RIFK_AMYMS
ID RIFK_AMYMS Reviewed; 388 AA.
AC O52552; G0FS65; Q44095;
DT 29-MAY-2013, integrated into UniProtKB/Swiss-Prot.
DT 13-NOV-2013, sequence version 2.
DT 03-AUG-2022, entry version 103.
DE RecName: Full=3-amino-5-hydroxybenzoate synthase {ECO:0000303|PubMed:21081954, ECO:0000303|PubMed:9497318};
DE Short=AHBA synthase {ECO:0000303|PubMed:21081954, ECO:0000303|PubMed:9497318};
DE EC=4.2.1.144 {ECO:0000269|PubMed:21081954, ECO:0000269|PubMed:9497318};
DE AltName: Full=Putative UDP-kanosamine synthase aminotransferase subunit {ECO:0000305|PubMed:21081954};
DE EC=2.6.1.- {ECO:0000305|PubMed:21081954};
GN Name=rifK; Synonyms=rifD; OrderedLocusNames=RAM_03205, AMES_0625;
OS Amycolatopsis mediterranei (strain S699) (Nocardia mediterranei).
OC Bacteria; Actinobacteria; Pseudonocardiales; Pseudonocardiaceae;
OC Amycolatopsis.
OX NCBI_TaxID=713604;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=S699;
RX PubMed=9512878; DOI=10.1016/s1074-5521(98)90141-7;
RA August P.R., Tang L., Yoon Y.J., Ning S., Mueller R., Yu T.W., Taylor M.,
RA Hoffmann D., Kim C.G., Zhang X., Hutchinson C.R., Floss H.G.;
RT "Biosynthesis of the ansamycin antibiotic rifamycin: deductions from the
RT molecular analysis of the rif biosynthetic gene cluster of Amycolatopsis
RT mediterranei S699.";
RL Chem. Biol. 5:69-79(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-11; 74-90 AND
RP 236-261, FUNCTION AS AHBA SYNTHASE, CATALYTIC ACTIVITY, COFACTOR, SUBSTRATE
RP SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY REGULATION,
RP IDENTIFICATION BY MASS SPECTROMETRY, SUBUNIT, DISRUPTION PHENOTYPE, AND
RP REACTION MECHANISM.
RC STRAIN=S699;
RX PubMed=9497318; DOI=10.1074/jbc.273.11.6030;
RA Kim C.G., Yu T.W., Fryhle C.B., Handa S., Floss H.G.;
RT "3-amino-5-hydroxybenzoic acid synthase, the terminal enzyme in the
RT formation of the precursor of mC7N units in rifamycin and related
RT antibiotics.";
RL J. Biol. Chem. 273:6030-6040(1998).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=S699;
RX PubMed=21914879; DOI=10.1128/jb.05819-11;
RA Verma M., Kaur J., Kumar M., Kumari K., Saxena A., Anand S., Nigam A.,
RA Ravi V., Raghuvanshi S., Khurana P., Tyagi A.K., Khurana J.P., Lal R.;
RT "Whole genome sequence of the rifamycin B-producing strain Amycolatopsis
RT mediterranei S699.";
RL J. Bacteriol. 193:5562-5563(2011).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=S699;
RX PubMed=23012281; DOI=10.1128/jb.01295-12;
RA Tang B., Zhao W., Zheng H., Zhuo Y., Zhang L., Zhao G.P.;
RT "Complete genome sequence of Amycolatopsis mediterranei S699 based on de
RT novo assembly via a combinatorial sequencing strategy.";
RL J. Bacteriol. 194:5699-5700(2012).
RN [5]
RP DISRUPTION PHENOTYPE.
RC STRAIN=S699;
RX PubMed=11278540; DOI=10.1074/jbc.m009667200;
RA Yu T.W., Muller R., Muller M., Zhang X., Draeger G., Kim C.G., Leistner E.,
RA Floss H.G.;
RT "Mutational analysis and reconstituted expression of the biosynthetic genes
RT involved in the formation of 3-amino-5-hydroxybenzoic acid, the starter
RT unit of rifamycin biosynthesis in amycolatopsis Mediterranei S699.";
RL J. Biol. Chem. 276:12546-12555(2001).
RN [6]
RP PUTATIVE FUNCTION AS UDP-KANOSAMINE SYNTHASE, CATALYTIC ACTIVITY,
RP INTERACTION WITH RIFL, KINETIC PARAMETERS, PATHWAY, AND MUTAGENESIS OF
RP PHE-88; ASP-159; HIS-162; GLN-185; LYS-188; ARG-219; TYR-226; ARG-236 AND
RP TYR-291.
