Harutyunyan, E. H.

Kuranova, I. P.

Obmolova, G. V.

Popov, A. N.

Safonova, T. N.

Teplyakov, A. V.

Revistes Catalanes amb Accés Obert

STRUCTURE OF FERROUS FORMS
OF THE YELLOW LUPIN LEGHEMOGLOBIN
T. N. SAFONO VA, A. V. TEPL YAKO V, G. V. OBMOL 0 VA,
A. N. POPOV, I. P. KURANOVA, E. H. HARUTYUNYAN
Institute of Crystallography , USSR Academy of Sciences , Moscow
Legume hemoglobin - leghemoglobin (Lb) - was discovered by
Kubo [ 1 ] in root nodules of leguminous plants. These nodules are a natu-
ral nitrogen-fixing system which is a result of the symbiosis of high plants
with the bacteria Rhysobium. Lb does not directly take part in nitrogen fi-
xation. Possessing very high affinity for oxygen (Pso = 0.05 torr), Lb has
a high combination rate constant k = 118 tM-'- sec' and a comparatively
fast dissociation rate constant k = 4.4 sec' [2]. These properties mean that
Lb may, on the one hand, maintain proper tension of oxygen in nodules
and, on the other hand, provide transport of oxygen.
In many respects (magnetic susceptibility data, spectroscopic data,
etc.) Lb resembles animal hemoglobins and myoglobins. Its molecular
weight is about 17000. Lb has the same type of polypeptide chain folding
as other hemoglobins. Lb consists of 7 a-helices and a porphyrine group
- the heme group (figure 1).
We have studied deoxy-Lb and three ferrous complexes of leghemol-
gobin with CO, NO and 0,. In nodules Lb was detected only in oxy and
deoxy ferrous states.
All experimental data sets were collected on a CARD-diffractometer
with a multiwire detector at the Institute of Crystallography in Moscow
[3]. Experimental data for LbO, were obtained in the atmosphere of argon
at -20" C. Data sets for other complexes were collected at room tempera-
ture.
All complexes have been refined by the Hendrickson-Konnert res-
trained least-square method [4]. Deoxv-Lb was refined by jack-Levitt
procedure [5]. The best results were obtained for Lb02. Models include
139, 150 and 254 water molecules for LbCO, LbNO and LbO2, respecti-
vely. Summary of the refinement is given in Table 1.
[But!I.Soc.Cat .Cien.],Vol.XIII,Num.1,1992
4'^ „ Y'..A..S.lIo.A'ol:4 F:7':-AL.
Table 1. Summary of the refinement.
Complex deoxy-Lb LbCO LbNO LbO,
Program J - L H-K H-K H-K
Resolution (A) 2.0 1.8 1.8 1.7
N of reflections, I o (1) 10172 10925 11512 13063
N , , of solvent atoms 68 139 150 254
R= IIF,,I- I F ,I/FI F ,,I(` %,) 20 18 18 15
: J-I. - Jack & Levitt ]5], H-K - Hendrickson & Konnert ]4].
Phe CD 1
Fig. 1. Polypeptide chain of leghemoglobin. Arrows indicate directions of helices.
I Butll.Soc.Cat.Cien.],VOI.XIII, Num.1,1992
STRUCTURE OF FERROUS FORMS 401
Ligands were localized on the difference electron density maps. In the
course of the refinement we did not use restraints for the bond between Fe
and the first ligand atom and for the angle Fe-L1-L2 (L1 - first ligand
atom, L2 - second ligand atom). Standard lengths for the bond between
two ligand atoms were 1.15, 1.13 and 1.22 A for LbCO, LbNo and Lb02,
respectively. Occupancies for ligand atoms were refined. Occupancies for
atoms of CO and NO ligands were 1.0. Occupancies for ligand atoms in
Lb02 were 0.4 and 0.5. Such low values of occupancies in the last case are
probably due to the disorder of the oxygen molecule.
The geometrical parametes for ligand binding are given in Table 2.
Fe-C bond in CO-complex is markedly shorter than the same bonds ob-
tained by X-ray analysis in CO-complexes of myoglobin [6] (2.27 A) and
erythrocruorin [7] (2.40 A). Still, these lengths determined by EXAFS-
spectroscopy [8] and Raman spectroscopy [9] in myoglobin (Mb) and
erythrocruorin (Ery) complexes are in good agreement (1.97 and 1.8 A)
with our results.
Stereochemistry of molecular oxygen binding has some specific featu-
res. Two oxygen atoms of the ligand are located at approximaltely equal
