4.5 Panel data analysis
4.5.2 Model fit comparison
Las fosfatidilinositol-fosfato-quinasas (PIPK) de tipo I y II presentan una organización similar: un dominio central con actividad quinasa (DQ), y regiones N- y C-terminales menos conservadas e implicadas en la interacción con otras proteínas (Fig. 2A). El DQ de las PIP5KI posee ~80% de identidad de secuencia entre las isoformas de una misma subfamilia (Sun, 2013), y tiene residuos altamente conservados implicados en la interacción con ATP, GTP ó Mg2+ y el reconocimiento específico del sustrato lipídico (Doughman et al., 2003a; Kunz et al., 2000; Rao et al., 1998).
1.2.1. El dominio quinasa y la especificidad de sustrato.
El DQ comprende la región central y constituye la mayor parte de la secuencia de las PIPK. En este dominio tiene lugar la transferencia del grupo γ-fosfato de alta energía del ATP ó el GTP al grupo 5-hidroxilo del PI4P para generar el PIP2. Dentro del DQ se encuentra una secuencia de unos 22 aa equivalente al denominado lazo de activación (LA) de las proteínas quinasas (PK) (Cox et al., 1994) (Fig. 2), implicada en el reconocimiento específico del sustrato, y una región poco conservada entre las PIP5KI de unos 53 aa conocida como inserto (Ins) que se encuentra desordenada en la estructura de PIP4KIIβ (Rao et al., 1998). Tres residuos altamente conservados dentro del DQ de las PIPK (K138, D266 y D350 en PIP5KIβ) parecen jugar un papel muy importante en la reacción de transferencia del grupo fosfato catalizada por estas enzimas de acuerdo con la estructura de PIP4KIIβ (Rao et al., 1998). La K138 interactuaría, en presencia de iones Mg2+ con los grupos α y β fosfatos del ATP que no se transfieren, el D266 actuaría como una base débil en la catálisis y el D350 interactuaría con los iones Mg2+ del complejo Mg2+-ATP.
Introducción
29
Los determinantes moleculares de la especificidad de sustrato en las PIP5KI y PIP4KII fueron identificados inicialmente por Kunz y colaboradores (Kunz et al., 2002; Kunz et al., 2000) como una secuencia de 25 aa, hacia la región C-terminal del DQ. Esta secuencia en la estructura de las PIP4KII se corresponde con el llamado lazo de activación (LA) de las proteínas quinasas (Rao et al., 1998). Aunque el LA se encuentra desordenado en la estructura cristalográfica de PIP4KIIβ (Rao et al., 1998), juega un importante papel en la función de estas quinasas. Su secuencia se encuentra muy conservada dentro de cada subfamilia de PIPK, pero varía de una subfamilia a otra lo cual sugirió que el LA estaría implicado en el reconocimiento y/o el acomodo del sustrato en el sitio catalítico (Fig. 2B).
Figura 2. Organización en dominios de las PIPK. (A) Representación esquemática de PIP5KIβ y PIP4KIIβ humanas. Los números indican los límites de cada dominio así como la longitud de la secuencia. El DQ presenta gran similitud entre las isoformas de una misma subfamilia. Dentro de este dominio se encuentra el inserto (Ins) y el lazo de activación (LA). (B) Alineamiento de secuencias del LA de las PIPK de tipo I y II humanas. Los residuos totalmente conservados entre todas las PIPK se muestran en azul; en verde y rosa se indican los conservados en cada tipo de proteínas.
Mediante la construcción de quinasas quiméricas intercambiando los LA de las PIP5KI y PIP4KII, Kunz y colaboradores (Kunz et al., 2000) demostraron que la PIP5KIβ que tenía el LA de la PIP4KIIβ cambiaba su especificidad de sustrato y se comportaba como una PIP4KIIβ localizándose además en el citosol celular. Por el contrario, la PIP4KIIβ que tenía el LA de la PIP5KIβ se localizaba en la membrana plasmática y se comportaba como una PIP5KIβ. Mutaciones en el LA de PIP5KIβ y PIP4KIIβ demostraron que la especificidad de sustrato y la localización en la membrana dependía del aminoácido PIP5KIβ(E362) y PIP4KIIβ(A381), respectivamente (Kunz et al., 2002).
A! PIP5KIβ" N-t! DQ! Ins! C-t! 18" 279" 332" 355" 376"399" 540 aa" LA! PIP4KIIβ" DQ! Ins! 291" N-t! 351" 410 416 aa" C-t! 22" LA! 373" 395" B! 355" 376"
and are situated so their amide groups interact with
the triphosphate backbone of ATP (Knighton et al.,
1991a, 1991b; Rao et al., 1998; Taylor et al., 1992,
1993).
