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Protein

Indole-3-glycerol phosphate lyase, chloroplastic

Gene

BX1

Organism
Zea mays (Maize)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate. In bacteria, tryptophan synthase alpha (TSA) activity is almost completely dependent on formation of an active alpha2beta2 complex with tryptophan synthase beta (TSB), and indole is usually not released during tryptophan synthesis. In maize, the TSA homolog BX1 catalyzes the formation of free indole from indole-3-glycerol phosphate, independently of TSB.1 Publication

Catalytic activityi

(1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate = indole + D-glyceraldehyde 3-phosphate.
L-serine + 1-C-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + D-glyceraldehyde 3-phosphate + H2O.

Kineticsi

  1. KM=0.013 mM for indole-3-glycerol phosphate1 Publication

    Pathway:i2,4-dihydroxy-1,4-benzoxazin-3-one biosynthesis

    This protein is involved in step 1 of the subpathway that synthesizes 2,4-dihydroxy-1,4-benzoxazin-3-one from indoleglycerol phosphate.
    Proteins known to be involved in the 5 steps of the subpathway in this organism are:
    1. Indole-3-glycerol phosphate lyase, chloroplastic (BX1)
    2. indole-2-monooxygenase (CYP71C4)
    3. indolin-2-one monooxygenase (CYP71C2)
    4. 3-hydroxyindolin-2-one monooxygenase (CYP71C1)
    5. Cytochrome P450 71C3 (CYP71C3)
    This subpathway is part of the pathway 2,4-dihydroxy-1,4-benzoxazin-3-one biosynthesis, which is itself part of Secondary metabolite biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes 2,4-dihydroxy-1,4-benzoxazin-3-one from indoleglycerol phosphate, the pathway 2,4-dihydroxy-1,4-benzoxazin-3-one biosynthesis and in Secondary metabolite biosynthesis.

    Pathway:iL-tryptophan biosynthesis

    This protein is involved in step 5 of the subpathway that synthesizes L-tryptophan from chorismate.
    Proteins known to be involved in the 5 steps of the subpathway in this organism are:
    1. no protein annotated in this organism
    2. no protein annotated in this organism
    3. N-(5'-phosphoribosyl)anthranilate isomerase (LOC100194071), N-(5'-phosphoribosyl)anthranilate isomerase (LOC100274239)
    4. no protein annotated in this organism
    5. Tryptophan synthase beta chain 1 (TSB1), Tryptophan synthase beta chain 2, chloroplastic (TSB2), Indole-3-glycerol phosphate lyase, chloroplastic (BX1)
    This subpathway is part of the pathway L-tryptophan biosynthesis, which is itself part of Amino-acid biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-tryptophan from chorismate, the pathway L-tryptophan biosynthesis and in Amino-acid biosynthesis.

    GO - Molecular functioni

    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Biological processi

    Amino-acid biosynthesis, Aromatic amino acid biosynthesis, Tryptophan biosynthesis

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-10162.
    BRENDAi4.1.2.8. 6752.
    UniPathwayiUPA00035; UER00044.
    UPA00872; UER00847.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Indole-3-glycerol phosphate lyase, chloroplastic (EC:4.1.2.8)
    Alternative name(s):
    Benzoxazineless 1
    Indole synthase
    Tryptophan synthase alpha chain (EC:4.2.1.20)
    Gene namesi
    Name:BX1
    OrganismiZea mays (Maize)
    Taxonomic identifieri4577 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaePACMAD cladePanicoideaeAndropogoneaeZea
    ProteomesiUP000007305 Componenti: Chromosome 4

    Organism-specific databases

    GrameneiP42390.
    MaizeGDBi102199.

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Chloroplast, Plastid

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transit peptidei1 – 5353ChloroplastSequence AnalysisAdd
    BLAST
    Chaini54 – 347294Indole-3-glycerol phosphate lyase, chloroplasticPRO_0000035782Add
    BLAST

    Expressioni

    Gene expression databases

    ExpressionAtlasiP42390. baseline and differential.

    Interactioni

    Subunit structurei

    Tetramer of two alpha and two beta chains for the tryptophan synthase activity. Homodimer of alpha chains for the indole-3-glycerol phosphate lyase activity.1 Publication

    Protein-protein interaction databases

    STRINGi4577.GRMZM2G085381_P03.

    Structurei

    Secondary structure

    1
    347
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi90 – 9910Combined sources
    Beta strandi104 – 1107Combined sources
    Helixi116 – 12813Combined sources
    Beta strandi132 – 1376Combined sources
    Helixi148 – 15811Combined sources
    Turni159 – 1613Combined sources
    Helixi164 – 17411Combined sources
    Helixi175 – 1773Combined sources
    Beta strandi182 – 1854Combined sources
    Helixi189 – 1924Combined sources
    Helixi197 – 2015Combined sources
    Beta strandi206 – 2083Combined sources
    Turni214 – 2163Combined sources
    Helixi217 – 22610Combined sources
    Beta strandi233 – 2353Combined sources
    Helixi241 – 25010Combined sources
    Beta strandi255 – 2584Combined sources
    Helixi273 – 28412Combined sources
    Beta strandi289 – 2935Combined sources
    Helixi298 – 3069Combined sources
    Beta strandi310 – 3145Combined sources
    Helixi316 – 3238Combined sources
    Beta strandi324 – 3274Combined sources
    Helixi328 – 34619Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1RD5X-ray2.02A/B87-347[»]
    1TJRX-ray2.30A/B87-347[»]
    ProteinModelPortaliP42390.
    SMRiP42390. Positions 87-347.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP42390.

