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Protein

Ligninase H2

Gene

GLG4

Organism
Phanerochaete chrysosporium (White-rot fungus) (Sporotrichum pruinosum)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Depolymerization of lignin. Catalyzes the C(alpha)-C(beta) cleavage of the propyl side chains of lignin.1 Publication

Catalytic activityi

1-(3,4-dimethoxyphenyl)-2-(2-methoxyphenoxy)propane-1,3-diol + H2O2 = 3,4-dimethoxybenzaldehyde + 2-methoxyphenol + glycolaldehyde + H2O.1 Publication
2 (3,4-dimethoxyphenyl)methanol + H2O2 = 2 (3,4-dimethoxyphenyl)methanol radical + 2 H2O.1 Publication

Cofactori

Protein has several cofactor binding sites:
  • heme bPROSITE-ProRule annotationNote: Binds 1 heme b (iron(II)-protoporphyrin IX) group per subunit.PROSITE-ProRule annotation
  • Ca2+Note: Binds 2 calcium ions per subunit.

Kineticsi

  1. KM=85 µM for H2O21 Publication
  2. KM=171 µM for (3,4-dimethoxyphenyl)methanol1 Publication

    pH dependencei

    Optimum pH is 2.3.1 Publication

    Pathwayi: lignin degradation

    This protein is involved in the pathway lignin degradation, which is part of Secondary metabolite metabolism.
    View all proteins of this organism that are known to be involved in the pathway lignin degradation and in Secondary metabolite metabolism.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sitei72Transition state stabilizer1
    Active sitei76Proton acceptor1
    Metal bindingi77Calcium 11
    Metal bindingi95Calcium 1; via carbonyl oxygen1
    Metal bindingi97Calcium 11
    Metal bindingi99Calcium 11
    Metal bindingi205Iron (heme axial ligand)1
    Metal bindingi206Calcium 21
    Metal bindingi223Calcium 21
    Metal bindingi225Calcium 21
    Metal bindingi228Calcium 2; via carbonyl oxygen1
    Metal bindingi230Calcium 21

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase, Peroxidase

    Keywords - Biological processi

    Hydrogen peroxide, Lignin degradation

    Keywords - Ligandi

    Calcium, Heme, Iron, Metal-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-14340.
    UniPathwayiUPA00892.

    Protein family/group databases

    CAZyiAA2. Auxiliary Activities 2.
    mycoCLAPiLPO2B_PHACH.
    PeroxiBasei2414. PcLiP04_BKMF1767.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ligninase H2 (EC:1.11.1.141 Publication)
    Alternative name(s):
    Diarylpropane peroxidase
    LG4
    Lignin peroxidase
    Gene namesi
    Name:GLG4
    Synonyms:LIP2
    OrganismiPhanerochaete chrysosporium (White-rot fungus) (Sporotrichum pruinosum)
    Taxonomic identifieri5306 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaBasidiomycotaAgaricomycotinaAgaricomycetesPolyporalesPhanerochaetaceaePhanerochaete

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Signal peptidei1 – 21Sequence analysisAdd BLAST21
    PropeptideiPRO_000002376622 – 282 Publications7
    ChainiPRO_000002376729 – 372Ligninase H2Add BLAST344

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Disulfide bondi31 ↔ 44
    Disulfide bondi43 ↔ 314
    Disulfide bondi63 ↔ 149
    Disulfide bondi278 ↔ 344
    Glycosylationi286N-linked (GlcNAc...)1 Publication1

    Keywords - PTMi

    Cleavage on pair of basic residues, Disulfide bond, Glycoprotein, Zymogen

    Expressioni

    Developmental stagei

    Ligninases are expressed during secondary metabolism, and are triggered by nutrient limitation.

    Structurei

    Secondary structure

    1372
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi41 – 46Combined sources6
    Helixi47 – 56Combined sources10
    Turni59 – 61Combined sources3
    Helixi65 – 78Combined sources14
    Helixi83 – 87Combined sources5
    Beta strandi95 – 98Combined sources4
    Helixi99 – 102Combined sources4
    Helixi104 – 107Combined sources4
    Helixi111 – 113Combined sources3
    Helixi116 – 130Combined sources15
    Helixi134 – 147Combined sources14
    Helixi180 – 191Combined sources12
    Helixi195 – 201Combined sources7
    Helixi202 – 206Combined sources5
    Beta strandi209 – 214Combined sources6
    Beta strandi220 – 224Combined sources5
    Helixi232 – 236Combined sources5
    Beta strandi245 – 247Combined sources3
    Beta strandi256 – 259Combined sources4
    Helixi265 – 272Combined sources8
    Turni274 – 276Combined sources3
    Helixi277 – 281Combined sources5
    Turni282 – 285Combined sources4
    Helixi287 – 302Combined sources16
    Turni303 – 305Combined sources3
    Helixi308 – 310Combined sources3
    Beta strandi311 – 313Combined sources3
    Helixi315 – 317Combined sources3
    Helixi337 – 339Combined sources3
    Beta strandi345 – 347Combined sources3
    Beta strandi356 – 359Combined sources4

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1QPAX-ray1.80A/B29-372[»]
    ProteinModelPortaliP11542.
    SMRiP11542.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP11542.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the peroxidase family. Ligninase subfamily.Curated

    Keywords - Domaini

    Signal

    Phylogenomic databases

    eggNOGiENOG410II1B. Eukaryota.
    ENOG410ZS1R. LUCA.