Based on the structural homology between the cat-
alytic domains of PIPKIIβ and protein kinases, as well as
the defined structures of protein kinases bound to ATP,
a model of PIPKIIβ bound to ATP was constructed.
This PIPKIIβ · ATP structural model revealed that the
catalytic site of PIPKIIβ accommodates ATP so that
the γ -phosphate of ATP is spatially oriented toward
the putative membrane association interface of the
PIPKIIβ, consistent for PIP kinase function. To assess if
this model would accommodate an endogenous PIP
substrate, PI5P, the preferred substrate for PIPKIIβ
was docked onto the PIPKIIβ · ATP structural model
using the structure of the PKI inhibitor peptide
bound to PKA · ATP as a guide. By this approach,
the PI5P was docked such that the 4-hydroxyl of
the myo-inositol ring is positioned for nucleophilic
substitution of the γ -phosphate of ATP (Knighton
et al., 1991a, 1991b; Rao et al., 1998; Taylor et al., 1992,
1993).
Consistent with the PIP kinase preference of PIP
as substrate, there are four basic residues in the PIP
kinase (R134, K218, R224, and K239) that are clustered
adjacent to the 5-phosphate of PI5P in the structural
representation of PIPKIIβ · ATP · PI5P (Figure 5). Basic
residues analogous to K218 and R224 are invariant in
all known PIP kinases, residues analogous to R134 are
conserved in most PIP kinases, and K239 analogs are
conserved in PIPKI and PIPKII subfamilies, but not in
PIPKIII. While the modeled PI5P binding site contains
a putative 5-phosphate binding pocket, the remainder
of the binding site is open and shallow. The openness
of the PIP binding site suggests an explanation for
the multiple substrate specificities of the PIP kinases;
in this structure, the PIP substrates are free to rotate
such that the 3-, 4-, or 5-phosphate could occupy the
highly basic and conserved phosphate-binding pocket.
In addition, the substrate-binding site is sufficiently
shallow allowing for movement of the 2-hydroxyl,
as there do not appear to be any interactions with
the 2-hydroxyl that would hinder this movement.
The structural model of the PIPKIIβ · ATP · PI5P is
internally consistent with the orientation of the ATP
binding site and the positioning of the PIPKIIβ on
membranes (Knighton et al., 1991a, 1991b; Rao et al.,
1998; Taylor et al., 1992, 1993) and as a result, appears
Figure 5
Structural representation of PIPKIIβ bound to PI5P
substrate and ATP. (A) Monomeric PIPKIIβ bound to substrate
and ATP is docked on a phospholipid interface. Some residues
have been removed from the PIPKIIβ structure to reveal the
binding pocket where ATP and PIP substrate bind. (B) Monomeric
PIPKIIβ bound to PIP substrate highlights the resolved residues
in the PIPKIIβ structure that mark the beginning and end of the
specificity loop. (C) The position of the specificity loop in the
PIPKIIβ structure as well as a sequence pileup of type I, II, and III
PIP kinase specificity loops are shown. The KK motif is important
for membrane targeting, while the glutamate of type I (E362) and
the alanine of type II (A381) PIP kinases is required for substrate
recognition.
to accommodate all major substrates of the PIP kinase
family.
The PIPKIIβ model, shown in Figure 5, does not
take into account key regions of the PIP kinase that
are disordered. Three regions within PIPKIIβ crystal
structure were unresolved including the N-terminal 33
residues, residues 304–342 from the highly variable
insert sequence that is found in the type I and II PIP
kinases, and of particular interest, a loop from 373–390
that spans the PIP binding site and coincides with
the specificity loop of protein kinases as illustrated in
Figure 5. The position of this loop suggests a key role
in generation of PI4,5P2
by the PIP kinases and these
regions of PIPKIIβ are likely to be critical to PIP kinase
function (Rao et al., 1998).
SIGNALING SPECIFICITY IS DEFINED
BY THE SPECIFICITY LOOP
The specificity loop of protein kinases is positioned
to modulate kinase activity as well as interactions
with and specificity toward protein substrates. The
22
J. N. Heck et al.
Critical Reviews in Biochemistry and Molecular Biology Downloaded from informahealthcare.com by Universidad Autonoma on 10/30/14
For personal use only.
and are situated so their amide groups interact with
the triphosphate backbone of ATP (Knighton et al.,
1991a, 1991b; Rao et al., 1998; Taylor et al., 1992,
1993).
Based on the structural homology between the cat-
alytic domains of PIPKIIβ and protein kinases, as well as
the defined structures of protein kinases bound to ATP,
a model of PIPKIIβ bound to ATP was constructed.
