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O52552

- RIFK_AMYMS

UniProt

O52552 - RIFK_AMYMS

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Protein

3-amino-5-hydroxybenzoate synthase

Gene
rifK, rifD, RAM_03205, AMES_0625
Organism
Amycolatopsis mediterranei (strain S699) (Nocardia mediterranei)
Status
Reviewed - 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. Can not utilize 5-deoxy-5-amino-3-dehydroquinate (aminoDHQ), 5-deoxy-5-aminoshikimate (aminoSA), quinate, 3-dehydroquinate, or 3-dehydroshikimate (DHS) as substrate.2 Publications
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.2 Publications

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-dehydroshikimate (1 Publication)2 Publications
  2. KM=0.122 mM for 5-amino-5-deoxy-3-dehydroshikimate (1 Publication)

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.

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.

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
Complete GO annotation...

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.

Miscellaneous databases

EvolutionaryTraceiO52552.

Family & Domainsi

Sequence similaritiesi

Belongs to the degT/dnrJ/eryC1 family.

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

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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

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti56 – 561A → G in AAA75105. 1 Publication
Sequence conflicti262 – 2621R → P in AAC01720. 1 Publication
Sequence conflicti262 – 2621R → P in AAA75105. 1 Publication
Sequence conflicti386 – 3861A → G in AAC01720. 1 Publication
Sequence conflicti386 – 3861A → G in AAA75105. 1 Publication

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

« Hide 'large scale' publications
  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: July 9, 2014
This is version 69 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

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

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