    Family & Domainsi

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi47 – 515Poly-Thr
    Compositional biasi52 – 12271Ala-richAdd
    BLAST

    Sequence similaritiesi

    Belongs to the TrpA family.Curated

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    HOGENOMiHOG000223816.
    KOiK13222.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_00131. Trp_synth_alpha.
    InterProiIPR013785. Aldolase_TIM.
    IPR011060. RibuloseP-bd_barrel.
    IPR018204. Trp_synthase_alpha_AS.
    IPR002028. Trp_synthase_suA.
    [Graphical view]
    PfamiPF00290. Trp_syntA. 1 hit.
    [Graphical view]
    SUPFAMiSSF51366. SSF51366. 1 hit.
    TIGRFAMsiTIGR00262. trpA. 1 hit.
    PROSITEiPS00167. TRP_SYNTHASE_ALPHA. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P42390-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAFAPKTSSS SSLSSALQAA QSPPLLLRRM SSTATPRRRY DAAVVVTTTT
    60 70 80 90 100
    TARAAAAAVT VPAAPPQAPA PAPVPPKQAA APAERRSRPV SDTMAALMAK
    110 120 130 140 150
    GKTAFIPYIT AGDPDLATTA EALRLLDGCG ADVIELGVPC SDPYIDGPII
    160 170 180 190 200
    QASVARALAS GTTMDAVLEM LREVTPELSC PVVLLSYYKP IMSRSLAEMK
    210 220 230 240 250
    EAGVHGLIVP DLPYVAAHSL WSEAKNNNLE LVLLTTPAIP EDRMKEITKA
    260 270 280 290 300
    SEGFVYLVSV NGVTGPRANV NPRVESLIQE VKKVTNKPVA VGFGISKPEH
    310 320 330 340
    VKQIAQWGAD GVIIGSAMVR QLGEAASPKQ GLRRLEEYAR GMKNALP
    Length:347
    Mass (Da):36,521
    Last modified:August 30, 2005 - v2
    Checksum:i110D4215101F2012
    GO

    Sequence cautioni

    The sequence CAA54131.1 differs from that shown. Reason: Frameshift at positions 69 and 84. Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X76713 Genomic DNA. Translation: CAA54131.1. Frameshift.
    AY254103 mRNA. Translation: AAP33667.1.
    AY254104 mRNA. Translation: AAP33668.1.
    PIRiS56665.
    RefSeqiNP_001105219.1. NM_001111749.1.
    UniGeneiZm.283.

    Genome annotation databases

    EnsemblPlantsiGRMZM2G085381_T01; GRMZM2G085381_P01; GRMZM2G085381.
    GeneIDi542117.
    KEGGizma:542117.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X76713 Genomic DNA. Translation: CAA54131.1. Frameshift.
    AY254103 mRNA. Translation: AAP33667.1.
    AY254104 mRNA. Translation: AAP33668.1.
    PIRiS56665.
    RefSeqiNP_001105219.1. NM_001111749.1.
    UniGeneiZm.283.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1RD5X-ray2.02A/B87-347[»]
    1TJRX-ray2.30A/B87-347[»]
    ProteinModelPortaliP42390.
    SMRiP42390. Positions 87-347.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi4577.GRMZM2G085381_P03.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblPlantsiGRMZM2G085381_T01; GRMZM2G085381_P01; GRMZM2G085381.
    GeneIDi542117.
    KEGGizma:542117.

    Organism-specific databases

    GrameneiP42390.
    MaizeGDBi102199.

    Phylogenomic databases

    HOGENOMiHOG000223816.
    KOiK13222.

    Enzyme and pathway databases

    UniPathwayiUPA00035; UER00044.
    UPA00872; UER00847.
    BioCyciMetaCyc:MONOMER-10162.
    BRENDAi4.1.2.8. 6752.

    Miscellaneous databases

    EvolutionaryTraceiP42390.

    Gene expression databases

    ExpressionAtlasiP42390. baseline and differential.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_00131. Trp_synth_alpha.
    InterProiIPR013785. Aldolase_TIM.
    IPR011060. RibuloseP-bd_barrel.
    IPR018204. Trp_synthase_alpha_AS.
    IPR002028. Trp_synthase_suA.
    [Graphical view]
    PfamiPF00290. Trp_syntA. 1 hit.
    [Graphical view]
    SUPFAMiSSF51366. SSF51366. 1 hit.
    TIGRFAMsiTIGR00262. trpA. 1 hit.
    PROSITEiPS00167. TRP_SYNTHASE_ALPHA. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    1. "Structure of a maize tryptophan synthase alpha subunit gene with pith enhanced expression."
      Kramer V.C., Koziel M.G.
      Plant Mol. Biol. 27:1183-1188(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: cv. CG000237.
    2. "Transformation of Nicotiana tabacum cv. Samsun with melanin and indigo genes."
      Jordaan A., Botha A.-M.
      Submitted (MAR-2003) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    3. Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES.
    4. "Crystal structure of tryptophan synthase alpha chain."
      Kulik V., Weyand M., Frey M., Dunn M., Schlichting I.
      Submitted (DEC-2004) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (2.02 ANGSTROMS) OF 86-347, SUBUNIT.

    Entry informationi

    Entry nameiTRPA_MAIZE
    AccessioniPrimary (citable) accession number: P42390
    Secondary accession number(s): Q84K75
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1995
    Last sequence update: August 30, 2005
    Last modified: June 24, 2015
    This is version 116 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Mutant rescue experiments indicate the existence of a second tryptophan synthase alpha gene whose product might be involved in tryptophan biosynthesis while BX1 might be restricted to free indol production.

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    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

    External Data

    Dasty 3

    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 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.