Chemistry Reference
In-Depth Information
Substrate
Intermediate
Product
MR
O
-
O
O
+2
Mg
-
O
-
O
OH
O
-
H
OH
H
HO
O
O
O
MLE
O
-
O
O
O
-
O
O
Mg
+2
H
-
O
-
O
H
O
-
H
H
Enolase
Mg
+2
OPO
3
-2
OPO
3
-2
O
O
-
OPO
3
-2
O
Mg
+2
-
O
O
-
-
O
CH
2
OH
CH
2
OH
CH
2
H
FIGURE 10.10
The substrates, enolate anion intermediates, and products of the MR; MLE and enolase reactions.
(Adapted from
Gerlt,
(MR) and the muconate lactonising enzyme (MLE) of Pseudomonas putida and enolase, the fifth glycolytic enzyme
referred to above. The three-dimensional structures of all three enzymes are remarkably superposable
(
Figure 10.11
)
. All three have a two-domain structure, with the active sites located at the interface between flexible
loops in the capping domain and the C-terminal barrel domain. The capping domain is formed by segments from the
N- and C-terminii of the polypeptide chain, while the barrel domain is formed from ends of the
b
-strands of the
modified TIM-barrel domain. Whereas the TIM molecule (Figure 3.7) has [(
b
/
a
)
8
b
], the enolase superfamily
b
a
)
7
b
instead has [(
]. All members of the superfamily contain ligands (nearly always Glu or Asp) for the essential
Mg
2
þ
, located at the ends of the third, fourth, and fifth
/
b
-strands, which is illustrated for enolase in
Figure 10.12
.
In enolase, the substrate, 2-phosphoglycerate (2-PGA) is coordinated to two Mg
2
þ
ions, one of which is
liganded to the three conserved carboxylate residues (Asp 246, Glu 295, and Asp 320). Currently, more than 600
enolase sequences have been identified in the databases, and all are thought to be isofunctional, catalyzing the
conversion of 2-PGA to phosphoenolpyruvate. In the MLE subclass of the superfamily, at least three reactions are
known to be catalysed
in addition to the lactonisation of muconate, succinylbenzoate synthase, and L-Ala-D/L-
Glu epimerase reactions are observed within the
e
300 members. The MR subclass catalyses at least five
reactions, mandelate racemisation and 4 sugar dehydratases. As in the MLE subclass, of the
w
400 members
w
identified, only
50% of these are functionally assigned.
w
ENZYMES OF NUCLEIC ACID METABOLISM
Clearly, since DNA and RNA molecules are polynucleotides, composed of an invariant sugar-phosphate backbone,
it comes as no surprise that many of the enzymes involved in their metabolism require Mg
2
þ
ions. We do not