RC STRAIN=S699;
RX PubMed=21081954; DOI=10.1038/ja.2010.139;
RA Floss H.G., Yu T.W., Arakawa K.;
RT "The biosynthesis of 3-amino-5-hydroxybenzoic acid (AHBA), the precursor of
RT mC7N units in ansamycin and mitomycin antibiotics: a review.";
RL J. Antibiot. 64:35-44(2011).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEXES WITH PYRIDOXAL
RP PHOSPHATE AND THE INHIBITOR GABACULINE, COFACTOR, AND PYRIDOXAL PHOSPHATE
RP AT LYS-188.
RC STRAIN=S699;
RX PubMed=10433690; DOI=10.1021/bi990018q;
RA Eads J.C., Beeby M., Scapin G., Yu T.W., Floss H.G.;
RT "Crystal structure of 3-amino-5-hydroxybenzoic acid (AHBA) synthase.";
RL Biochemistry 38:9840-9849(1999).
CC -!- FUNCTION: Catalyzes the dehydration and aromatization of 5-amino-5-
CC deoxy-3-dehydroshikimate (aminoDHS) to 3-amino-5-hydroxybenzoate
CC (AHBA), a compound that then serves as the starter unit for the
CC assembly of a polyketide during the biosynthesis of rifamycin B and
CC other ansamycin antibiotics. Cannot utilize 5-deoxy-5-amino-3-
CC dehydroquinate (aminoDHQ), 5-deoxy-5-aminoshikimate (aminoSA), quinate,
CC 3-dehydroquinate, or 3-dehydroshikimate (DHS) as substrate.
CC {ECO:0000269|PubMed:21081954, ECO:0000269|PubMed:9497318}.
CC -!- FUNCTION: In a complex with RifL, RifK may have a second function in
CC the AHBA pathway, acting as a transaminase introducing the nitrogen
CC into the first pathway intermediate, UDP-3-keto-D-glucose, to give UDP-
CC kanosamine. Appears to use glutamine as the nitrogen donor; NH(4)(+) or
CC asparagine are 30% less effective as nitrogen donors and neither
CC glutamate nor aspartate show activity. {ECO:0000269|PubMed:21081954}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-deoxy-5-amino-3-dehydroshikimate = 3-amino-5-hydroxybenzoate
CC + H(+) + H2O; Xref=Rhea:RHEA:35771, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:71959, ChEBI:CHEBI:71963;
CC EC=4.2.1.144; Evidence={ECO:0000269|PubMed:21081954,
CC ECO:0000269|PubMed:9497318};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-glutamine + UDP-3-oxo-alpha-D-glucose = 2-oxoglutaramate +
CC UDP-alpha-D-kanosamine; Xref=Rhea:RHEA:35775, ChEBI:CHEBI:16769,
CC ChEBI:CHEBI:58359, ChEBI:CHEBI:71964, ChEBI:CHEBI:71965;
CC Evidence={ECO:0000305|PubMed:21081954};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000269|PubMed:10433690, ECO:0000269|PubMed:9497318};
CC Note=Binds 1 pyridoxal phosphate per subunit.
CC {ECO:0000269|PubMed:10433690, ECO:0000269|PubMed:9497318};
CC -!- ACTIVITY REGULATION: AHBA synthase activity is activated by 3-deoxy-D-
CC arabinoheptulosonic acid 7-phosphate (DAHP), an intermediate in the
CC shikimate pathway, and is irreversibly inhibited by gabaculine (5-
CC amino-1,3-cyclohexadiene-1-carboxylate). {ECO:0000269|PubMed:9497318}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.164 mM for 5-amino-5-deoxy-3-dehydroshikimate
CC {ECO:0000269|PubMed:9497318};
CC KM=0.122 mM for 5-amino-5-deoxy-3-dehydroshikimate
CC {ECO:0000269|PubMed:21081954};
CC Note=kcat is 6.82 sec(-1) for AHBA synthase activity.
CC {ECO:0000269|PubMed:21081954};
CC pH dependence:
CC Optimum pH is 7.5 for AHBA synthase activity. Retains its activity
CC over a broad range of pH. Over 84% of the maximum activity of AHBA
CC synthase is maintained over a pH range from 7.0 to 9.0.
CC {ECO:0000269|PubMed:9497318};
CC Temperature dependence:
CC Optimum temperature is 33 degrees Celsius for AHBA synthase activity.
CC Retains its activity over a broad range of temperature. Over 84% of
CC the maximum activity of AHBA synthase is maintained over a
CC temperature range from 28 to 50 degrees Celsius.
CC {ECO:0000269|PubMed:9497318};
CC -!- PATHWAY: Antibiotic biosynthesis; rifamycin B biosynthesis.
CC {ECO:0000269|PubMed:21081954}.
CC -!- SUBUNIT: Homodimer (PubMed:9497318). Can interact with RifL
CC (PubMed:21081954). {ECO:0000269|PubMed:21081954,
CC ECO:0000269|PubMed:9497318}.
