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Protein

3-amino-5-hydroxybenzoate synthase

Gene

rifK

Organism
Amycolatopsis mediterranei (strain S699) (Nocardia mediterranei)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the dehydration and aromatization of 5-amino-5-deoxy-3-dehydroshikimate (aminoDHS) to 3-amino-5-hydroxybenzoate (AHBA), a compound that then serves as the starter unit for the assembly of a polyketide during the biosynthesis of rifamycin B and other ansamycin antibiotics. Cannot utilize 5-deoxy-5-amino-3-dehydroquinate (aminoDHQ), 5-deoxy-5-aminoshikimate (aminoSA), quinate, 3-dehydroquinate, or 3-dehydroshikimate (DHS) as substrate.1 Publication
In a complex with RifL, RifK may have a second function in the AHBA pathway, acting as a transaminase introducing the nitrogen into the first pathway intermediate, UDP-3-keto-D-glucose, to give UDP-kanosamine. Appears to use glutamine as the nitrogen donor; NH4+ or asparagine are 30% less effective as nitrogen donors and neither glutamate nor aspartate show activity.1 Publication

Catalytic activityi

5-amino-5-deoxy-3-dehydroshikimate = 3-amino-5-hydroxybenzoate + H2O.1 Publication
UDP-3-keto-alpha-D-glucose + L-glutamine = UDP-alpha-D-kanosamine + L-glutaramate.1 Publication

Cofactori

pyridoxal 5'-phosphate2 PublicationsNote: Binds 1 pyridoxal phosphate per subunit.2 Publications

Enzyme regulationi

AHBA synthase activity is activated by 3-deoxy-D-arabinoheptulosonic acid 7-phosphate (DAHP), an intermediate in the shikimate pathway, and is irreversibly inhibited by gabaculine (5-amino-1,3-cyclohexadiene-1-carboxylate).1 Publication

Kineticsi

kcat is 6.82 sec(-1) for AHBA synthase activity.1 Publication

Manual assertion based on experiment ini

  • Ref.6
    "The biosynthesis of 3-amino-5-hydroxybenzoic acid (AHBA), the precursor of mC7N units in ansamycin and mitomycin antibiotics: a review."
    Floss H.G., Yu T.W., Arakawa K.
    J. Antibiot. 64:35-44(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: PUTATIVE FUNCTION AS UDP-KANOSAMINE SYNTHASE, INTERACTION WITH RIFL, KINETIC PARAMETERS, PATHWAY, MUTAGENESIS OF PHE-88; ASP-159; HIS-162; GLN-185; LYS-188; ARG-219; TYR-226; ARG-236 AND TYR-291.

  1. KM=0.164 mM for 5-amino-5-deoxy-3-dehydroshikimate2 Publications
  2. KM=0.122 mM for 5-amino-5-deoxy-3-dehydroshikimate2 Publications

    pH dependencei

    Optimum pH is 7.5 for AHBA synthase activity. Retains its activity over a broad range of pH. Over 84% of the maximum activity of AHBA synthase is maintained over a pH range from 7.0 to 9.0.1 Publication

    Temperature dependencei

    Optimum temperature is 33 degrees Celsius for AHBA synthase activity. Retains its activity over a broad range of temperature. Over 84% of the maximum activity of AHBA synthase is maintained over a temperature range from 28 to 50 degrees Celsius.1 Publication

    Pathwayi: rifamycin B biosynthesis

    This protein is involved in the pathway rifamycin B biosynthesis, which is part of Antibiotic biosynthesis.1 Publication
    View all proteins of this organism that are known to be involved in the pathway rifamycin B biosynthesis and in Antibiotic biosynthesis.

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase, Transferase

    Keywords - Biological processi

    Antibiotic biosynthesis

    Keywords - Ligandi

    Pyridoxal phosphate

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-14078.
    BRENDAi4.2.1.144. 313.
    UniPathwayiUPA01029.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    3-amino-5-hydroxybenzoate synthase (EC:4.2.1.144)
    Short name:
    AHBA synthase
    Alternative name(s):
    Putative UDP-kanosamine synthase aminotransferase subunit (EC:2.6.1.-)
    Gene namesi
    Name:rifK
    Synonyms:rifD
    Ordered Locus Names:RAM_03205, AMES_0625
    OrganismiAmycolatopsis mediterranei (strain S699) (Nocardia mediterranei)
    Taxonomic identifieri713604 [NCBI]
    Taxonomic lineageiBacteriaActinobacteriaPseudonocardialesPseudonocardiaceaeAmycolatopsis
    Proteomesi
    • UP000006138 Componenti: Chromosome

