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PubMed1995

The structure of deoxy- and oxy-leghaemoglobin from lupin.

The leghaemoglobins have oxygen affinities 11 to 24 times higher than that of sperm whale myoglobin, due mainly to higher rates of association. To find out why, we have determined the structures of deoxy- and oxy-leghaemoglobin II of the lupin at 1.7 A resolution. Results confirm the general features found in previous X-ray analyses of this protein. The unique feature that has now emerged is the rotational freedom of the proximal histidine. In deoxy-leghaemoglobin the imidazole oscillates between two alternative orientations, eclipsing either the lines N1-N3 or N2-N4 of the porphyrin; in oxy-leghaemoglobin it is fixed in a staggered orientation. The iron atom moves from a position 0.30 A from the plane of the pyrrole nitrogen atoms in deoxy- to a position in the plane in oxy-leghaemoglobin while the Fe- bond distance remains constant at 2.02 A. The Fe-O-O angle is 152 degrees, as in human haemoglobin. The oxygen is hydrogen-bonded to the distal histidine at N epsilon 2-O1 and N epsilon 2-O2 distance of 2.95 A and 2.68 A, respectively. The porphyrin is ruffled equally in deoxy- and oxy-leghaemoglobins, due to rotations of the pyrrols about the N-Fe-N bonds, causing the methine bridges to deviate by up to 0.32 A from the mean porphyrin plane. The only feature capable of accounting for the high on-rate of the reaction with oxygen are the mobilities of the proximal histidine and distal histidine residues in deoxy-leghaemoglobin. The eclipsed positions of the proximal histidine in deoxy-leghaemoglobin maximize steric hindrance with the porphyrin nitrogen atoms and minimize pi-->p electron donation, while its staggered position in oxy-leghaemoglobin reverses both these effects. Together with the oscillation of the imidazole between the two orientations, these two factors may reduce the activation energy for the reaction of leghaemoglobin with oxygen. The distal histidine is in a fixed position in the haem pocket in the crystal, but must be swinging in and out of the pocket at a high rate in solution to allow the oxygen to enter.

Crystallography, X-Ray↗
PubMed1996

The binding of carbon monoxide and nitric oxide to leghaemoglobin in comparison with other haemoglobins.

Haemoglobins have the ability to discriminate between oxygen and other diatomic molecules. To further understanding of this process the X-ray crystal structures of carbonmonoxy and nitrosyl-leghaemoglobin have been determined at 1.8 A resolution. The ligand geometry is discussed in detail and the controversial issue of bent versus linear carbon monoxide binding is addressed. The bond angle of 160 degrees for CO-leghaemoglobin is in conflict with recent spectroscopy results on myoglobin but is consistent with angles obtained for myoglobin X-ray crystal structures. In contrast to the numerous carbon monoxide studies, very little stereochemical information is available for the nitric oxide adduct of haemoglobin. This is provided by the X-ray structure of NO-leghaemoglobin, which conforms to expected geometry with an Fe-NO angle of 147 degrees and a lengthened iron-proximal histidine bond. Thus crystallographic evidence is given for the predicted weakening of this bond on the binding of nitric oxide.

Binding Sites↗
PubMed1997

Multiple sequence threading: an analysis of alignment quality and stability.

Methods that compare a protein sequence directly to a structure can be divided into those that construct a molecular model (threading methods) and those that perform a sequence alignment with the structure encoded as a sequence of structural states (one-dimensional/three-dimensional (1D/3D) matching). The former take into account the internal packing of the molecule but the latter do not. On the other hand, it is simple to include multiple sequence data in a 1D/3D comparison but difficult in a threading method. Here, a protein sequence/structure alignment method is described that uses a combination of matching predicted and observed residue exposure, predicted and observed secondary structure (1D/3D) together with pairwise packing interactions in the core (threading). Using a variety of distantly related and analogous protein structures, the multiple sequence threading (MST) method was compared to a single sequence threading (SST) method (that uses complex potentials of mean-force) and also to a multiple sequence alignment (MSA) program. It was found that the MST method produced alignments that were better than the best that could be obtained with either the SST or MSA method. The method was found to be stable to error in both secondary structure prediction and predicted exposure and also under variation of the key parameters (fully described in an Appendix). The contribution of the pairwise term was found to be small but without it, the correct alignments were less stable and structurally unreasonable deletions were observed when matching against larger structures. Using the parameters derived for alignment, the method was able to recognise related folds in the structure databank with a specificity comparable to other methods.

