Elizabeth E. Millard (1),
Aaron Downs (3) and David
Marcey (2)
© David Marcey, 2001
I. Overview of Hin Recombinase Function
II. Structural Features of the Hin Domain
III. Structural Features of the Hin-DNA Binding Site
IV. DNA-HIN Interactions
V. Relavent WWW Sites
VI. References
Note: This exhibit is best viewed if the cue buttons ( ) are pressed in sequence and if the viewer does not independently manipulate the molecule on the left.
Hin recombinase catalyzes a site-specific DNA inversion in the Salmonella
chromosome, shown schematically at left.
(A) The recombination event regulates the alternate expression of two flagellin
genes, H2 and H1 (not shown). The hin
gene encodes hin recombinase protein and lies between
two 14 bp inverted repeats, hixL and hixR.
Also contained between these repeats is the H2 promoter
(P), responsible for driving transcription of the H2 operon. The operon
is transcribed when the promoter is oriented near the structural genes H2
and rH1. This transcription is followed by translation
of the H2 flagellin protein and of the rH1
protein, a repressor of H1 flagellin gene transcription. Thus, in the
situation just described, the H2 flagellin gene is expressed but the H1 flagellin
gene is silent.
(B) Hin recombinase is responsible for binding
hixL and hixR,
looping out intervening DNA. There is also a cis-acting site on the
DNA that is bound by two dimers of the Fis protein (not shown), forming a synaptic
complex with hixL, hixR,
and the bound hin protein. This complex is called
the invertasome complex, and its formation permits the recombination sites to
be properly aligned for the recombination event. Hin recombinase
can then catalyze homologous recombination between the repeats, now oriented
in parallel. This results in a reversible switch of the orientation of the ~1,000
bp segment containing the hin gene and the
H2 promoter (P).
(C) As a consequence of the inversion, transcription of the H2 operon is shut off, and the resulting absence of rH1 repressor allows expression of the H1 gene, producing H1 flagellin.
Shown
at left is the carboxy-terminal 52-amino acid DNA-binding domain (the Hin
domain) of the Hin recombinase molecule, complexed with a hixL DNA recombination
half site. The Hin domain contains a three a-helix
bundle with the carboxy-terminal a-helix
(helix 3) of this bundle inserted into the major goove of the DNA parallel
to the base pairs (not to the floor of the groove itself).
a helix 1
is oriented parallel to the axis of the DNA, and
a- helix 2
is positioned in a almost antiparallel manner to helix 1.
There is an angle of -25o between the helix axes. Helices 2
and 3 form a helix-turn-helix motif (HTH) that is similar
to those found in other prokaryotic regulatory DNA-binding proteins.
The three a-helices are amphipathic, having hydrophobic
residues tightly packed agaist one another in a hydrophobic core . Ile152 and Leu156
of helix 1 interact with Leu165
and Phe169 of helix
2, and Val173, Leu176,
and Phe180 of helix
3 also point into this hydophobic core.
Ile144, located on the amino-terminal
arm of the Hin protein, closes this hydrophobic pocket
. These hydrophobic forces play a major role in the stabilization of
the folding of the Hin protein.
There are also hydrogen bonds in the Hin domain that supplement the stabiliztion
of the peptide by the hydrophobic interactions. For example, Arg162,
located at the beginning of helix 2, is hydrogen
bonded to the main chain carbonyl oxygens of Phe180,
which is the final residue of helix 3, and Pro181
. The Hin peptide is further stabilized by the orientation of most
of the charged side chains in the Hin domain. These
are either in contact with the DNA, or exposed to solvent (water) .
The Hin domain also includes two flanking extended amino- and carboxy-terminal polypeptides that contact the bases of the DNA along two different regions in the minor groove .
Hin recombinase binds to each recombination site on standard B-form DNA as
a dimer, and the final 52 amino acids of the two monomers bind to a 26-bp recombination
site. The recombination site is made up of two 12-bp inverted repeats seperated
by a 2-bp core region where DNA strand exchange occurs (13 of these base pairs
are shown here) . The amino-terminal catalytic domain of Hin recombinase, consisting
of 138 amino acids, is positioned in part over the core nucleotides (not shown).
When complexed with Hin recombinase, the DNA remains relatively straight and
is not significantly bent around the protein. This could be explained in part
by the fact that the DNA half site contains a short run of five
AT base pairs . This segment of DNA may be regarded as a region of A-tract DNA,
characterized by a straight, unbent axis, a large propeller twist, and a narrow
minor groove. However, when this small section of A-tract DNA is complexed with
the Hin protein, the minor groove is considerably wider (approx. 6.5-8.5 Å)
than it would be for typical A-tracts (3.5-4.5 Å). Also, propeller twist
is large (approximately -16o) all along the DNA-Hin complex, but
is not significantly larger in the A-tract region.
The Hin protein contacts an unusually large amount of surface area on the DNA : the DNA half-site monomer loses 1816 Å2 of its static solvent accessible surface area when it is bound by the Hin protein.