distances from the Fe atom (Fe-L1 is 2.00 A, Fe-L2 is 2.17 A). The angle
Fe-L1-L2 is 81° but not 120° as predicted by Pauling [10]. The values of
this angle in model systems are 129° and 131° [11, 12], in Mb02 and Ery02
- 115° and 170°, respectively.
Table 2. Geometrical parameters of ligand binding.
Complexes deoxy-Lb LbCO LbNO Lb02
Distances (A)
Fe-L1 - 1.95 1.79 2.00
Fe-Nv2 (His) 2.25 2.27 2.20 2.21
AFe 0.08 0.02 0.03 0.30
ACM 0.13 0.27 0.20 0.25
Angles (degrees)
Fe-L1-L,3>,
- 151 154 81
between Fe-L1 and the
normal to the heme
plane - 0.6 8.6 20.1
torsion angle
C°-N`3-Fe-N14 -55 -60 -60 16
') Ape - distance between Fe atom and the heme plane.
2") AC,,, - average deviation of methine C atoms from the heme plane.
3'") L„ L2 - atoms of the ligand.
4*) C°, N°, - atoms of the proximal His, Ni - atom of the heme.
[Butll.Soc.Cat.Cien.],Vol.X111,N6m.1,1992
402 T.N. SAFONOVA ETA 1, -
Angles Fe-L1-L2 are 151, 154 and 81° for CO, NO and O2 comple-
xes. Angles between Fe-L1 bond and the normal to the heme plane are 0.6,
8.6 and 20 ° for CO, NO and 02 complexes, respectively. Probably the li-
gand's bent binding geometry is largely determined by its direct interac-
tion with the heme than with the protein environement.
The binding of the ligands in CO and NO complexes causes a shift of
the Fe atom towards the ligand into the heme plane and the rotation of the
heme relative to the globin. On the contrary, transition of Lb from deoxy
to oxy-form causes the shift of Fe in the direction of the proximal His
(figure 2). The distance between Fe and the heme plane is 0.30 A. Thus,
the most important difference of Lb02 from other ferrous Lb derivatives
lies in the relationship between the Fe atom and the heme.
Oxygenation leads to the 70° rotation of the His F11 imidazole ring
thus breaking the hydrogen bond between His F11 and Len F7. In this
conformation the angle between the imidazole ring and the heme plane is
71°. Due to the rotation of the proximal His ring the plane of imidazole
ring passes through the line connecting two nitrogen atoms of the heme.
The angle between planes of proximal and distal His changes from 74 to
124°.
NHS
Fig. 2. The heme, proximal His and the ligand in LbO2.
[ButII.'.CdC.Ci&n.],Vol. XI11,NUm . 1,1992
STRUCTURI: OF FERROUS I ORA1S 403
Table 3. Mean -square deviations of C„-coordinates ( 1) and all atom coordinates (2) in
CO, NO and OZ complexes after superimposition with deoxy-Lb.
Complex LbCO1 2
LbNO
1 2 1
LbO,
2
Helices
A 0.17 0.31 0.19 0.34 0.22 0.41
B 0.16 0 . 28 0.18 0.30 0.15 0.36
C 0.17 0.32 0 . 17 0.38 0.15 0.35
E 0.19 0.35 0.18 0.39 0.32 01 .40
F 0.22 0.51 0.23 0.44 0.35 0.70
G 0.18 0.38 0.16 0.44 0.20 0.36
H 0.21 0.47 0.17 0.42 0.31 0.48
Non-helical regions
NA 0.63 0.87 0.61 0.70 1.00 1.07
CD 0.26 0.50 0.26 0.59 0.28 0.59
EF 0.19 0.33 0.12 0.30 0.24 0.46
FG 0.14 0.26 0.17 0.25 0.29 0.32
GH 0.10 0.26 0.21 0.26 0.23 0.36
Theheme - 0.30 - 0.19 - 1.08
R.m.s. deviation 0.21 0.40 0.21 0.41 0.30 0.51
Average deviations of heme methine bridges are 0.27, 0.20 and 0.25 A
for CO, NO and 02 complexes, respectively. These deviations are equal to
rotation of pyrrole rings relative to the least-square plane of the heme
through 6°. In deoxy-Lb this average deviation is 0.13 A. So we can
suggest that maximum distortion of the heme electron system occurs due
to the binding of CO and 02 ligands. The degree of the heme ruffle is
dependent only on the valent and spin state of the Fe atom, but not on the
size of the ligand. This suggestion is confirmed by the geometry of ferrous
Lb complex with nitrozobenzole, where the average deviation of methine
bridges is only 0.18 A.
Oxygenation changes the degree but not the character of the heme
distortion. Therefore the type of the heme distortion should be connected