This PIPKIIβ · ATP structural model revealed that the
catalytic site of PIPKIIβ accommodates ATP so that
the γ -phosphate of ATP is spatially oriented toward
the putative membrane association interface of the
PIPKIIβ, consistent for PIP kinase function. To assess if
this model would accommodate an endogenous PIP
substrate, PI5P, the preferred substrate for PIPKIIβ
was docked onto the PIPKIIβ · ATP structural model
using the structure of the PKI inhibitor peptide
bound to PKA · ATP as a guide. By this approach,
the PI5P was docked such that the 4-hydroxyl of
the myo-inositol ring is positioned for nucleophilic
substitution of the γ -phosphate of ATP (Knighton
et al., 1991a, 1991b; Rao et al., 1998; Taylor et al., 1992,
1993).
Consistent with the PIP kinase preference of PIP
as substrate, there are four basic residues in the PIP
kinase (R134, K218, R224, and K239) that are clustered
adjacent to the 5-phosphate of PI5P in the structural
representation of PIPKIIβ · ATP · PI5P (Figure 5). Basic
residues analogous to K218 and R224 are invariant in
all known PIP kinases, residues analogous to R134 are
conserved in most PIP kinases, and K239 analogs are
conserved in PIPKI and PIPKII subfamilies, but not in
PIPKIII. While the modeled PI5P binding site contains
a putative 5-phosphate binding pocket, the remainder
of the binding site is open and shallow. The openness
of the PIP binding site suggests an explanation for
the multiple substrate specificities of the PIP kinases;
in this structure, the PIP substrates are free to rotate
such that the 3-, 4-, or 5-phosphate could occupy the
highly basic and conserved phosphate-binding pocket.
In addition, the substrate-binding site is sufficiently
shallow allowing for movement of the 2-hydroxyl,
as there do not appear to be any interactions with
the 2-hydroxyl that would hinder this movement.
The structural model of the PIPKIIβ · ATP · PI5P is
internally consistent with the orientation of the ATP
binding site and the positioning of the PIPKIIβ on
membranes (Knighton et al., 1991a, 1991b; Rao et al.,
1998; Taylor et al., 1992, 1993) and as a result, appears
Figure 5
Structural representation of PIPKIIβ bound to PI5P
substrate and ATP. (A) Monomeric PIPKIIβ bound to substrate
and ATP is docked on a phospholipid interface. Some residues
have been removed from the PIPKIIβ structure to reveal the
binding pocket where ATP and PIP substrate bind. (B) Monomeric
PIPKIIβ bound to PIP substrate highlights the resolved residues
in the PIPKIIβ structure that mark the beginning and end of the
specificity loop. (C) The position of the specificity loop in the
PIPKIIβ structure as well as a sequence pileup of type I, II, and III
PIP kinase specificity loops are shown. The KK motif is important
for membrane targeting, while the glutamate of type I (E362) and
the alanine of type II (A381) PIP kinases is required for substrate
recognition.
to accommodate all major substrates of the PIP kinase
family.
The PIPKIIβ model, shown in Figure 5, does not
take into account key regions of the PIP kinase that
are disordered. Three regions within PIPKIIβ crystal
structure were unresolved including the N-terminal 33
residues, residues 304–342 from the highly variable
insert sequence that is found in the type I and II PIP
kinases, and of particular interest, a loop from 373–390
that spans the PIP binding site and coincides with
the specificity loop of protein kinases as illustrated in
Figure 5. The position of this loop suggests a key role
in generation of PI4,5P2
by the PIP kinases and these
regions of PIPKIIβ are likely to be critical to PIP kinase
function (Rao et al., 1998).
SIGNALING SPECIFICITY IS DEFINED
BY THE SPECIFICITY LOOP
The specificity loop of protein kinases is positioned
to modulate kinase activity as well as interactions
with and specificity toward protein substrates. The
22
J. N. Heck et al.
Critical Reviews in Biochemistry and Molecular Biology Downloaded from informahealthcare.com by Universidad Autonoma on 10/30/14
For personal use only.
hPIP5KIα" hPIP5KIβ" hPIP5Kγ" hPIP4KIIα" hPIP4KIIβ" hPIP4KIIγ" Lazo de Activación! F! L! F! V! M! I! L! L! L! L! L! L! V! V! V! E! E! E! H! H! H! H! H! H! V! V! V! H! Y! H! D! D! D! G! G! G! D! D! D! T! T! T! R! R! R! F! F! L! A! A! A! H! H! Y! D! D! D! H! H! H! A! G! A! A!G! G!A! A! A! I! I! I!