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    MB myoglobin [ Physeter catodon (sperm whale) ]

    Gene ID: 102975021, updated on 8-Jun-2024

    Summary

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    Gene symbol
    MB
    Gene description
    myoglobin
    See related
    Ensembl:ENSPCTG00005011582
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Physeter catodon
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Artiodactyla; Whippomorpha; Cetacea; Odontoceti; Physeteridae; Physeter
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    chromosome: Un
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2023_04 current ASM283717v5 (GCF_002837175.3) Unplaced Scaffold NW_021145510.1 (28809..39467, complement)
    102 previous assembly ASM283717v2 (GCF_002837175.2) Unplaced Scaffold NW_021145510.1 (28809..39467, complement)

    NW_021145510.1Genomic Context describing neighboring genes Neighboring gene apolipoprotein L6-like

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Influence of the heme distal pocket on nitrite binding orientation and reactivity in Sperm Whale myoglobin. Tse W, et al. Biochem J, 2021 Feb 26. PMID 33543749, Free PMC Article
    2. sw ApoMb Amyloid Aggregation under Nondenaturing Conditions: The Role of Native Structure Stability. Katina NS, et al. Biophys J, 2017 Sep 5. PMID 28877500, Free PMC Article
    3. Intermediate States of Apomyoglobin: Are They Parts of the Same Area of Conformations Diagram? Balobanov VA, et al. Biochemistry (Mosc), 2017 May. PMID 28601072
    4. Benchmarking Rapid TLES Simulations of Gas Diffusion in Proteins: Mapping O2 Migration and Escape in Myoglobin as a Case Study. Shadrina MS, et al. J Chem Theory Comput, 2016 Apr 12. PMID 26938707
    5. Structures of K42N and K42Y sperm whale myoglobins point to an inhibitory role of distal water in peroxidase activity. Wang C, et al. Acta Crystallogr D Biol Crystallogr, 2014 Nov. PMID 25372675

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Influence of the heme distal pocket on nitrite binding orientation and reactivity in Sperm Whale myoglobin.
      Title: Influence of the heme distal pocket on nitrite binding orientation and reactivity in Sperm Whale myoglobin.
    2. Study investigated the effect of amino acid substitutions on propensity of the completely helical protein sperm whale apomyoglobin (sw ApoMb) for amyloid formation from its structured state in the absence of denaturing agents; demonstrated that stability of the protein native state determines both protein aggregation propensity and structural peculiarities of formed aggregates.
      Title: sw ApoMb Amyloid Aggregation under Nondenaturing Conditions: The Role of Native Structure Stability.
    3. The current report presents spectral properties of sperm whale apomyoglobin studied over a wide range of conditions with the use of circular dichroism and fluorescence techniques.
      Title: Intermediate States of Apomyoglobin: Are They Parts of the Same Area of Conformations Diagram?
    4. A temperature-controlled locally enhanced sampling (TLES) simulation examines multiple diffusion trajectories per simulation by accommodating multiple noninteracting copies of a gas molecule that diffuse independently, while the protein and water molecules experience an average interaction from all copies. Using TLES this study presents mapping O2 migration and escape in Myoglobin.
      Title: Benchmarking Rapid TLES Simulations of Gas Diffusion in Proteins: Mapping O2 Migration and Escape in Myoglobin as a Case Study.
    5. Data suggest that adding hydrophilicity (such as in I107E mutation) to distal pocket is at origin of increase in nitric oxide reductase (NOR) activity in sperm whale myoglobin; proton transfer appears important in biocatalysis by P. aeruginosa NOR.
      Title: Effect of Outer-Sphere Side Chain Substitutions on the Fate of the trans Iron-Nitrosyl Dimer in Heme/Nonheme Engineered Myoglobins (Fe(B)Mbs): Insights into the Mechanism of Denitrifying NO Reductases.
    6. The crystal structures of the K42Y and K42N mutants revealed that the substitutions at position 42 elongate the distances between the distal His55 and the heme iron and also the hydrogen-bonding distances between His55 and the Fe-coordinated water.
      Title: Structures of K42N and K42Y sperm whale myoglobins point to an inhibitory role of distal water in peroxidase activity.
    7. Nitrite binds to oxy myoglobin to generate an undetectable ferrous-peroxynitrate intermediate, whose decay leads to nitrate and ferryl. The ferryl is then reduced to met by the excess nitrite.
      Title: Involvement of ferryl in the reaction between nitrite and the oxy forms of globins.
    8. Data from studies on recombinant/mutant proteins suggest apomyoglobin folding exhibits several energetic bottlenecks that frustrate folding; relief of any one of major identified bottlenecks is insufficient to speed progression to transition state.
      Title: Probing the non-native H helix translocation in apomyoglobin folding intermediates.
    Submit: New GeneRIF Correction

    General gene information

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    Homology

    Gene Ontology Provided by RefSeq

    Function Evidence Code Pubs
    enables heme binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables oxygen binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in oxygen transport IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in extracellular exosome IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    myoglobin
    Names
    nitrite reductase MB
    pseudoperoxidase MB
    NP_001277651.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001290722.1 → NP_001277651.1  myoglobin

      See identical proteins and their annotated locations for NP_001277651.1

      Status: PROVISIONAL

      Source sequence(s)
      AB271144
      UniProtKB/Swiss-Prot
      P02185, Q0KIY8
      Related
      ENSPCTP00005016290.1, ENSPCTT00005017972.1
      Conserved Domains (1) summary
      cl21461
      Location:6 → 154
      Globin-like; Globin-like protein superfamily

    RefSeqs of Annotated Genomes: GCF_002837175.3-RS_2023_04

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference ASM283717v5 Primary Assembly

    Genomic

    1. NW_021145510.1 Reference ASM283717v5 Primary Assembly

      Range
      28809..39467 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P02185.2 GenPept UniProtKB/Swiss-Prot:P02185

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.