with the affinity of hemoglobins to molecular oxygen. In myoglobin and
hemoglobins the domeshaped distortion of the heme is observed and their
affinity to oxygen is significantly lower than in Lb.
In deoxy-Lb both propionic acids of the heme are oriented towards
the distal side, thus covering the heme pocket. In CO, NO and 02 com-
plexes one of these residues turns away towards the proximal side.
[Butll.Soc.Cat. Cien.j,Vol.XIII,NUm.1,1992
404 T..\. SAt'O,AO1'A L:T:1L.
In the course of ligand binding some conformational changes in the
side chains, in the secondary structure and in the heme occur. The most
mobile is the N-terminus of the molecule. Results of the superimposition
of CO, NO and 0, complexes with deoxy-Lb based on C,,-atoms are gi-
ven in Table 3. Ligand binding causes rotation of the heme relative to the
protein part. This rotaton for CO and NO complexes can be described as
a rotation of the protein about the line that passes through the Fe atom pa-
rallel to B-helix. The angle of rotation in the CO complex is larger than in
the NO complex. The direction of rotation in Lb02 is opposite to that ob-
served in CO and NO complexes.
The main peculiarity of oxygen binding is the marked disorder of 02
molecule. It may be due either to the different geometry of binding in dif-
ferent Lb molecules or to significant thermal motion of oxygen molecule.
It may be possible that it is this ability of Lb to bind oxygen in arbitrary
orientation that provides the high affinity of Lb to oxygen.
Systems of hydrogen bonds and ionic interactions in these complexes
were compared. It was shown that the principal differences are observed
on the surface of the molecule. Still, there are also some changes in the
bonds, in which heme pocket residues take part.
ABSTRACT
Crystal structures of deoxy-leghemoglobin and three ferrous complexes of leg-
hemoglobin (Lb) with CO, NO and 02 were studied by X-ray analysis at 2.0, 1.8, 1.8
and 1.7 A resolution for deoxy-Lb, LhCO, LhNO and LbO2, respectively. All expe-
rimental data arrays were collected on a CARD-diffractometer with a multiwire
detector. Experimental data for LbO, were obtained at -20° C. Data arrays for other
complexes were collected at room temperature. All the complexes were refined by the
Hendrickson-Konnert method. Deoxy-Lb was refined by Jack-Levitt procedure. The
final R-values are 0.20, 0.18, 0.18 and 0.15 for deoxv-Lb, LbCO, LbNO and LbO,
respectively. Angles Fc-L,-L, are 151, 154 and 81° for CO, NO and 02 complexes.
The binding of the ligands in CO and NO complexes causes a shift of the Fe atom
towards the ligand into the heme plane. On the contrary, transition of Lb from deoxv
to oxy-form causes the shift of Fe in the direction of the proximal His. The distance
between Fe and the heme plane in LhO, is 0.30 A. Oxygenation leads to the 70°
rotation of the His F11 imidazole ring. Geometrical parameters of the heme show that
the degree of the heme ruffle is dependent only on the valent and spin state of the Fe
atom, but not on the size of the ligand. Oxygenation changes the degree but not the
character of the heme distortion. The main peculiarity of oxygen binding is the
marked disorder of 0, molecule (occupancies for ligand atoms 0.4 and 0.5). It may be
due either to the different geometry of binding in different Lb molecules or to
significant thermal motion of 0, molecule. It may be possible that it is this ability of
Lb to bind 0, in arbitrary orientation that provides the high affinity of Lb to oxygen.
I Butll.5oc.Cat .Cic11 . ],Vol. X I I I, Nun,.1,1992
STRUCTURE 01 1 L'RROUS FORMS 405
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[Butll.Soc.Ca t.CiOn.],Vo!.X1I1,N6m .1,1992


Structure of ferrous forms of the yellow lupin leghemoglobin

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