Understanding Nucleoside Monophosphate Kinases: The Role of Enzymes in Energy Transfer

so far in our discussion on enzymes we focused on two types of enzymes we discussed proteases and carbonic

anhydrase --is now we're going to focus on a third type of enzyme found our body known as nucleoside monophosphate kinase

or simply and MP kinases now nmp kinases catalyze the transfer of a Fuss Forel group from some type of nucleoside

triphosphate for example ATP molecule onto another molecule namely the nucleoside monophosphate or nmp and to

this and to basically show what that means let's take a look at the following general chemical equation so we have two

reactants two substrate molecules and this reaction is catalyzed by some type of an MP kinase now in this particular

case because i'm using ATP as a specific nucleotide triphosphate the name of the nfe kinase molecule is adenylate kinase

and so adenylate kinase will catalyze the transfer of this purple terminal force Forel group from the ATP molecule

onto this region of the nucleoside monophosphate and we ultimately form the nucleoside diphosphate and the adenosine

diphosphate so this losses of phosphorus and this gains of a spoil group so in this reaction we have two substrate

molecules the ATP as well as the end MP now what do we have to know about nucleoside monophosphate time ASIS well

there are three things that you have to keep in mind about these enzymes and let's begin by discussing the first one

so an MP kinase molecules for example adenylate kinase or guanylate kinase so guanylate kinase basically catalyzes the

transfer of the phosphoryl groups from gtp on to some type of an MP so if we study the three-dimensional structure of

all these different types of and P kindnesses for example these two we're going to see a region that is conserved

it remains the same when we go from one molecule one enzyme one kinase to another kinase and this is the region

shown here so if we begin at the beginning of the polypeptide chain this is where we're gonna be and so we

basically move along the polypeptide chain and this is the first beta sheet that we come across and then we continue

moving and we move through this coloured loop and this coloured loop is known as the P loop structure and we'll see why

we call it the P loop in just a moment then we have the first alpha helix and then we continue we have the second beta

sheets then we continue we have the second alpha helix we continue we have the third beta sheet and so forth and we

continue all the way until we get to the end now what's so special about this colored loop

well this loop is known as the peel and the reason we called the P loop is because this polypeptide section is the

section that contains the amino acids that are responsible for actually binding to and interacting with the ATP

molecule and more specifically it will interact with the negative charges on this triphosphate group of that ATP

molecule and if we study the sequence of nucleotides among the different types of nmp kinases on that P loop this is what

we're going to see so it's relatively conserved so we have a glycine bolotov followed by four X's where the X

basically describes some type of arbitrary amino acid and then we have glycine and lysine now what we see

happen is the NH groups that are basically found on the backbone of this P loop will interact will form hydrogen

bonds with the negative charges of these oxygen on the triphosphate and like and likewise if we have any residue that

contains a positive charge so if we have basic residues such as lysine and our Janene Fallon appeal ooh those will also

form interactions with this triphosphate and so it's the P loop structure found inside this domain of the enzyme that

actually is responsible for binding and interacting with this substrate molecule the triphosphate group of that

particular nucleoside triphosphate so in the case of adenylate kinase it's the triphosphate group of the ATP that the P

loop actually interacts with now the second thing you have to know about nucleoside monophosphate kinase is is

they use a specific mechanism of enzyme catalysis known as metal ion catalysis now we actually discussed metal ion

catalysis previously when we discuss proteases and carbonic anhydrase --is but the major difference between that

type of metal ion catalysis and the metal ion catalysis that takes place within an MP kinases is here that metal

ion doesn't actually interact with the active sites enzyme but it interacts with the substrate molecule itself so we

see that n MP kinases require the presence of a metal atom such as magnesium or a manganese and so we have

to have some type of diving divalent metal atom by valence simply means it has a charge of positive 2 so to

demonstrate why this is so let's suppose we have the ATP molecule as our substrate so this is the ATP so we have

our adenine base 2 shirt component and the triphosphate group and so the reason we need that magnesium or the manganese

the reason we need a divalent positive metal ion is because the positive metal ion will interact with the negative

charges on the oxygen molecule on the ax oxygen atoms of a triphosphate and by interacting with the oxygen they will

create a conformational change in that substrate molecule and by inducing that conformational

change they will create a shape they will give the ATP molecule a shape that is appropriate for the shape of that

active side so we need the divalent metal atom to basically give the ATP substrate molecule the appropriate shape

so that it can actually enter and bind to the active side of that nucleoside monophosphate kinase so before the ntp