A. Overview
As shown above, the carboxy-terminal a-helix of
the Hin protein interacts with the major groove of the DNA, while the flanking
amino- and carboxy-terminal chains interact with the minor groove. Specific binding of the Hin peptide
to DNA requires both the major groove interactions involving a-helix
3 and minor groove interactions involving the
amino-terminal sequence Gly139-Arg140-Pro141-Arg142
. The carboxy-terminal eight-amino acids
also contribute to base sequence recognition, and cross the phosphodiester backbone
of DNA, inserting into the minor groove in a novel DNA-protein complex . The binding affinity of the Hin dimer to the full recombination site
is approximately 100-fold higher than the binding affinity of the Hin monomer
to a recombination half-site, indicating that cooperative interactions between
the Hin monomers may contribute to sequence recognition as well.
B. Major Groove Interactions
1. Nonspecific interactions
Helix 3 is the only helix in the Hin protein that
interacts directly with DNA (the other two helices are not positioned close
enough to the DNA to allow any interaction to take place). However, Gln163,
at the amino terminus of helix 2, indirectly contacts
the DNA through a hydrogen bond to Tyr177
in helix 3. Tyr177
in turn interacts with phosphate P19 on the DNA
. There are five nonspecific interactions between
helix 3 and the phosphate backbone that help to position this helix properly
in the major groove and allow for specific recognition interactions. The side
chain of Tyr177 interacts with phosphate
P19 on one edge of the major groove, while Tyr179
interacts with phosphate P8 directly across the groove
on its other edge . Additionally, one of the terminal -NH2 groups of the Arg178
side chain forms a hydrogen bond with the remaining oxygen of phosphate
P8 . Also, the side chain of Thr175
and the main chain amide of Gly172 form
hydrogen bonds with phosphate P9 .
2. Specific Interactions
Specific base sequence recognition between the Hin peptide and DNA also occurs,
involving only the side chains of Ser174
and Arg178, and two water molecules (not
shown) . The side chain of Ser174 forms
a hydrogen bond with the N-7 atom of base A10, and
one a-helix-turn away from this position, the terminal
-NH2 of Arg178 forms a hydrogen
bond with the N-7 atom of base G9. Another nitrogen
of Arg178 donates a hydrogen
bond to water molecule 1, which hydrogen bonds to the O-4 atom of base
T22. One of the remaining protons of water molecule 1 forms a hydrogen
bond with water molecule 2, which also forms hydrogen bonds with the N-6 and
N-7 atoms of base A21 and with the carbonyl oxygen
of Ser174. The interaction of Hin with
DNA through these solvent H2O molecules allows Hin to "read" adjacent
AT's in the major groove.
On the basis of these specific and nonspecific interactions, it is possible
to imagine a mechanism whereby Hin could slide along the DNA in a nonspecific
fashion until it encoutered its correct recognition sequence.
C. Minor Groove Interactions
1. The amino-terminal arm
The amino-terminal arm (Gly139 to His147)
of the Hin peptide adopts an extended conformation, and Gly139
and Arg140 are located within the minor
groove when the Hin peptide is bound to DNA. The side chain of Arg140
forms a hydrogen bond with the N-3 atom of base A26,
and the unusually high propeller twist (26o) of this base pair allows
for another hydrogen bond to be formed between the main chain amide of Arg140
and the O-2 atom of base T6. Also, Gly139
participates in Van der Waals interactions with base pair
5 .
Pro141 arches across one wall of the
minor groove, and there is a hydrogen bond between Arg142
and phosphate P8 . This interaction may be involved in directing the amino-terminal arm
of the Hin peptide into the minor groove. It is also be possible that Ile144
(discussed above) is important in restricting the movement of the amino terminal
arm, thereby positioning Arg142 favorably
for hydrogen bonding to phosphate P8 .
2. The carboxyl-terminal tail
The carboxyl-terminal tail crosses the
phosphodiester backbone of the DNA at the outer edge of the recombination site
and then curves around to follow the minor groove back toward the center of
the 13-bp recombination half-site. The six most caboxyl-terminal
amino acid residues adopt an extended conformation and lie within the
minor groove. However, the side chains of these amino acids make no contacts
with the floor of the minor groove and instead point outward, leaving the polypeptide
backbone to rest against the bases.
The main chain carbonyl group of Ile185 forms a hydrogen bond with the N-2 atom of base G-14, the main chain -NH group of Lys187 forms a hydrogen bond with to the O-2 atom of base T20, the main chain amide of Asn190 interacts with the O-2 atom of base T22, and the side chain of Asn190 interacts with the N-3 atom of base A10.
The
R.E.D. Gallery: Another image and brief description of Hin Recombinase (as
well as several other molecules, including the Fis protein)
Current
Research on the interaction of Hin recombinase with the Fis protein, and
other levels regulation of transcription of the flagellin gene (Kelly T. Hughes)
Phase variation of Salmonella flagellar antigens
Feng, J.-A., Johnson, R. C., and R. E. Dickerson (1994). Hin Recombinase Bound to DNA: The Origin of Specificity in Major and Minor Groove Interactions. Science 263: 348-355 .
Silverman, M., and M. Simon, in Mobile Genetic Elements, J.A. Shapiro, ed.. Academic Press, 1983.
1,
Kenyon College, Gambier, Ohio. A first draft of this exhibit was created for
D. Marcey's Molecular Biology class, Biology 63.
2, Kenyon College, Gambier, Ohio. Present address: California Lutheran University.
Address correspondence to this author (see below).
3, Kenyon College, Gambier, Ohio. This author transferred RasMol script files
into the body of the exhibit text.