Algorithms↗
PubMed1998

Dynamic sequence databank searching with templates and multiple alignment.

Sequence databank searches are often performed iteratively, taking the results of a search to form a probe (either a pattern or profile) for a subsequent scan of the databank. The advantage of this approach is that, as more sequences are drawn into the probe, it should, in principle be possible to detect increasingly distant members of the family. This approach works well when supervised by an "expert" who has a good "eye" for the quality of the sequence alignment and whether novel matches should be rejected or incorporated into the probe. However, all attempts to automate the process have proved difficult, as the process is inherently unstable. Errors in the alignment, or the misalignment of a non-family member, lead to a deterioration of the probe specificity, so allowing further incorrect sequences to be identified. Here, a combination of two methods is used to provide a check on such instability. A pattern matching (template) search method is used (with a BLAST-like pre-filter for speed) to return sequence segments for alignment in a standard multiple alignment program (MULTAL). Sequences are aligned only to a fixed limit of similarity and any sequences or sub-families that have not joined the original "seed" family are rejected. The remaining core family then provides the basis for a subsequent pattern derivation and databank search. The constant check by the multiple alignment phase allows the search phase to be pushed continually towards the boundary of similarity. This is maintained by lowering the cutoff on the scores of acceptable sequences each time the family remains the same over successive search cycles. The procedure was observed to be stable under misalignments and to have an ability to recognise distantly related family members across super-families that was comparable to Psi-BLAST. The method is applied to the analysis of the hormone-binding domains of the insulin and related growth-factor receptors.

Azurin↗
PubMed1996

The pea early nodulin gene PsENOD7 maps in the region of linkage group I containing sym2 and leghaemoglobin.

The early nodulin gene, PsENOD7, is expressed in pea root nodules induced by Rhizobium leguminosarum bv. viciae, but not in other plant organs. In situ hybridization showed that this gene is transcribed during nodule maturation in the infected cells of the proximal part of the prefixation zone II. At the transition of zone II into interzone II-III, the level of PsENOD7 mRNA drops markedly. PsENOD7 has no significant homology to other genes. RFLP mapping studies have shown that PsENOD7 is located in linkage group I between the leghaemoglobin genes and sym2.

Amino Acid Sequence↗
PubMed1993

The pea late nodulin gene PsNOD6 is homologous to the early nodulin genes PsENOD3/14 and is expressed after the leghaemoglobin genes.

The pea late nodulin gene PsNOD6 has been cloned and sequenced. PsNOD6 is homologous to the pea early nodulin genes PsNOD3 and PsENOD14. In situ hybridization experiments showed that, like the PsENOD3 and PsENOD14 genes, the PsNOD6 gene is only expressed in the infected cell type. The PsNOD6 gene is first expressed at the transition of the pre-fixation zone II into the interzone II-III (the amyloplast-rich zone preceding the fixation zone III), whereas the early nodulin genes PsENOD3 and PsENOD14 are already induced in the pre-fixation zone II. Thus these nodulin genes encoding homologous proteins are induced at consecutive stages of nodule development. The expression of the late nodulin genes encoding leghaemoglobin precedes the expression of the late nodulin gene PsNOD6. Therefore these late nodulin genes have to be regulated by different mechanisms despite the fact they are expressed in the same cell type. This conclusion is consistent with the fact that PsNOD6 lacks one of the conserved regions occurring in the promoters of all other late nodulin genes studied.

Amino Acid Sequence↗
PubMed1991

Synchronous expression of leghaemoglobin genes in Medicago truncatula during nitrogen-fixing root nodule development and response to exogenously supplied nitrate.

Two leghaemoglobin genes from the diploid, autogamous Medicago truncatula (Mtlb1 and Mtlb2) have been cloned and their nucleotide sequences determined. The deduced amino acid sequences encoded by these two genes differ significantly (18%), confirming that they belong to different sub-groups of Medicago leghaemoglobin genes. RNAse protection experiments have been used to show that both genes are transcriptionally active, and are expressed specifically in the nitrogen-fixing root nodule of M. truncatula. Whilst Mtlb1 mRNA is present at approximatively 3-fold higher steady-state levels than Mtlb2 mRNA, the transcription of both genes is triggered concomitantly during nodule development (5 days after inoculation with Rhizobium meliloti), and the ratio of the steady-state levels of the two mRNA species remains constant throughout nodule maturation. When the growth medium of nodulated M. truncatula is supplemented with 5 mM KNO3 over a period of 2-3 days there is a progressive drop in specific nitrogen fixation activity to only 20-25% of the original level. This is accompanied with a parallel and synchronous reduction in the quantities of mRNA corresponding to both Mtlb1 and Mtlb2. By contrast, the expression of the nodule parenchyma-specific gene ENOD2 is not significantly modified following nitrate treatment, clearly demonstrating differences in tissue-specific gene regulation in response to combined nitrogen.

