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Protein

Aclacinomycin 10-hydroxylase RdmB

Gene

rdmB

Organism
Streptomyces purpurascens
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the biosynthesis of the anthracycline aclacinomycin which is an aromatic polyketide antibiotic that exhibits high cytotoxicity and is widely applied in the chemotherapy of a variety of cancers. In vivo and in vitro, RdmB catalyzes the removal of the carboxylic group from the C-10 position of 15-demethoxyaclacinomycin T coupled to hydroxylation at the same C-10 position. It could also catalyze the removal of the carboxylic group at the C-10 position of 15-demethoxy-epsilon-rhodomycin coupled to hydroxylation at the same C-10 position to yield rhodomycin B. The reaction catalyzes by RdmB is intriguing, since the enzyme does not use any of the cofactors usually associated with hydroxylases such as flavins and/or metal ions to activate molecular oxygen.2 Publications

Catalytic activityi

15-demethoxyaclacinomycin + reduced acceptor + O2 + H+ = 10-decarboxymethylaclacinomycin + CO2 + acceptor + H2O.2 Publications

Enzyme regulationi

Inhibited by sinefungin and S-adenosyl-L-homocysteine.1 Publication

Pathwayi: aclacinomycin biosynthesis

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

Pathwayi: rhodomycin biosynthesis

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei171 – 1711S-adenosyl-L-methionine2 Publications
Binding sitei190 – 1901S-adenosyl-L-methionine; via carbonyl oxygen2 Publications
Binding sitei213 – 2131S-adenosyl-L-methionine2 Publications
Binding sitei255 – 2551S-adenosyl-L-methionine2 Publications
Binding sitei260 – 2601Substrate1 Publication

GO - Molecular functioni

  • carboxy-lyase activity Source: UniProtKB
  • O-methyltransferase activity Source: InterPro

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Antibiotic biosynthesis

Keywords - Ligandi

S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-18185.
UniPathwayiUPA01042.
UPA01043.

Names & Taxonomyi

Protein namesi
Recommended name:
Aclacinomycin 10-hydroxylase RdmB (EC:4.1.1.-)
Alternative name(s):
15-demethoxy-epsilon-rhodomycin 10-hydroxylase
15-demethoxyaclacinomycin T
Gene namesi
Name:rdmB
OrganismiStreptomyces purpurascens
Taxonomic identifieri1924 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaStreptomycetalesStreptomycetaceaeStreptomyces

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi165 – 1651C → S: Approximately equally active as the native enzyme. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 374374Aclacinomycin 10-hydroxylase RdmBPRO_0000425720Add
BLAST

Interactioni

Subunit structurei

Homodimer and homotetramer in equilibrium.3 Publications

Structurei

Secondary structure

1
374
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi14 – 229Combined sources
Turni23 – 253Combined sources
Helixi28 – 3811Combined sources
Helixi41 – 466Combined sources
Helixi52 – 598Combined sources
Helixi63 – 7513Combined sources
Beta strandi78 – 803Combined sources
Helixi95 – 984Combined sources
Helixi106 – 1105Combined sources
Helixi115 – 1206Combined sources
Helixi121 – 1255Combined sources
Helixi126 – 1327Combined sources
Helixi137 – 1415Combined sources
Helixi145 – 1517Combined sources
Helixi153 – 1619Combined sources
Helixi164 – 1663Combined sources
Turni168 – 1714Combined sources
Helixi172 – 1765Combined sources
Beta strandi185 – 1895Combined sources
Helixi195 – 2039Combined sources
Beta strandi208 – 2136Combined sources
Helixi215 – 22713Combined sources
Turni231 – 2333Combined sources
Beta strandi234 – 2385Combined sources
Beta strandi249 – 2568Combined sources
Helixi258 – 2603Combined sources
Helixi263 – 27614Combined sources
Beta strandi277 – 28711Combined sources
Helixi297 – 31216Combined sources
Helixi319 – 3279Combined sources
Turni328 – 3303Combined sources
Beta strandi331 – 3399Combined sources
Beta strandi342 – 3454Combined sources
Beta strandi348 – 3558Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1QZZX-ray2.10A1-374[»]
1R00X-ray2.50A1-374[»]
1XDSX-ray2.30A/B1-374[»]
1XDUX-ray2.70A1-374[»]
ProteinModelPortaliQ54527.
SMRiQ54527. Positions 10-357.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ54527.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni240 – 2412S-adenosyl-L-methionine binding

Sequence similaritiesi

Phylogenomic databases

KOiK15958.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
3.40.50.150. 1 hit.
InterProiIPR016461. O-MeTrfase_COMT.
IPR001077. O_MeTrfase_2.
IPR029063. SAM-dependent_MTases.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF00891. Methyltransf_2. 1 hit.
[Graphical view]
PIRSFiPIRSF005739. O-mtase. 1 hit.
SUPFAMiSSF46785. SSF46785. 1 hit.
SSF53335. SSF53335. 1 hit.

