P02238 · LGB3_SOYBN
- ProteinLeghemoglobin 3
- GeneLB3
- StatusUniProtKB reviewed (Swiss-Prot)
- Amino acids144 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
Function
function
Leghemoglobin that reversibly binds oxygen O2 through a pentacoordinated heme iron (PubMed:29100196).
In root nodules, facilitates the diffusion of oxygen to the bacteroids while preventing the bacterial nitrogenase from being inactivated by buffering dioxygen, nitric oxide and carbon monoxide, and promoting the formation of reactive oxygen species (ROS, e.g. H2O2) (PubMed:17540516, PubMed:22308405, PubMed:29701804, PubMed:32297921).
This role is essential for symbiotic nitrogen fixation (SNF) (PubMed:17540516, PubMed:32297921).
In root nodules, facilitates the diffusion of oxygen to the bacteroids while preventing the bacterial nitrogenase from being inactivated by buffering dioxygen, nitric oxide and carbon monoxide, and promoting the formation of reactive oxygen species (ROS, e.g. H2O2) (PubMed:17540516, PubMed:22308405, PubMed:29701804, PubMed:32297921).
This role is essential for symbiotic nitrogen fixation (SNF) (PubMed:17540516, PubMed:32297921).
Features
Showing features for binding site.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Binding site | 46 | heme b (UniProtKB | ChEBI) | ||||
Sequence: S | ||||||
Binding site | 62 | O2 (UniProtKB | ChEBI) | ||||
Sequence: H | ||||||
Binding site | 65 | heme b (UniProtKB | ChEBI) | ||||
Sequence: K | ||||||
Binding site | 93 | Fe (UniProtKB | ChEBI) of heme b (UniProtKB | ChEBI); proximal binding residue | ||||
Sequence: H | ||||||
Binding site | 96 | heme b (UniProtKB | ChEBI) | ||||
Sequence: K |
GO annotations
all annotations | all molecular function | nucleotide binding | molecular_function | nucleic acid binding | dna binding | chromatin binding | dna-binding transcription factor activity | rna binding | cytoskeletal motor activity | catalytic activity | nuclease activity | signaling receptor binding | structural molecule activity | transporter activity | binding | protein binding | translation factor activity, rna binding | lipid binding | kinase activity | transferase activity | hydrolase activity | oxygen binding | enzyme regulator activity | carbohydrate binding | signaling receptor activity | translation regulator activity | transcription regulator activity | other molecular function | all biological process | carbohydrate metabolic process | generation of precursor metabolites and energy | nucleobase-containing compound metabolic process | dna metabolic process | translation | lipid metabolic process | transport | response to stress | cell cycle | cell communication | signal transduction | cell-cell signaling | multicellular organism development | circadian rhythm | biological_process | metabolic process | catabolic process | biosynthetic process | response to light stimulus | response to external stimulus | tropism | response to biotic stimulus | response to abiotic stimulus | response to endogenous stimulus | embryo development | post-embryonic development | fruit ripening | abscission | pollination | flower development | cellular process | programmed cell death | photosynthesis | cellular component organization | cell growth | protein metabolic process | cellular homeostasis | secondary metabolic process | reproductive process | cell differentiation | protein modification process | growth | epigenetic regulation of gene expression | response to chemical | anatomical structure development | regulation of molecular function | other biological process | all cellular component | cellular_component | extracellular region | cell wall | intracellular anatomical structure | nucleus | nuclear envelope | nucleoplasm | nucleolus | cytoplasm | mitochondrion | lysosome | endosome | vacuole | peroxisome | endoplasmic reticulum | golgi apparatus | cytosol | ribosome | cytoskeleton | plasma membrane | chloroplast | plastid | thylakoid | membrane | external encapsulating structure | other cellular component | |||
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Aspect | Term | |
---|---|---|
Cellular Component | cytosol | |
Cellular Component | nucleus | |
Molecular Function | heme binding | |
Molecular Function | metal ion binding | |
Molecular Function | oxygen binding | |
Molecular Function | oxygen carrier activity | |
