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Fig. 7.5 A portion of an enzyme (histidine decarboxylase) viewed as the network of atoms of
amino acid residues linked together through both covalent and non-covalent bonds. D ¼ aspartic
acid; E ¼ glutamic acid; I ¼ isoleucine; R ¼ arginine; S ¼ serine. Solid lines and the ribbon
indicate covalent bonds, and dotted lines and empty space indicate non-covalent interactions
(Downloaded from the web site of Jon D. Robertus, University of Texas, http://research.cm.
utexas.edu/jrobertus )
As an example of an enzyme viewed as an atomic network, let us examine
histidine decarboxylase (HDC), a portion of which is shown in Fig. 7.5 .This
enzyme catalyzes the removal of carbon dioxide from amino acid histidine:
HDC
Hisitidine
!
Histamine
þ
CO 2
(7.15)
HDC exists as a trimer (i.e., three identical units combined to form a functional
unit). Each unit consists of a linear chain of 662 amino acids (molecular weight
¼
74,017 Daltons). Each of the three active sites is located at the interface between
two HDC molecules. Each HDC molecule can exist in two conformational states
denoted as T and R . Low pH and high histidine concentration favor the R confor-
mation which has a high affinity for histidine, while high pH favors the T confor-
mation which has a low affinity for histidine:
H þ $
HDC( T
Þþ
HDC( R
Þ
(7.16)
One active site of HDC in the R form is shown in Fig. 7.5 . The active site is partially
formed by helix B from a neighboringmolecule. At acidic pH, two protons are trapped
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