Sequencei

Sequence statusi: Complete.

Q54527-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSSSSPGEPL EPTDQDLDVL LKNLGNLVTP MALRVAATLR LVDHLLAGAD
60 70 80 90 100
TLAGLADRTD THPQALSRLV RHLTVVGVLE GGEKQGRPLR PTRLGMLLAD
110 120 130 140 150
GHPAQQRAWL DLNGAVSHAD LAFTGLLDVV RTGRPAYAGR YGRPFWEDLS
160 170 180 190 200
ADVALADSFD ALMSCDEDLA YEAPADAYDW SAVRHVLDVG GGNGGMLAAI
210 220 230 240 250
ALRAPHLRGT LVELAGPAER ARRRFADAGL ADRVTVAEGD FFKPLPVTAD
260 270 280 290 300
VVLLSFVLLN WSDEDALTIL RGCVRALEPG GRLLVLDRAD VEGDGADRFF
310 320 330 340 350
STLLDLRMLT FMGGRVRTRD EVVDLAGSAG LALASERTSG STTLPFDFSI
360 370
LEFTAVSEEA APAAQASEAL PAQE
Length:374
Mass (Da):39,797
Last modified:November 1, 1996 - v1
Checksum:i427F37F5C59EEAD2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U10405 Genomic DNA. Translation: AAA83421.1.

Genome annotation databases

KEGGiag:AAA83421.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U10405 Genomic DNA. Translation: AAA83421.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1QZZX-ray2.10A1-374[»]
1R00X-ray2.50A1-374[»]
1XDSX-ray2.30A/B1-374[»]
1XDUX-ray2.70A1-374[»]
ProteinModelPortaliQ54527.
SMRiQ54527. Positions 10-357.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

KEGGiag:AAA83421.

Phylogenomic databases

KOiK15958.

Enzyme and pathway databases

UniPathwayiUPA01042.
UPA01043.
BioCyciMetaCyc:MONOMER-18185.

Miscellaneous databases

EvolutionaryTraceiQ54527.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
3.40.50.150. 1 hit.
InterProiIPR016461. O-MeTrfase_COMT.
IPR001077. O_MeTrfase_2.
IPR029063. SAM-dependent_MTases.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF00891. Methyltransf_2. 1 hit.
[Graphical view]
PIRSFiPIRSF005739. O-mtase. 1 hit.
SUPFAMiSSF46785. SSF46785. 1 hit.
SSF53335. SSF53335. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Hybrid anthracycline antibiotics: production of new anthracyclines by cloned genes from Streptomyces purpurascens in Streptomyces galilaeus."
    Niemi J., Ylihonko K., Hakala J., Parssinen R., Kopio A., Mantsala P.
    Microbiology 140:1351-1358(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 25489 / DSM 40310 / JCM 4509 / NBRC 13077 / Maria 515.
  2. "Nucleotide sequences and expression of genes from Streptomyces purpurascens that cause the production of new anthracyclines in Streptomyces galilaeus."
    Niemi J., Mantsala P.
    J. Bacteriol. 177:2942-2945(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 25489 / DSM 40310 / JCM 4509 / NBRC 13077 / Maria 515.
  3. "Modifications of aclacinomycin T by aclacinomycin methyl esterase (RdmC) and aclacinomycin-10-hydroxylase (RdmB) from Streptomyces purpurascens."
    Wang Y., Niemi J., Airas K., Ylihonko K., Hakala J., Mantsala P.
    Biochim. Biophys. Acta 1480:191-200(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-8, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT.
    Strain: ATCC 25489 / DSM 40310 / JCM 4509 / NBRC 13077 / Maria 515.
  4. "Crystal structure of aclacinomycin-10-hydroxylase, a S-adenosyl-L-methionine-dependent methyltransferase homolog involved in anthracycline biosynthesis in Streptomyces purpurascens."
    Jansson A., Niemi J., Lindqvist Y., Mantsala P., Schneider G.
    J. Mol. Biol. 334:269-280(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEX WITH S-ADENOSYL-L-METHIONINE, SUBUNIT.
  5. "Aclacinomycin 10-hydroxylase is a novel substrate-assisted hydroxylase requiring S-adenosyl-L-methionine as cofactor."
    Jansson A., Koskiniemi H., Erola A., Wang J., Mantsala P., Schneider G., Niemi J.
    J. Biol. Chem. 280:3636-3644(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) IN COMPLEX WITH S-ADENOSYL-L-METHIONINE AND SUBSTRATE, FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF CYS-165, ENZYME REGULATION, REACTION MECHANISM, SUBUNIT.

Entry informationi

Entry nameiRDMB_STREF
AccessioniPrimary (citable) accession number: Q54527
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 19, 2014
Last sequence update: November 1, 1996
Last modified: December 9, 2015
This is version 93 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Although RdmB shows significant similarity to methyltransferase family, it can not act as a methyltransferase.

Keywords - Technical termi

3D-structure, 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

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.