    Family and domain databases

    CDDicd00692. ligninase. 1 hit.
    InterProiIPR010255. Haem_peroxidase.
    IPR002016. Haem_peroxidase_pln/fun/bac.
    IPR001621. Ligninase.
    IPR024589. Ligninase_C.
    IPR019794. Peroxidases_AS.
    IPR019793. Peroxidases_heam-ligand_BS.
    [Graphical view]
    PfamiPF00141. peroxidase. 1 hit.
    PF11895. Peroxidase_ext. 1 hit.
    [Graphical view]
    PRINTSiPR00462. LIGNINASE.
    PR00458. PEROXIDASE.
    SUPFAMiSSF48113. SSF48113. 1 hit.
    PROSITEiPS00435. PEROXIDASE_1. 1 hit.
    PS00436. PEROXIDASE_2. 1 hit.
    PS50873. PEROXIDASE_4. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P11542-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAFKQLLAAL SVALTLQVTQ AAPNLDKRVA CPDGVHTASN AACCAWFPVL
    60 70 80 90 100
    DDIQQNLFHG GQCGAEAHEA LRMVFHDSIA ISPKLQSQGK FGGGGADGSI
    110 120 130 140 150
    ITFSSIETTY HPNIGLDEVV AIQKPFIAKH GVTRGDFIAF AGAVGVSNCP
    160 170 180 190 200
    GAPQMQFFLG RPEATQAAPD GLVPEPFHTI DQVLARMLDA GGFDEIETVW
    210 220 230 240 250
    LLSAHSIAAA NDVDPTISGL PFDSTPGQFD SQFFVETQLR GTAFPGKTGI
    260 270 280 290 300
    QGTVMSPLKG EMRLQTDHLF ARDSRTACEW QSFVNNQTKL QEDFQFIFTA
    310 320 330 340 350
    LSTLGHDMNA MTDCSEVIPA PKPVNFGPSF FPAGKTHADI EQACASTPFP
    360 370
    TLITAPGPSA SVARIPPPPS PN
    Length:372
    Mass (Da):39,523
    Last modified:February 1, 1991 - v2
    Checksum:iA17AD0AB5FE1A290
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti312T → I in AAA33733 (PubMed:3440521).Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X15599 Genomic DNA. Translation: CAA33621.1.
    M18743 mRNA. Translation: AAA33733.1.
    PIRiS06043. OPJGH2.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X15599 Genomic DNA. Translation: CAA33621.1.
    M18743 mRNA. Translation: AAA33733.1.
    PIRiS06043. OPJGH2.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1QPAX-ray1.80A/B29-372[»]
    ProteinModelPortaliP11542.
    SMRiP11542.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein family/group databases

    CAZyiAA2. Auxiliary Activities 2.
    mycoCLAPiLPO2B_PHACH.
    PeroxiBasei2414. PcLiP04_BKMF1767.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Phylogenomic databases

    eggNOGiENOG410II1B. Eukaryota.
    ENOG410ZS1R. LUCA.

    Enzyme and pathway databases

    UniPathwayiUPA00892.
    BioCyciMetaCyc:MONOMER-14340.

    Miscellaneous databases

    EvolutionaryTraceiP11542.

    Family and domain databases

    CDDicd00692. ligninase. 1 hit.
    InterProiIPR010255. Haem_peroxidase.
    IPR002016. Haem_peroxidase_pln/fun/bac.
    IPR001621. Ligninase.
    IPR024589. Ligninase_C.
    IPR019794. Peroxidases_AS.
    IPR019793. Peroxidases_heam-ligand_BS.
    [Graphical view]
    PfamiPF00141. peroxidase. 1 hit.
    PF11895. Peroxidase_ext. 1 hit.
    [Graphical view]
    PRINTSiPR00462. LIGNINASE.
    PR00458. PEROXIDASE.
    SUPFAMiSSF48113. SSF48113. 1 hit.
    PROSITEiPS00435. PEROXIDASE_1. 1 hit.
    PS00436. PEROXIDASE_2. 1 hit.
    PS50873. PEROXIDASE_4. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiLIG4_PHACH
    AccessioniPrimary (citable) accession number: P11542
    Secondary accession number(s): P14153
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1989
    Last sequence update: February 1, 1991
    Last modified: November 30, 2016
    This is version 120 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.