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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)DescriptionActionsGraphical viewLength
Binding sitei171S-adenosyl-L-methionine2 Publications1
Binding sitei190S-adenosyl-L-methionine; via carbonyl oxygen2 Publications1
Binding sitei213S-adenosyl-L-methionine2 Publications1
Binding sitei255S-adenosyl-L-methionine2 Publications1
Binding sitei260Substrate1 Publication1

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)DescriptionActionsGraphical viewLength
Mutagenesisi165C → S: Approximately equally active as the native enzyme. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004257201 – 374Aclacinomycin 10-hydroxylase RdmBAdd BLAST374

Interactioni

Subunit structurei

Homodimer and homotetramer in equilibrium.3 Publications

Structurei

Secondary structure

1374
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi14 – 22Combined sources9
Turni23 – 25Combined sources3
Helixi28 – 38Combined sources11
Helixi41 – 46Combined sources6
Helixi52 – 59Combined sources8
Helixi63 – 75Combined sources13
Beta strandi78 – 80Combined sources3
Helixi95 – 98Combined sources4
Helixi106 – 110Combined sources5
Helixi115 – 120Combined sources6
Helixi121 – 125Combined sources5
Helixi126 – 132Combined sources7
Helixi137 – 141Combined sources5
Helixi145 – 151Combined sources7
Helixi153 – 161Combined sources9
Helixi164 – 166Combined sources3
Turni168 – 171Combined sources4
Helixi172 – 176Combined sources5
Beta strandi185 – 189Combined sources5
Helixi195 – 203Combined sources9
Beta strandi208 – 213Combined sources6
Helixi215 – 227Combined sources13
Turni231 – 233Combined sources3
Beta strandi234 – 238Combined sources5
Beta strandi249 – 256Combined sources8
Helixi258 – 260Combined sources3
Helixi263 – 276Combined sources14
Beta strandi277 – 287Combined sources11
Helixi297 – 312Combined sources16
Helixi319 – 327Combined sources9
Turni328 – 330Combined sources3
Beta strandi331 – 339Combined sources9
Beta strandi342 – 345Combined sources4
Beta strandi348 – 355Combined sources8

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiQ54527.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni240 – 241S-adenosyl-L-methionine binding2

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1QZZX-ray2.10A1-374[»]
1R00X-ray2.50A1-374[»]
1XDSX-ray2.30A/B1-374[»]
1XDUX-ray2.70A1-374[»]
ProteinModelPortaliQ54527.
SMRiQ54527.
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...

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: November 2, 2016
This is version 97 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 cannot 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.