)(1-2-3)
  Loop2* 2 141(1)(1-3)
  Loop3* 2 189(2)(2-1)
    194(1)(1-3-2)
    212(3)(3-2)
    213(3)(3-1-2)
    228(2)(2-1-3)
G-protein s-alpha (1azs C) [19,26,29] Cat site DomC1 in 1,4 and DomC2 in 1 50(1)(1-4-3)
  GSP BS DomC1 in 1 and Dom C2 in 4 58(1)(1-4)
  Adenylyl cyclase BS*
-Binding only*
DomC2 in 4,1 and DomC1 in 1
2
173(4)(4-1-5)
201(4)(4-1-3)
  -Binding and transmission* DomC2 in 4,1 and DomC1 in 1  
G-protein beta-gamma (1tbg A) [19,79] PLC-beta2 BS* 4 61(4)(4-3-2)
  -Binding only* 3,2,4 63(4)(4-3-2)
  -Binding and transmission* 4 105(4)(4-3)
    150(3)(3-4)
    151(3)(3-4)
    190(3)(3-2)
    192(3)(3-2)
    234(2)(2-3)
    258(2)(2-1-3)
    289(2)(2-4)
    318(2)(2-4)
    320(2)(2-4)
Cytochrome P450eryF (1eup A) [32] Hem BS 2,6 102(6)(6-2-4)
  Andro1 BS 6 238(6)(6-3)
  Andro2 BS 3 349(2)(2-5-6)
  1. The functional site divisions into modules are indicated. *The information on these sites was extracted from the reference indicated in the first column. Dom denotes those functional sites divided into several domains according to the CATH database. The FCCRs linking functional modules are listed (the first number in parentheses represents the module to which the FCCR belongs and the numbers in the following parentheses are the modules it connects). BS, binding site; Cat, catalytic site. AB, chains A and B; AF2 helix, activation function 2 helix; FBP, fructose1,6-bisphosphate; PEP, phosphoenolpyruvate; PLC, phospholipase C.