    Pathology & Biotechi

    Disruption phenotypei

    Inactivation of the gene encoding AHBA synthase results in loss of rifamycin formation; production of the antibiotic is restored when the mutant is supplemented with AHBA. Cells lacking this gene do not accumulate aminoDHS, aminoDHQ, or their spontaneous aromatization product, protocatechuate.2 Publications

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi88F → A: Loss of AHBA synthase activity. 1 Publication1
    Mutagenesisi159D → A, E or K: Loss of AHBA synthase activity. 1 Publication1
    Mutagenesisi162H → L: 2-fold decrease in AHBA synthase activity. 1 Publication1
    Mutagenesisi185Q → E, H or L: Loss of AHBA synthase activity. 1 Publication1
    Mutagenesisi188K → D: Loss of AHBA synthase activity. 1 Publication1
    Mutagenesisi219R → A: 10-fold decrease in AHBA synthase activity. 1 Publication1
    Mutagenesisi226Y → F: Loss of AHBA synthase activity. 1 Publication1
    Mutagenesisi236R → A: Loss of AHBA synthase activity. 1 Publication1
    Mutagenesisi291Y → A: Loss of AHBA synthase activity. 1 Publication1
    Mutagenesisi291Y → F: 7-fold decrease in AHBA synthase activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemoved1 Publication
    ChainiPRO_00004224002 – 3883-amino-5-hydroxybenzoate synthaseAdd BLAST387

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei188N6-(pyridoxal phosphate)lysine1

    Interactioni

    Subunit structurei

    Homodimer. Can interact with RifL.1 Publication

    Structurei

    Secondary structure

    1388
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi17 – 28Combined sources12
    Turni34 – 36Combined sources3
    Helixi39 – 50Combined sources12
    Beta strandi54 – 60Combined sources7
    Helixi62 – 72Combined sources11
    Beta strandi80 – 87Combined sources8
    Helixi90 – 97Combined sources8
    Beta strandi101 – 105Combined sources5
    Turni109 – 111Combined sources3
    Helixi116 – 122Combined sources7
    Beta strandi127 – 130Combined sources4
    Helixi135 – 137Combined sources3
    Helixi142 – 152Combined sources11
    Helixi173 – 175Combined sources3
    Beta strandi176 – 178Combined sources3
    Beta strandi180 – 183Combined sources4
    Beta strandi188 – 190Combined sources3
    Beta strandi192 – 194Combined sources3
    Beta strandi196 – 200Combined sources5
    Helixi205 – 214Combined sources10
    Helixi239 – 249Combined sources11
    Helixi252 – 271Combined sources20
    Beta strandi291 – 296Combined sources6
    Helixi302 – 314Combined sources13
    Beta strandi319 – 321Combined sources3
    Helixi326 – 328Combined sources3
    Helixi330 – 334Combined sources5
    Helixi342 – 347Combined sources6
    Helixi350 – 358Combined sources9
    Beta strandi359 – 363Combined sources5
    Helixi364 – 368Combined sources5
    Helixi371 – 387Combined sources17

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1B9HX-ray2.00A1-388[»]
    1B9IX-ray2.00A1-388[»]
    ProteinModelPortaliO52552.
    SMRiO52552.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO52552.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the degT/dnrJ/eryC1 family.Curated

    Phylogenomic databases

    KOiK16016.
    OMAiYMAMFRV.
    OrthoDBiPOG091H08GO.

    Family and domain databases

    CDDicd00616. AHBA_syn. 1 hit.
    Gene3Di3.40.640.10. 1 hit.
    3.90.1150.10. 1 hit.
    InterProiIPR000653. DegT/StrS_aminotransferase.
    IPR015424. PyrdxlP-dep_Trfase.
    IPR015421. PyrdxlP-dep_Trfase_major_sub1.
    IPR015422. PyrdxlP-dep_Trfase_major_sub2.
    [Graphical view]
    PfamiPF01041. DegT_DnrJ_EryC1. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000390. PLP_StrS. 1 hit.
    SUPFAMiSSF53383. SSF53383. 1 hit.

    Sequencei

    Sequence statusi: Complete.