CC -!- DISRUPTION PHENOTYPE: Inactivation of the gene encoding AHBA synthase
CC results in loss of rifamycin formation; production of the antibiotic is
CC restored when the mutant is supplemented with AHBA. Cells lacking this
CC gene do not accumulate aminoDHS, aminoDHQ, or their spontaneous
CC aromatization product, protocatechuate. {ECO:0000269|PubMed:11278540,
CC ECO:0000269|PubMed:9497318}.
CC -!- MISCELLANEOUS: Mechanistic studies show that the enzyme-bound pyridoxal
CC phosphate forms a Schiff's base with the amino group of 5-amino-5-
CC deoxy-3-dehydroshikimate and catalyzes both an alpha,beta-dehydration
CC and a stereospecific 1,4-enolization of the substrate.
CC {ECO:0000305|PubMed:9497318}.
CC -!- SIMILARITY: Belongs to the degT/dnrJ/eryC1 family. {ECO:0000305}.
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DR EMBL; AF040570; AAC01720.1; -; Genomic_DNA.
DR EMBL; U33061; AAA75105.1; -; Genomic_DNA.
DR EMBL; CP002896; AEK39133.1; -; Genomic_DNA.
DR EMBL; CP003729; AFO74161.1; -; Genomic_DNA.
DR PIR; I39599; I39599.
DR RefSeq; WP_013222557.1; NC_018266.1.
DR PDB; 1B9H; X-ray; 2.00 A; A=1-388.
DR PDB; 1B9I; X-ray; 2.00 A; A=1-388.
DR PDBsum; 1B9H; -.
DR PDBsum; 1B9I; -.
DR AlphaFoldDB; O52552; -.
DR SMR; O52552; -.
DR STRING; 713604.RAM_03205; -.
DR EnsemblBacteria; AEK39133; AEK39133; RAM_03205.
DR KEGG; amm:AMES_0625; -.
DR KEGG; amn:RAM_03205; -.
DR PATRIC; fig|713604.12.peg.666; -.
DR HOGENOM; CLU_033332_7_1_11; -.
DR OMA; YMAMFRV; -.
DR OrthoDB; 1722208at2; -.
DR BioCyc; MetaCyc:MON-14078; -.
DR BRENDA; 4.2.1.144; 313.
DR UniPathway; UPA01029; -.
DR EvolutionaryTrace; O52552; -.
DR Proteomes; UP000006138; Chromosome.
DR GO; GO:0016829; F:lyase activity; IEA:UniProtKB-KW.
DR GO; GO:0016740; F:transferase activity; IEA:UniProtKB-KW.
DR GO; GO:0017000; P:antibiotic biosynthetic process; IEA:UniProtKB-KW.
DR CDD; cd00616; AHBA_syn; 1.
DR Gene3D; 3.40.640.10; -; 1.
DR Gene3D; 3.90.1150.10; -; 1.
DR InterPro; IPR000653; DegT/StrS_aminotransferase.
DR InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR PANTHER; PTHR30244; PTHR30244; 1.
DR Pfam; PF01041; DegT_DnrJ_EryC1; 1.
DR PIRSF; PIRSF000390; PLP_StrS; 1.
DR SUPFAM; SSF53383; SSF53383; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Antibiotic biosynthesis; Direct protein sequencing; Lyase;
KW Pyridoxal phosphate; Reference proteome; Transferase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:9497318"
FT CHAIN 2..388
FT /note="3-amino-5-hydroxybenzoate synthase"
FT /id="PRO_0000422400"
FT MOD_RES 188
FT /note="N6-(pyridoxal phosphate)lysine"
FT MUTAGEN 88
FT /note="F->A: Loss of AHBA synthase activity."
FT /evidence="ECO:0000269|PubMed:21081954"
FT MUTAGEN 159
FT /note="D->A,E,K: Loss of AHBA synthase activity."
FT /evidence="ECO:0000269|PubMed:21081954"
FT MUTAGEN 162
FT /note="H->L: 2-fold decrease in AHBA synthase activity."
FT /evidence="ECO:0000269|PubMed:21081954"
FT MUTAGEN 185
FT /note="Q->E,H,L: Loss of AHBA synthase activity."
FT /evidence="ECO:0000269|PubMed:21081954"
FT MUTAGEN 188
FT /note="K->D: Loss of AHBA synthase activity."
FT /evidence="ECO:0000269|PubMed:21081954"
FT MUTAGEN 219
FT /note="R->A: 10-fold decrease in AHBA synthase activity."
FT /evidence="ECO:0000269|PubMed:21081954"
FT MUTAGEN 226
FT /note="Y->F: Loss of AHBA synthase activity."
FT /evidence="ECO:0000269|PubMed:21081954"
FT MUTAGEN 236
FT /note="R->A: Loss of AHBA synthase activity."
