Figure 3.
FIG. 3. Structures of the small domains of enzymes from the
Acy1/M20 family. A, topology diagram for the lid domain in L.
delbrueckii PepV and the dimerization domains from both monomers
in Pseudomonas sp. CPG2. Subdomains 1 (gray) and 2 (white) of
PepV show apparent similarity. However, strands 8 and 12 are
only found in subdomain 1, and strands 3 and 7 are only found in
subdomain 2. The -sheet composed of the
latter two strands is also present in the dimerization domain of
CPG2. B, backbone trace superposition of subdomains 1 and 2 in
the lid domain of PepV (blue) and the two associated
dimerization domains in CPG2 (red and green). Known active site
residues in PepV are shown in a stick representation, from left
to right, Arg350, Asn217 (both carboxyl-terminal docking), and
His269 (transition state stabilization). Corresponding residues
from CPG2 are also shown. The enlargement above additionally
shows the corresponding residues in PepT. Arg288 from CPG2 (red)
and Arg280 from PepT (yellow) reside in the monomer, which
superimposes with subdomain 1 of PepV. Asn275 and His229 from
CPG2 (green) and His223 in PepT (purple) are recruited from the
opposite monomer which superimposes with subdomain 2 of PepV. In
the structure of CPG2, the side chain of His229 shows a [1]
rotation by about 90° relative to the other two structures
and coordinates an additional interdimeric zinc ion in the
protein crystal (not shown). C, multiple sequence alignment of
the small domains in the PepV enzymes from L. delbrueckii
(PEPV_LACDL) and Lactococcus lactis subsp. cremoris MG1363
(PEPV_LACLC) and from CPG2 (CBPG_PSES6), PepT (PEPT_SALTY), and
hAcy1 (ACY1_HUMAN). Subdomain 1 and 2 in the lid domain of PepV
are abbreviated sd1 and sd2, respectively. The alignment was
assembled using an available alignment of the two PepV enzymes
(15) and structure-based alignments of CPG2 to sd1 in L.
Delbrueckii (29) and CPG2 to PepT (24). The sequences of the
dimerization domain in hAcy1 and CPG2 were aligned manually.
Strands (s) and helices (h), as identified in the crystal
structures of PepV, CPG2, and PepT, are printed in red and blue,
respectively. Their numbering in sd1 and sd2 of L. delbrueckii
PepV is indicated in the corresponding colors above the aligned
sequences. Residues that interact with the bound transition
state analog Asp [PO[2]CH[2]]AlaOH in the
PepV structure are in yellow boxes. Greek letters indicate the
sites of rearrangement generated by the insertion of sd2 in the
sequence of sd1 and their sequel.
The above figure is reprinted
by permission from the ASBMB:
J Biol Chem
(2003,
278,
44496-44504)
copyright 2003.
-sheet composed of the
latter two strands is also present in the dimerization domain of
CPG2. B, backbone trace superposition of subdomains 1 and 2 in
the lid domain of PepV (blue) and the two associated
dimerization domains in CPG2 (red and green). Known active site
residues in PepV are shown in a stick representation, from left
to right, Arg350, Asn217 (both carboxyl-terminal docking), and
His269 (transition state stabilization). Corresponding residues
from CPG2 are also shown. The enlargement above additionally
shows the corresponding residues in PepT. Arg288 from CPG2 (red)
and Arg280 from PepT (yellow) reside in the monomer, which
superimposes with subdomain 1 of PepV. Asn275 and His229 from
CPG2 (green) and His223 in PepT (purple) are recruited from the
opposite monomer which superimposes with subdomain 2 of PepV. In
the structure of CPG2, the side chain of His229 shows a 
[1]
rotation by about 90° relative to the other two structures
and coordinates an additional interdimeric zinc ion in the
protein crystal (not shown). C, multiple sequence alignment of
the small domains in the PepV enzymes from L. delbrueckii
(PEPV_LACDL) and Lactococcus lactis subsp. cremoris MG1363
(PEPV_LACLC) and from CPG2 (CBPG_PSES6), PepT (PEPT_SALTY), and
hAcy1 (ACY1_HUMAN). Subdomain 1 and 2 in the lid domain of PepV
are abbreviated sd1 and sd2, respectively. The alignment was
assembled using an available alignment of the two PepV enzymes
(15) and structure-based alignments of CPG2 to sd1 in L.
Delbrueckii (29) and CPG2 to PepT (24). The sequences of the
dimerization domain in hAcy1 and CPG2 were aligned manually.
Strands (s) and helices (h), as identified in the crystal
structures of PepV, CPG2, and PepT, are printed in red and blue,
respectively. Their numbering in sd1 and sd2 of L. delbrueckii
PepV is indicated in the corresponding colors above the aligned
sequences. Residues that interact with the bound transition
state analog Asp 
[PO[2]CH[2]]AlaOH in the
PepV structure are in yellow boxes. Greek letters indicate the
sites of rearrangement generated by the insertion of sd2 in the
sequence of sd1 and their sequel.