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

    O52552-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MNARKAPEFP AWPQYDDAER NGLVRALEQG QWWRMGGDEV NSFEREFAAH
    60 70 80 90 100
    HGAAHALAVT NGTHALELAL QVMGVGPGTE VIVPAFTFIS SSQAAQRLGA
    110 120 130 140 150
    VTVPVDVDAA TYNLDPEAVA AAVTPRTKVI MPVHMAGLMA DMDALAKISA
    160 170 180 190 200
    DTGVPLLQDA AHAHGARWQG KRVGELDSIA TFSFQNGKLM TAGEGGAVVF
    210 220 230 240 250
    PDGETEKYET AFLRHSCGRP RDDRRYFHKI AGSNMRLNEF SASVLRAQLA
    260 270 280 290 300
    RLDEQIAVRD ERWTLLSRLL GAIDGVVPQG GDVRADRNSH YMAMFRIPGL
    310 320 330 340 350
    TEERRNALVD RLVEAGLPAF AAFRAIYRTD AFWELGAPDE SVDAIARRCP
    360 370 380
    NTDAISSDCV WLHHRVLLAG EPELHATAEI IADAVARA
    Length:388
    Mass (Da):42,211
    Last modified:November 13, 2013 - v2
    Checksum:i6537B1541C0410F0
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti56A → G in AAA75105 (PubMed:9497318).Curated1
    Sequence conflicti262R → P in AAC01720 (PubMed:9512878).Curated1
    Sequence conflicti262R → P in AAA75105 (PubMed:9497318).Curated1
    Sequence conflicti386A → G in AAC01720 (PubMed:9512878).Curated1
    Sequence conflicti386A → G in AAA75105 (PubMed:9497318).Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF040570 Genomic DNA. Translation: AAC01720.1.
    U33061 Genomic DNA. Translation: AAA75105.1.
    CP002896 Genomic DNA. Translation: AEK39133.1.
    CP003729 Genomic DNA. Translation: AFO74161.1.
    PIRiI39599.
    RefSeqiWP_013222557.1. NC_018266.1.

    Genome annotation databases

    EnsemblBacteriaiAEK39133; AEK39133; RAM_03205.
    AFO74161; AFO74161; AMES_0625.
    KEGGiamm:AMES_0625.
    amn:RAM_03205.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF040570 Genomic DNA. Translation: AAC01720.1.
    U33061 Genomic DNA. Translation: AAA75105.1.
    CP002896 Genomic DNA. Translation: AEK39133.1.
    CP003729 Genomic DNA. Translation: AFO74161.1.
    PIRiI39599.
    RefSeqiWP_013222557.1. NC_018266.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1B9HX-ray2.00A1-388[»]
    1B9IX-ray2.00A1-388[»]
    ProteinModelPortaliO52552.
    SMRiO52552.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAEK39133; AEK39133; RAM_03205.
    AFO74161; AFO74161; AMES_0625.
    KEGGiamm:AMES_0625.
    amn:RAM_03205.

    Phylogenomic databases

    KOiK16016.
    OMAiYMAMFRV.
    OrthoDBiPOG091H08GO.

    Enzyme and pathway databases

    UniPathwayiUPA01029.
    BioCyciMetaCyc:MONOMER-14078.
    BRENDAi4.2.1.144. 313.

    Miscellaneous databases

    EvolutionaryTraceiO52552.

    Family and domain databases

    CDDicd00616. AHBA_syn. 1 hit.
    Gene3Di3.40.640.10. 1 hit.
    3.90.1150.10. 1 hit.
    InterProiIPR000653. DegT/StrS_aminotransferase.
    IPR015424. PyrdxlP-dep_Trfase.
    IPR015421. PyrdxlP-dep_Trfase_major_sub1.
    IPR015422. PyrdxlP-dep_Trfase_major_sub2.
    [Graphical view]
    PfamiPF01041. DegT_DnrJ_EryC1. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000390. PLP_StrS. 1 hit.
    SUPFAMiSSF53383. SSF53383. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiRIFK_AMYMS
    AccessioniPrimary (citable) accession number: O52552
    Secondary accession number(s): G0FS65, Q44095
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 29, 2013
    Last sequence update: November 13, 2013
    Last modified: November 2, 2016
    This is version 81 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Mechanistic studies show that the enzyme-bound pyridoxal phosphate forms a Schiff's base with the amino group of 5-amino-5-deoxy-3-dehydroshikimate and catalyzes both an alpha,beta-dehydration and a stereospecific 1,4-enolization of the substrate.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, 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

    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.