FT /evidence="ECO:0000269|PubMed:21081954"
FT MUTAGEN 291
FT /note="Y->A: Loss of AHBA synthase activity."
FT /evidence="ECO:0000269|PubMed:21081954"
FT MUTAGEN 291
FT /note="Y->F: 7-fold decrease in AHBA synthase activity."
FT /evidence="ECO:0000269|PubMed:21081954"
FT CONFLICT 56
FT /note="A -> G (in Ref. 2; AAA75105)"
FT /evidence="ECO:0000305"
FT CONFLICT 262
FT /note="R -> P (in Ref. 1; AAC01720 and 2; AAA75105)"
FT /evidence="ECO:0000305"
FT CONFLICT 386
FT /note="A -> G (in Ref. 1; AAC01720 and 2; AAA75105)"
FT /evidence="ECO:0000305"
FT HELIX 17..28
FT /evidence="ECO:0007829|PDB:1B9H"
FT TURN 34..36
FT /evidence="ECO:0007829|PDB:1B9H"
FT HELIX 39..50
FT /evidence="ECO:0007829|PDB:1B9H"
FT STRAND 54..60
FT /evidence="ECO:0007829|PDB:1B9H"
FT HELIX 62..72
FT /evidence="ECO:0007829|PDB:1B9H"
FT STRAND 80..87
FT /evidence="ECO:0007829|PDB:1B9H"
FT HELIX 90..97
FT /evidence="ECO:0007829|PDB:1B9H"
FT STRAND 101..105
FT /evidence="ECO:0007829|PDB:1B9H"
FT TURN 109..111
FT /evidence="ECO:0007829|PDB:1B9H"
FT HELIX 116..122
FT /evidence="ECO:0007829|PDB:1B9H"
FT STRAND 127..130
FT /evidence="ECO:0007829|PDB:1B9H"
FT HELIX 135..137
FT /evidence="ECO:0007829|PDB:1B9H"
FT HELIX 142..152
FT /evidence="ECO:0007829|PDB:1B9H"
FT HELIX 173..175
FT /evidence="ECO:0007829|PDB:1B9H"
FT STRAND 176..178
FT /evidence="ECO:0007829|PDB:1B9H"
FT STRAND 180..183
FT /evidence="ECO:0007829|PDB:1B9H"
FT STRAND 188..190
FT /evidence="ECO:0007829|PDB:1B9H"
FT STRAND 192..194
FT /evidence="ECO:0007829|PDB:1B9H"
FT STRAND 196..200
FT /evidence="ECO:0007829|PDB:1B9H"
FT HELIX 205..214
FT /evidence="ECO:0007829|PDB:1B9H"
FT HELIX 239..249
FT /evidence="ECO:0007829|PDB:1B9H"
FT HELIX 252..271
FT /evidence="ECO:0007829|PDB:1B9H"
FT STRAND 291..296
FT /evidence="ECO:0007829|PDB:1B9H"
FT HELIX 302..314
FT /evidence="ECO:0007829|PDB:1B9H"
FT STRAND 319..321
FT /evidence="ECO:0007829|PDB:1B9H"
FT HELIX 326..328
FT /evidence="ECO:0007829|PDB:1B9H"
FT HELIX 330..334
FT /evidence="ECO:0007829|PDB:1B9H"
FT HELIX 342..347
FT /evidence="ECO:0007829|PDB:1B9H"
FT HELIX 350..358
FT /evidence="ECO:0007829|PDB:1B9H"
FT STRAND 359..363
FT /evidence="ECO:0007829|PDB:1B9H"
FT HELIX 364..368
FT /evidence="ECO:0007829|PDB:1B9H"
FT HELIX 371..387
FT /evidence="ECO:0007829|PDB:1B9H"
SQ SEQUENCE 388 AA; 42211 MW; 6537B1541C0410F0 CRC64;
MNARKAPEFP AWPQYDDAER NGLVRALEQG QWWRMGGDEV NSFEREFAAH HGAAHALAVT
NGTHALELAL QVMGVGPGTE VIVPAFTFIS SSQAAQRLGA VTVPVDVDAA TYNLDPEAVA
AAVTPRTKVI MPVHMAGLMA DMDALAKISA DTGVPLLQDA AHAHGARWQG KRVGELDSIA
TFSFQNGKLM TAGEGGAVVF PDGETEKYET AFLRHSCGRP RDDRRYFHKI AGSNMRLNEF
SASVLRAQLA RLDEQIAVRD ERWTLLSRLL GAIDGVVPQG GDVRADRNSH YMAMFRIPGL
TEERRNALVD RLVEAGLPAF AAFRAIYRTD AFWELGAPDE SVDAIARRCP NTDAISSDCV
WLHHRVLLAG EPELHATAEI IADAVARA
