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O52552 (RIFK_AMYMS) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 69. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
3-amino-5-hydroxybenzoate synthase

Short name=AHBA synthase
EC=4.2.1.144
Alternative name(s):
Putative UDP-kanosamine synthase aminotransferase subunit
EC=2.6.1.-
Gene names
Name:rifK
Synonyms:rifD
Ordered Locus Names:RAM_03205, AMES_0625
OrganismAmycolatopsis mediterranei (strain S699) (Nocardia mediterranei) [Complete proteome] [HAMAP]
Taxonomic identifier713604 [NCBI]
Taxonomic lineageBacteriaActinobacteriaActinobacteridaeActinomycetalesPseudonocardineaePseudonocardiaceaeAmycolatopsis

Protein attributes

Sequence length388 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.2 Ref.6

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. Ref.2 Ref.6

Catalytic activity

5-amino-5-deoxy-3-dehydroshikimate = 3-amino-5-hydroxybenzoate + H2O. Ref.2

UDP-3-keto-alpha-D-glucose + L-glutamine = UDP-alpha-D-kanosamine + L-glutaramate. Ref.2

Cofactor

Binds 1 pyridoxal phosphate per subunit. Ref.2 Ref.7

Enzyme regulation

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). Ref.2

Pathway

Antibiotic biosynthesis; rifamycin B biosynthesis. Ref.6

Subunit structure

Homodimer. Can interact with RifL. Ref.2

Disruption phenotype

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. Ref.2 Ref.5

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 (Ref.2).

Sequence similarities

Belongs to the degT/dnrJ/eryC1 family.

Biophysicochemical properties

Kinetic parameters:

kcat is 6.82 sec(-1) for AHBA synthase activity (Ref.6).

KM=0.164 mM for 5-amino-5-deoxy-3-dehydroshikimate (Ref.2) Ref.2 Ref.6

KM=0.122 mM for 5-amino-5-deoxy-3-dehydroshikimate (Ref.6)

pH dependence:

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 dependence:

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.

Ontologies

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.2
Chain2 – 3883873-amino-5-hydroxybenzoate synthase
PRO_0000422400

Amino acid modifications

Modified residue1881N6-(pyridoxal phosphate)lysine

Experimental info

Mutagenesis881F → A: Loss of AHBA synthase activity. Ref.6
Mutagenesis1591D → A, E or K: Loss of AHBA synthase activity. Ref.6
Mutagenesis1621H → L: 2-fold decrease in AHBA synthase activity. Ref.6
Mutagenesis1851Q → E, H or L: Loss of AHBA synthase activity. Ref.6
Mutagenesis1881K → D: Loss of AHBA synthase activity. Ref.6
Mutagenesis2191R → A: 10-fold decrease in AHBA synthase activity. Ref.6
Mutagenesis2261Y → F: Loss of AHBA synthase activity. Ref.6
Mutagenesis2361R → A: Loss of AHBA synthase activity. Ref.6
Mutagenesis2911Y → A: Loss of AHBA synthase activity. Ref.6
Mutagenesis2911Y → F: 7-fold decrease in AHBA synthase activity. Ref.6
Sequence conflict561A → G in AAA75105. Ref.2
Sequence conflict2621R → P in AAC01720. Ref.1
Sequence conflict2621R → P in AAA75105. Ref.2
Sequence conflict3861A → G in AAC01720. Ref.1
Sequence conflict3861A → G in AAA75105. Ref.2

Secondary structure

.............................................................. 388
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
O52552 [UniParc].

Last modified November 13, 2013. Version 2.
Checksum: 6537B1541C0410F0

FASTA38842,211
        10         20         30         40         50         60 
MNARKAPEFP AWPQYDDAER NGLVRALEQG QWWRMGGDEV NSFEREFAAH HGAAHALAVT 

        70         80         90        100        110        120 
NGTHALELAL QVMGVGPGTE VIVPAFTFIS SSQAAQRLGA VTVPVDVDAA TYNLDPEAVA 

       130        140        150        160        170        180 
AAVTPRTKVI MPVHMAGLMA DMDALAKISA DTGVPLLQDA AHAHGARWQG KRVGELDSIA 

       190        200        210        220        230        240 
TFSFQNGKLM TAGEGGAVVF PDGETEKYET AFLRHSCGRP RDDRRYFHKI AGSNMRLNEF 

       250        260        270        280        290        300 
SASVLRAQLA RLDEQIAVRD ERWTLLSRLL GAIDGVVPQG GDVRADRNSH YMAMFRIPGL 

       310        320        330        340        350        360 
TEERRNALVD RLVEAGLPAF AAFRAIYRTD AFWELGAPDE SVDAIARRCP NTDAISSDCV 

       370        380 
WLHHRVLLAG EPELHATAEI IADAVARA 

« Hide

References

« Hide 'large scale' references
[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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF040570 Genomic DNA. Translation: AAC01720.1.
U33061 Genomic DNA. Translation: AAA75105.1.
CP002896 Genomic DNA. Translation: AEK39133.1.
CP003729 Genomic DNA. Translation: AFO74161.1.
PIRI39599.
RefSeqYP_005528590.1. NC_017186.1.
YP_006547106.1. NC_018266.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1B9HX-ray2.00A1-388[»]
1B9IX-ray2.00A1-388[»]
ProteinModelPortalO52552.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAEK39133; AEK39133; RAM_03205.
AFO74161; AFO74161; AMES_0625.
GeneID12122913.
13406227.
KEGGamm:AMES_0625.
amn:RAM_03205.

Organism-specific databases

CMRSearch...

Phylogenomic databases

KOK16016.

Enzyme and pathway databases

BioCycMetaCyc:MONOMER-14078.
UniPathwayUPA01029.

Family and domain databases

Gene3D3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
InterProIPR000653. DegT/StrS_aminotransferase.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]
PfamPF01041. DegT_DnrJ_EryC1. 1 hit.
[Graphical view]
PIRSFPIRSF000390. PLP_StrS. 1 hit.
SUPFAMSSF53383. SSF53383. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceO52552.

Entry information

Entry nameRIFK_AMYMS
AccessionPrimary (citable) accession number: O52552
Secondary accession number(s): G0FS65, Q44095
Entry history
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 statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways