Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Basket 0
(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

O52552

- RIFK_AMYMS

UniProt

O52552 - RIFK_AMYMS

Protein

3-amino-5-hydroxybenzoate synthase

Gene

rifK

Organism
Amycolatopsis mediterranei (strain S699) (Nocardia mediterranei)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
    • BLAST
    • Align
    • Format
    • Add to basket
    • History
      Entry version 70 (01 Oct 2014)
      Sequence version 2 (13 Nov 2013)
      Previous versions | rss
    • Help video
    • Feedback
    • Comment

    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. Can not 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

    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

    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

    GO - Molecular functioni

    1. lyase activity Source: UniProtKB-KW
    2. pyridoxal phosphate binding Source: InterPro
    3. transferase activity Source: UniProtKB-KW

    GO - Biological processi

    1. antibiotic biosynthetic process Source: UniProtKB-KW

    Keywords - Molecular functioni

    Lyase, Transferase

    Keywords - Biological processi

    Antibiotic biosynthesis

    Keywords - Ligandi

    Pyridoxal phosphate

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-14078.
    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 lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesPseudonocardineaePseudonocardiaceaeAmycolatopsis
    ProteomesiUP000006138: 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)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi88 – 881F → A: Loss of AHBA synthase activity. 1 Publication
    Mutagenesisi159 – 1591D → A, E or K: Loss of AHBA synthase activity. 1 Publication
    Mutagenesisi162 – 1621H → L: 2-fold decrease in AHBA synthase activity. 1 Publication
    Mutagenesisi185 – 1851Q → E, H or L: Loss of AHBA synthase activity. 1 Publication
    Mutagenesisi188 – 1881K → D: Loss of AHBA synthase activity. 1 Publication
    Mutagenesisi219 – 2191R → A: 10-fold decrease in AHBA synthase activity. 1 Publication
    Mutagenesisi226 – 2261Y → F: Loss of AHBA synthase activity. 1 Publication
    Mutagenesisi236 – 2361R → A: Loss of AHBA synthase activity. 1 Publication
    Mutagenesisi291 – 2911Y → A: Loss of AHBA synthase activity. 1 Publication
    Mutagenesisi291 – 2911Y → F: 7-fold decrease in AHBA synthase activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 3883873-amino-5-hydroxybenzoate synthasePRO_0000422400Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei188 – 1881N6-(pyridoxal phosphate)lysine

    Interactioni

    Subunit structurei

    Homodimer. Can interact with RifL.1 Publication

    Structurei

    Secondary structure

    1
    388
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi17 – 2812
    Turni34 – 363
    Helixi39 – 5012
    Beta strandi54 – 607
    Helixi62 – 7211
    Beta strandi80 – 878
    Helixi90 – 978
    Beta strandi101 – 1055
    Turni109 – 1113
    Helixi116 – 1227
    Beta strandi127 – 1304
    Helixi135 – 1373
    Helixi142 – 15211
    Helixi173 – 1753
    Beta strandi176 – 1783
    Beta strandi180 – 1834
    Beta strandi188 – 1903
    Beta strandi192 – 1943
    Beta strandi196 – 2005
    Helixi205 – 21410
    Helixi239 – 24911
    Helixi252 – 27120
    Beta strandi291 – 2966
    Helixi302 – 31413
    Beta strandi319 – 3213
    Helixi326 – 3283
    Helixi330 – 3345
    Helixi342 – 3476
    Helixi350 – 3589
    Beta strandi359 – 3635
    Helixi364 – 3685
    Helixi371 – 38717

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1B9HX-ray2.00A1-388[»]
    1B9IX-ray2.00A1-388[»]
    ProteinModelPortaliO52552.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO52552.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the degT/dnrJ/eryC1 family.Curated

    Phylogenomic databases

    KOiK16016.

    Family and domain databases

    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

    MNARKAPEFP AWPQYDDAER NGLVRALEQG QWWRMGGDEV NSFEREFAAH    50
    HGAAHALAVT NGTHALELAL QVMGVGPGTE VIVPAFTFIS SSQAAQRLGA 100
    VTVPVDVDAA TYNLDPEAVA AAVTPRTKVI MPVHMAGLMA DMDALAKISA 150
    DTGVPLLQDA AHAHGARWQG KRVGELDSIA TFSFQNGKLM TAGEGGAVVF 200
    PDGETEKYET AFLRHSCGRP RDDRRYFHKI AGSNMRLNEF SASVLRAQLA 250
    RLDEQIAVRD ERWTLLSRLL GAIDGVVPQG GDVRADRNSH YMAMFRIPGL 300
    TEERRNALVD RLVEAGLPAF AAFRAIYRTD AFWELGAPDE SVDAIARRCP 350
    NTDAISSDCV WLHHRVLLAG EPELHATAEI IADAVARA 388
    Length:388
    Mass (Da):42,211
    Last modified:November 13, 2013 - v2
    Checksum:i6537B1541C0410F0
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti56 – 561A → G in AAA75105. (PubMed:9497318)Curated
    Sequence conflicti262 – 2621R → P in AAC01720. (PubMed:9512878)Curated
    Sequence conflicti262 – 2621R → P in AAA75105. (PubMed:9497318)Curated
    Sequence conflicti386 – 3861A → G in AAC01720. (PubMed:9512878)Curated
    Sequence conflicti386 – 3861A → G in AAA75105. (PubMed:9497318)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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.
    RefSeqiYP_005528590.1. NC_017186.1.
    YP_006547106.1. NC_018266.1.