Amino Acid Sequence↗
PubMed1991

Characterization and genomic organization of a highly expressed late nodulin gene subfamily in soybeans.

A soybean nodulin cDNA clone (E41) hybrid-selected mRNA for three in vitro translation products with apparent molecular weights of 26 kDa, 25 kDa and 24 kDa. Based on Southern analysis of soybean genomic DNA, combined with mapping and sequencing of genomic clones, we identified four genes that are related to E41, one of which was identified to be the previously characterized N-20 gene. Our data indicate the linkage of three of the genes, of which one is a truncated version and suggest that they originated by gene duplication combined with deletion and conversion. The genes are highly expressed and we postulate that the sequence conservation in the 5' and 3' flanking regions of all four genes, has a functional role in their expression. Hybrid-selected translation products of E41 are not immunoprecipitable with antibody to the soluble fraction of nodules suggesting that they are membrane associated. The N-20 gene, which is a member of this gene subfamily, showed sequence similarity to four previously characterized nodulin genes and a phylogenetic tree is proposed based on the extent of sequence similarity.

Base Sequence↗
PubMed2005

Oxyleghemoglobin scavenges nitrogen monoxide and peroxynitrite: a possible role in functioning nodules?

It has been demonstrated that the NO* produced by nitric oxide synthase or by the reduction of nitrite by nitrate reductase plays an important role in plants' defense against microbial pathogens. The detection of nitrosyl Lb in nodules strongly suggests that NO* is also formed in functional nodules. Moreover, NO* may react with superoxide (which has been shown to be produced in nodules by various processes), leading to the formation of peroxynitrite. We have determined the second-order rate constants of the reactions of soybean oxyleghemoglobin with nitrogen monoxide and peroxynitrite. At pH 7.3 and 20 degrees C, the values are on the order of 10(8) and 10(4) M-1 s-1, respectively. In the presence of physiological amounts of CO2 (1.2 mM), the second-order rate constant of the reaction of oxyleghemoglobin peroxynitrite is even larger (10(5) M-1 s-1). The results presented here clearly show that oxyleghemoglobin is able to scavenge any NO* and peroxynitrite formed in functional nodules. This may help to stop NO* triggering a plant defense reaction.

Free Radical Scavengers↗
PubMed1975

Involvement of oxyleghaemoglobin and cytochrome P-450 in an efficient oxidative phosphorylation pathway which supports nitrogen fixation in Rhizobium.

Cellular ATP level, ATP/ADP ratio and nitrogenase activity rise when oxyleghaemoglobin is added to respiring suspensions of Rhizobium japonicum bacteroids from soybean root nodules. Increased gaseous O2 tension is much less efficient than oxyleghaemoglobin in stimulation of bacteroid ATP production. Studies with the inhibitor carbonyl cyanide m-chlorophenylhydrazone show this ATP to be generated as a consequence of oxidative phosphorylation. N-Phenylimidazole, a specific cytochrome P-450 inhibitor, also lowers the efficiency of bacteroid oxidative phosphorylation. An approximately linear relationship is observed between ATP/ADP ratio and nitrogenase activity as N-phenylimidazole concentration is lowered. It is suggested that cytochrome P-450 is a component of the leghaemoglobin-facilitated respiration pathway and that it may act as intracellular O2 carrier rather than terminal oxidase. A less efficient oxidase appears to function when cytochrome P-450 is inhibited.

Adenosine Diphosphate↗
PubMed1976

Synthesis and turnover of leghaemoglobin in lupin root nodules.

1. The problem of whether leghaemoglobin is synthesized on plant of bacterial ribosomes in root nodules of yellow lupin has been examined. 2. Leghaemoglobin, soluble plant protein and soluble bacteroid protein were labelled with 14C administered by uptake of 14CO2. 3. Exposure of roots to 1 mM D-threo-chloramphenicol resulted in inhibition of soluble bacteroid protein synthesis, but leghaemoglobin synthesis and soluble plant protein synthesis were unaffected. This result is consistent with leghaemoglobin being synthesized on plant ribosomes. 4. After nitrogen-fixing plants had been supplied with a pulse of 14CO2, the decay of specific radioactivity of nodule protein fractions was observed. Leghaemoglobin had an apparent half-life of 18 days and is a stable protein in nitrogen-fixing yellow lupin nodules.