substrate in this particular ATP in this particular case ATP can bind onto the active side of that kinase the NCP must

bind to a divalent metal atom such as magnesium or manganese so what happens is two oxygens on this triphosphate

interact with our magnesium atom so we have the alpha oxygens we have the beta oxygens these two and then we have these

are the gamma oxygens because this is the alpha phosphorus atom the beta phosphorus atom and the gamma phosphorus

atom and so the magnesium can either interact with the alpha and beta oxygens or with the alpha and gamma oxygens or

as in this particular case the beta and gamma oxygens and each time the magnesium interacts with two different

oxygens that creates its own unique its own unique conformation and so different enzymes require a different interaction

because different enzymes require a different shape and in this particular case for adenylate kinase the magnesium

must interact with these two oxygen atoms to give the proper orientation and shape to basically be able to bind into

the active side of that and MP kinase now not only with the magnesium interact with two oxygen atoms of the

triphosphate of the substrate but the magnesium will also be stabilized by four different water molecules and that

will give a stabilizing octahedral arrangement so these are the two oxygens that

come from the triphosphate group and these are the four oxygens and so the partially negative oxygen of these water

molecules will form bonds coordinate bonds with this magnesium atom and this will stabilize that structure and create

a conformational change that will basically bridge that active site structure and the structure of this

particular substrate molecules so the magnesium will interact with two oxygen atoms on the ATP molecule as well as

four water molecules and the interaction will hold that substrate in a well-defined conformation a well-defined

shape that is suitable for the shape of the active site found in that enzyme and so ultimately we see that the metal ion

serves as a bridge between the substrate molecule and the enzyme without that metal ion the substrate would not be

able to bind into the active site because it would not have the proper orientation and so ultimately it's the

ATP metal ion complex that is the substrate of that active site because only when the metal atom binds with the

ATP molecule will the interactions between the active site and the substrate be perfect and very

stabilizing interactions now the final thing that I'd like to mention about n MP kinases is that they not only use the

metal ion catalysis but they also use catalysis by proximity and orientation and to see what we mean by that let's

take a look at the structure of our and MP kinase namely the adenylate kinase and so this is the domain that we

basically spoke of earlier and this is our P loop so what happens is once the magnesium binds onto the ATP molecule

that creates a correct conformation and then the ATP magnesium complex can move in

to the active side of this molecule and bind with that P loop structure and once it binds with the P loop structure that

creates a localized change in conformation and that localized chain creates a more extensive change in the

entire structure of that particular enzyme and in particular if we examine the purple region this is known as the

lid domain of the kinase as it binds on to the P loop this basically closes down just like a lip closes on top of a can

and so in the same way this lid basically closes down and it induces a conformational change that traps that

ATP molecule in the proper orientation so that now the other substrate the nmp can bind onto the active side and it

binds in such a way so that the terminal phase for the ATP is in close proximity and in the proper orientation with

respect to this and MP molecule and that's exactly why what we mean by catalysis by proximity and orientation

what the active side does is it creates it induces this change that brings these two substrate molecules in close

proximity and arranges them in a proper orientation which basically decreases the energy of transition and it

basically catalyzed the transfer of this phosphoryl groups of ATP onto the end MP in addition because these two substrate

molecules are essentially trapped in the active site nothing else can actually come in because this entire lid domain

closes off and so other molecules for example water molecules will not be able to enter the active site and that means

the water molecules will not be able to hydrolyze this section and so that will decrease the likelihood that any

competing react we'll take place because remember the problem is if we don't have the nmp

kinase and these two molecules are in the presence of water water will be very likely to actually hydrolyze and break

this bond here and what that means is instead of transferring the force for Allah and that force for group will be

transferred on to the water molecule and so what the enzyme does is it utilizes catalysis by proximity it closes off the

active site and keeps away the water molecules and so no competing reactions can actually take place so once again as

the ATP magnesium substrate binds to the P loop as it as this complex binds unto this P loop here it induces a local

conformational change in the section of that causes a more extensive change and so the lid domain essentially closes off

and then the binding of that second substrate the and MP molecule instead the active site creates additional

changes and this causes catalysis by proximity so these changes in conformation hold the two substrates

close together so in close proximity and gives them the proper orientation that basically promotes the transfer of the

phosphoric so it decreases the energy of the transition state decreases the activation energy barrier and prevents

any competing reactions for actually taking place so nmp kinases do not only utilize the metal ion catalysis

mechanism but they also utilize catalysis by proximity and orientation