Table 3.

Proposed roles of conserved residues in vertebrate PTP domainsa

Motif (residues in PTP1B)ConservationConservation in 3DProposed roles of residues
Motif 1
 40–46NXXKNR YMediumpTyr-recognition loop: restricts substrate specificity to pTyr (Asn44, coordinates Asn68 which links Arg257; Arg45, putative substrate binding site, electrostatic attraction of ligand; Tyr46, hydrophobic packing with phosphotyrosine residue of substrate)
 40–46NXX( K/R )NR Y
Motif 2
 53–59DXXRVX L LowConserved secondary structure (β1 sheet), surface exposed (Arg56, H bonds to Asp65; Ile57, hydrophobic core cluster [residues 57, 67, 69, 82, 98]; Leu59, hydrophobic core)
 53–59DXXR( V/I )X L
Motif 3
 65–69D Y INA MediumCore structure (Tyr66, coordinates Asn44 through hydrogen bonding; Ile67, hydrophobic core cluster [residues 57, 67, 69, 82, 98]; Asn68, H bonds with Arg257; Ala69, hydrophobic core cluster [residues 57, 67, 69, 82, 98])
 65–70D Y INA( N/S )
Motif 4
 82–87 IAX Q GP HighCore structure surrounding PTP loop (Ile82, hydrophobic core cluster [residues 57, 67, 69, 82, 98]; Ala83, packs or surrounds the PTP loop; Gln85, H bonds with highly buried water molecule; Gly86, packs or surrounds the PTP loop; Pro87, packs or surrounds PTP loop)
 81–87(F/Y)(I/V)AX Q GP
Motif 5
 91–100 TXXDFW XMXW MediumConserved secondary structure (α2 helix) (Asp94, contributes to conserved subdomain at the “back side”; Phe95, energetically favored T-stacking arrangement with invariant Trp96; Trp96, H bonds to backbone of invariant Tyr124; Met98, hydrophobic core cluster [residues 57, 67, 69, 82, 98]; Trp100, contributes to conserved subdomain at the back side)
 91–101 TXXDFW X( M/L/V )X(W)(E/Q)
Motif 6
 107–111IV M XTMediumHydrophobic core structure (Ile107, hydrophobic core structure packs with invariant Trp96; Val108, hydrophobic core structure packs with invariant Trp96; Met109, packs with invariant Trp125; Thr111, packs with PTP loop)
 107–111( I/L/V )(V/I) M XT
Motif 7
 120–126KCXX Y WP LowHydrophobic core structure (Lys120, interacts with Asp181 [ligand induced]; Tyr124, H bonds with His214, stabilizing T-stacking arrangement with Trp125; Trp125, favored T arrangement of aromatic ring system with Tyr124)
 120–126KCXX Y WP
Motif 8
 179–185 W PDXGX P LowWPD loop, surface exposed, movable, contains general acid (Trp179, center of movable WPD loop, mediating motion of loop; Pro180, H bonds to NH2 of Arg221, mediating motion of loop; Asp181, general acid catalyst; Gly183, energetically favorable in loop motion [acts as hinge]; Pro185, energetically favorable in loop movement [no backbone H bonding])
 176–185( Y/F )XX W PDXGX P
Motif 9
 210–223 PXXV HCS AG X GR T G HighPTP loop surrounding active site Cys where seven successive main-chain nitrogens coordinate three phosphate oxyanions (Pro210, structural hydrophobic core; His214, lowers pKa of Cys215; Cys215, nucleophile; Ser216, H bonds with Tyr46 stabilizing its interaction with substrate; Ala217, phosphotyrosine binding, nonpolar interaction with substrate phenyl; Gly218, phosphotyrosine binding; Gly220, phosphotyrosine binding; Arg221, H bonds with phosphate oxygens [transition-state stabilization]; Thr222, lower pKa of Cys215)
 210–223 PXX(V/I) HCS AG X GR ( T/S ) G
Motif 10
 262–269 QTXXQYXFLowThe Q loop: interaction with active site water molecule (Gln262, H bonds with scissile oxygen and active site water molecule; Gln266, H bonds with active site water molecule; Tyr267, defines α6′ helix structure; Phe269, defines α6′ helix structure)
 261–269( V/I/L )QTXXQYXF
  • a Motifs are numbered (M1 to M10) in order of appearance in the primary amino acid sequence alignment (Fig.1). Amino acids are numbered according to human PTP1B. Conserved residues were identified from our multiple-sequence alignment of 113 vertebrate PTP domains (available athttp://www.science.nononordisk.com /ptp), and domain D2 sequences were not used in these evaluations. Underscored bold letters represent invariant amino acids. Residues in bold letters are conserved in ≥90% of the sequences, and nonbold letters represent ≥80% conservation. Sequence conservation of each motif was calculated according to (i) amino acid identity (top sequence) and (ii) amino acid similarity (bottom sequence), where X represents any amino acid (Fig. 1). Consensus substitution groups are defined as follows: 1, DN; 2, EQ; 3, ST; 4, KR; 5, FYW; 6, LIVM. Residue conservation in the immediate three-dimensional (3D) surroundings was determined using Cα-regiovariation score analysis (Fig. 5).