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. 2014 Apr 10;53(17):2752–2767. doi: 10.1021/bi4014215

Table 1. Summary of Pre-Steady-State Kinetic Parameters and Functional Consequences of Various RB69pol Variants.

subdomain residue functional interactions with RB69pol amino acid substitution kpol (s–1) or kexo (s–1)a Kd (μM) kpol/Kd (μM–1 s–1) ref
palm Y391 HB to Y567, HB network at minor groove Y → A 155 980 1.5 × 10–1 (60)
      Y → F 312 90 3.5  
  D411 ligands to metal ion at pol site D → A inactive     (53)
  L415 HB to β-phosphate of the incoming dNTP L → A 11 3 3.7 (82)
      L → G 58 9 6.4  
      L → M 375 12 31.3  
  Y416 “sugar gate”, sterically blocks the 2′-OH group of an incoming rNTP Y → A 22 70 3.1 × 10–1 (54)
      Y → F 36 209 1.7 × 10–1  
  T587 HB to Y567, HB network at minor groove T → A 0.8 0.7 1.1 × 10–1 (60)
  Y619 HB to a water molecule, HB network at minor groove Y → F 14 NDb NDb (53)
  D621 HB to K706, HB network at the minor groove D → A 1.3 166 7.8 × 10–3 (53)
  T622 HB to D621, anchors the side chain of D623 T → A 0.2 NDb NDb (53)
  D623 ligands to metal ion at pol site D → A inactive     (53)
  S624 ligands to metal ion at pol site via a water molecule S → C 4.5 18 2.5 × 10–1 (53)
  E686 ligands to metal ion at pol site via a water molecule E → A 7 58 1.2 × 10–1 (53)
  K706 HB to D621 and base at position n – 2 of primer strand K → R 0.1 NDb NDb (53)
fingers R482 HB to γ-phosphate of the incoming dNTP R → A 0.2 1100 1.8 × 10–4 (58)
  K486 HB to γ-phosphate of dNTP via a water molecule K → A 3.3 71 4.6 × 10–2 (58)
  K560 HB to α,γ-phosphate of the incoming dNTP K → A 0.8 790 1.0 × 10–3 (58)
  L561 anchoring the templating base at the major groove L → A 101 50 2.0 (61)
  N564 HB to β-phosphate of dNTP N → A 23 250 9.2 × 10–2 (58)
  S565 anchoring the templating base S → G 157 48 3.3 (76)
  Y567 HB to Y391, HB network at minor groove Y → A 213 68 3.1 (60)
      Y → F 7.5 2400 3.1 × 10–3  
thumb Y708 HB to 3′-terminal phosphodiester bond (primer strand) Y → A 6 34 1.8 × 10–1 (53)
  E716 ligands to a third metal ion at the pol site E → A 200 NDb NDb (53)
exonuclease E116 ligands to metal ion at the exo site E → A 2.8 × 10–4a     (42)
  D222 ligands to metal ion at the exo site D → A inactivea     (42)
  K302 anchors the side chain of D327 K → A 1.0 × 10–2a     (42)
  Y323 HB to Q171, anchors the backbone of D327 Y → F 5.8 × 10–3a     (42)
  D327 ligands to metal ion at the exo site D → A inactivea     (42)
a

Indicates the excision rate for RB69pol variants.

b

Not determined.