    Genome annotation databases

    EnsemblBacteriaiAEK39133; AEK39133; RAM_03205.
    AFO74161; AFO74161; AMES_0625.
    GeneIDi12122913.
    13406227.
    KEGGiamm:AMES_0625.
    amn:RAM_03205.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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 .
    PIRi I39599.
    RefSeqi YP_005528590.1. NC_017186.1.
    YP_006547106.1. NC_018266.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1B9H X-ray 2.00 A 1-388 [» ]
    1B9I X-ray 2.00 A 1-388 [» ]
    ProteinModelPortali O52552.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AEK39133 ; AEK39133 ; RAM_03205 .
    AFO74161 ; AFO74161 ; AMES_0625 .
    GeneIDi 12122913.
    13406227.
    KEGGi amm:AMES_0625.
    amn:RAM_03205.

    Phylogenomic databases

    KOi K16016.

    Enzyme and pathway databases

    UniPathwayi UPA01029 .
    BioCyci MetaCyc:MONOMER-14078.

    Miscellaneous databases

    EvolutionaryTracei O52552.

    Family and domain databases

    Gene3Di 3.40.640.10. 1 hit.
    3.90.1150.10. 1 hit.
    InterProi IPR000653. DegT/StrS_aminotransferase.
    IPR015424. PyrdxlP-dep_Trfase.
    IPR015421. PyrdxlP-dep_Trfase_major_sub1.
    IPR015422. PyrdxlP-dep_Trfase_major_sub2.
    [Graphical view ]
    Pfami PF01041. DegT_DnrJ_EryC1. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF000390. PLP_StrS. 1 hit.
    SUPFAMi SSF53383. SSF53383. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Biosynthesis of the ansamycin antibiotic rifamycin: deductions from the molecular analysis of the rif biosynthetic gene cluster of Amycolatopsis mediterranei S699."
      August P.R., Tang L., Yoon Y.J., Ning S., Muller R., Yu T.W., Taylor M., Hoffmann D., Kim C.G., Zhang X., Hutchinson C.R., Floss H.G.
      Chem. Biol. 5:69-79(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: S699.
    2. "3-amino-5-hydroxybenzoic acid synthase, the terminal enzyme in the formation of the precursor of mC7N units in rifamycin and related antibiotics."
      Kim C.G., Yu T.W., Fryhle C.B., Handa S., Floss H.G.
      J. Biol. Chem. 273:6030-6040(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-11; 74-90 AND 236-261, FUNCTION AS AHBA SYNTHASE, CATALYTIC ACTIVITY, COFACTOR, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, IDENTIFICATION BY MASS SPECTROMETRY, SUBUNIT, DISRUPTION PHENOTYPE, REACTION MECHANISM.
      Strain: S699.
    3. "Whole genome sequence of the rifamycin B-producing strain Amycolatopsis mediterranei S699."
      Verma M., Kaur J., Kumar M., Kumari K., Saxena A., Anand S., Nigam A., Ravi V., Raghuvanshi S., Khurana P., Tyagi A.K., Khurana J.P., Lal R.
      J. Bacteriol. 193:5562-5563(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: S699.
    4. "Complete genome sequence of Amycolatopsis mediterranei S699 based on de novo assembly via a combinatorial sequencing strategy."
      Tang B., Zhao W., Zheng H., Zhuo Y., Zhang L., Zhao G.P.
      J. Bacteriol. 194:5699-5700(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: S699.
    5. "Mutational analysis and reconstituted expression of the biosynthetic genes involved in the formation of 3-amino-5-hydroxybenzoic acid, the starter unit of rifamycin biosynthesis in amycolatopsis Mediterranei S699."
      Yu T.W., Muller R., Muller M., Zhang X., Draeger G., Kim C.G., Leistner E., Floss H.G.
      J. Biol. Chem. 276:12546-12555(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: DISRUPTION PHENOTYPE.
      Strain: S699.
    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; ADP-159; HIS-162; GLN-185; LYS-188; ARG-219; TYR-226; ARG-236 AND TYR-291.
      Strain: S699.
    7. "Crystal structure of 3-amino-5-hydroxybenzoic acid (AHBA) synthase."
      Eads J.C., Beeby M., Scapin G., Yu T.W., Floss H.G.
      Biochemistry 38:9840-9849(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEXES WITH PYRIDOXAL PHOSPHATE AND THE INHIBITOR GABACULINE, COFACTOR, PYRIDOXAL PHOSPHATE AT LYS-188.
      Strain: S699.

    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: October 1, 2014
    This is version 70 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

    External Data

    Dasty 3