Biological Process | nitrogen fixation | |
Biological Process | nodulation | |
Biological Process | response to cobalt ion | |
Biological Process | response to hydrogen sulfide | |
Biological Process | response to nitrogen compound |
Keywords
- Biological process
- Ligand
Names & Taxonomy
Protein names
- Recommended nameLeghemoglobin 3
- Short namesGmLb3
- Alternative names
Gene names
Organism names
- Strain
- Taxonomic lineageEukaryota > Viridiplantae > Streptophyta > Embryophyta > Tracheophyta > Spermatophyta > Magnoliopsida > eudicotyledons > Gunneridae > Pentapetalae > rosids > fabids > Fabales > Fabaceae > Papilionoideae > 50 kb inversion clade > NPAAA clade > indigoferoid/millettioid clade > Phaseoleae > Glycine > Glycine subgen. Soja
Accessions
- Primary accessionP02238
- Secondary accessions
Proteomes
Genome annotation databases
Subcellular Location
PTM/Processing
Features
Showing features for initiator methionine, modified residue, chain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Initiator methionine | 1 | Removed | ||||
Sequence: M | ||||||
Modified residue | 2 | N-acetylvaline | ||||
Sequence: V | ||||||
Chain | PRO_0000193002 | 2-144 | Leghemoglobin 3 | |||
Sequence: VAFTEKQDALVSSSFEAFKANIPQYSVVFYTSILEKAPAAKDLFSFLANGVDPTNPKLTGHAEKLFALVRDSAGQLKASGTVVADAALGSVHAQKAVTDPQFVVVKEALLKTIKAAVGDKWSDELSRAWEVAYDELAAAIKKA | ||||||
Modified residue | 26 | Nitrated tyrosine | ||||
Sequence: Y | ||||||
Modified residue | 31 | Nitrated tyrosine | ||||
Sequence: Y | ||||||
Modified residue | 46 | Phosphoserine | ||||
Sequence: S | ||||||
Modified residue | 134 | Nitrated tyrosine | ||||
Sequence: Y |
Post-translational modification
Nitrated mainly at Tyr-31 and, to a lower extent, at Tyr-26 and Tyr-134, in effective nodules and particularly in hypoxic conditions; this mechanism may play a protective role in the symbiosis by buffering toxic peroxynitrite NO2- (PubMed:17259612, PubMed:22308405, PubMed:25603991).
Nitration level decrease during nodule senescence (PubMed:17259612, PubMed:22308405, PubMed:25603991).
Nitration level decrease during nodule senescence (PubMed:17259612, PubMed:22308405, PubMed:25603991).
Phosphorylation at Ser-46 disrupts the molecular environment of its porphyrin ring oxygen binding pocket, thus leading to a reduced oxygen consumption and to the delivery of oxygen O2 to symbiosomes.
Keywords
- PTM
Proteomic databases
Expression
Tissue specificity
Specifically expressed in root nodules.
Induction
Negatively regulated by cobalt (Co) in a dose-dependent manner (PubMed:18838253).
Induced by hydrogen sulfide H2S (PubMed:31204904).
Suppressed by exposure to excess nitrogen (N); this repression is associated with nodule greening and reduced biological nitrogen fixation (BN) efficiency (PubMed:32297921).
Induced by iron-based nanomaterial (Fe-NMs) (PubMed:36479882).
Induced by hydrogen sulfide H2S (PubMed:31204904).
Suppressed by exposure to excess nitrogen (N); this repression is associated with nodule greening and reduced biological nitrogen fixation (BN) efficiency (PubMed:32297921).
Induced by iron-based nanomaterial (Fe-NMs) (PubMed:36479882).
Developmental stage
Interaction
Structure
Family & Domains
Features
Showing features for domain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Domain | 3-144 | Globin | ||||
Sequence: AFTEKQDALVSSSFEAFKANIPQYSVVFYTSILEKAPAAKDLFSFLANGVDPTNPKLTGHAEKLFALVRDSAGQLKASGTVVADAALGSVHAQKAVTDPQFVVVKEALLKTIKAAVGDKWSDELSRAWEVAYDELAAAIKKA |
Sequence similarities
Belongs to the plant globin family.
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length144
- Mass (Da)15,374
- Last updated2007-01-23 v2
- ChecksumE03D27BC73997DB5
Features
Showing features for sequence conflict.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Sequence conflict | 100 | in Ref. 4; AA sequence | ||||
Sequence: D → N | ||||||
Sequence conflict | 102 | in Ref. 4; AA sequence | ||||
Sequence: Q → E | ||||||
Sequence conflict | 106 | in Ref. 4; AA sequence | ||||
Sequence: Missing | ||||||
Sequence conflict | 143-144 | in Ref. 4; AA sequence | ||||
Sequence: KA → AK |
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
V00453 EMBL· GenBank· DDBJ | CAA23731.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
BT092268 EMBL· GenBank· DDBJ | ACU16517.1 EMBL· GenBank· DDBJ | mRNA | ||
CM000843 EMBL· GenBank· DDBJ | KRH34687.1 EMBL· GenBank· DDBJ | Genomic DNA |