Chloramphenicol↗
PubMed1981

Regulation of the expression of leghaemoglobin genes in effective and ineffective root nodules of soybean.

The expression of leghaemoglobin genes in effective and ineffective (unable to fix nitrogen) root nodules of soybean developed by Rhizobium japonicum strains 61A76, 61A24 and SM5 was measured by using a cDNA probe or a cloned leghaemoglobin sequence and in vitro translation of Lb-mRNA. Hybridization of the poly(A)-containing nodule polysomal RNA from 3-week-old nodules with a kinetically purified Lb-cDNA or with plasmid (pLbl) containing a leghaemoglobin sequence showed that Lb-mRNA is present in ineffective nodules formed by strains SM5 and 61A24 at reduced levels. Of the two major classes of electrophoretically distinguishable leghaemoglobins in soybean, LbS was not synthesized in 3-week-old strain 61A24-induced nodules while both sorts of leghaemoglobin were synthesized and accumulated in ineffective nodules formed by strain SM5 of Rhizobium. Ineffective nodules formed by strain 61A24 are green inside and do not appear to accumulate leghaemoglobin as measured by the haemochromogen assay, although low levels of apoleghaemoglobin were detected using leghaemoglobin antibodies. SM5-induced nodules were found to have about half as much as leghaemoglobin of the of effective (61A76-induced) nodules. This study demonstrates that while the appearance of leghaemoglobin is independent of nitrogenase activity in bacteroids, its synthesis is influenced to different degrees both by a mutation (SM5) and incompatibility (61A24) of Rhizobium. The primary regulation appears to be at the level of transcription or processing of mRNA since ineffective nodules contain Lb-mRNA approximately in proportion to the amount of apoleghaemoglobin present in these nodules.

Gene Expression Regulation↗
PubMed1976

A search for a leghaemoglobin-like compound in root nodules of Trema cannabina Lour.

Root nodules collected from the non-leguminous plant Trema cannabina Lour. grown under natural field conditions were examined for the presence of leghaemoglobin. No trace of any soluble haemoglobin-like compound could be detected by spectrophotometric analysis or molecular weight comparison studies, although a small amount of soluble haemoprotein with peroxidase activity was isolated. Possible alternatives to the possession of a leghaemoglobin in non-legume/Rhizobium N2-fixing associations are discussed.

Binding Sites↗
PubMed1979

Leghaemoglobin from Trifolium subterraneum. Purification and characterization.

Leghaemoglobin from the subclover, Trifolium subterraneum cultivar Woogenellup, has been fractionated into at least four electrophoretically distinct components using the ion-exchange chromatographic procedure described by Appleby et al. (Appebly, C.A., Nicola, N.A., Hurrell, J.G.R. and Leach, S.J. (1975) Biochemistry 14, 4444--4450) for soybean leghaemoglobins. Unlike those of soybean, the subclover leghaemoglobins showed no evidence of autoxidation under identical isolation procedures, implying that these proteins have an unusually stable ferrous oxidation state. Circular dichroism in the far-ultraviolet (200--240 nm) indicated a high helicity (approx. 70%) as has been reported for other species of leghaemoglobins. However, circular dichroism in the near-ultraviolet region (240--300 nm) indicated that the haem-protein interactions may be considerably different in the subclover leghaemoglobins and this may explain their atypical resistance to autoxidation and the absence of nicotinate binding in these proteins.

Binding Sites↗
PubMed1987

Hydrophobic cluster analysis: an efficient new way to compare and analyse amino acid sequences.

A new method for comparing and aligning protein sequences is described. This method, hydrophobic cluster analysis (HCA), relies upon a two-dimensional (2D) representation of the sequences. Hydrophobic clusters are determined in this 2D pattern and then used for the sequence comparisons. The method does not require powerful computer resources and can deal with distantly related proteins, even if no 3D data are available. This is illustrated in the present report by a comparison of human haemoglobin with leghaemoglobin, a comparison of the two domains of liver rhodanese (thiosulphate sulphurtransferase) and a comparison of plastocyanin and azurin.

Amino Acid Sequence↗