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Protein

Acireductone dioxygenase

Gene

mtnD

Organism
Yersinia pestis (strain Pestoides F)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Catalyzes 2 different reactions between oxygene and the acireductone 1,2-dihydroxy-3-keto-5-methylthiopentene (DHK-MTPene) depending upon the metal bound in the active site. Fe-containing acireductone dioxygenase (Fe-ARD) produces formate and 2-keto-4-methylthiobutyrate (KMTB), the alpha-ketoacid precursor of methionine in the methionine recycle pathway. Ni-containing acireductone dioxygenase (Ni-ARD) produces methylthiopropionate, carbon monoxide and formate, and does not lie on the methionine recycle pathway.UniRule annotation

Catalytic activityi

1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2 = 3-(methylthio)propanoate + formate + CO.UniRule annotation
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2 = 4-(methylthio)-2-oxobutanoate + formate.UniRule annotation

Cofactori

Protein has several cofactor binding sites:
  • Fe cationUniRule annotationNote: Binds 1 Fe cation per monomer.UniRule annotation
  • Ni2+UniRule annotationNote: Binds 1 nickel ion per monomer.UniRule annotation

Pathwayi: L-methionine biosynthesis via salvage pathway

This protein is involved in step 5 of the subpathway that synthesizes L-methionine from S-methyl-5-thio-alpha-D-ribose 1-phosphate.UniRule annotation
Proteins known to be involved in the 6 steps of the subpathway in this organism are:
  1. Methylthioribose-1-phosphate isomerase (mtnA)
  2. Methylthioribulose-1-phosphate dehydratase (mtnB)
  3. Enolase-phosphatase E1 (mtnC)
  4. Enolase-phosphatase E1 (mtnC)
  5. Acireductone dioxygenase (mtnD)
  6. no protein annotated in this organism
This subpathway is part of the pathway L-methionine biosynthesis via salvage pathway, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-methionine from S-methyl-5-thio-alpha-D-ribose 1-phosphate, the pathway L-methionine biosynthesis via salvage pathway and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei96 – 961May play a role in metal incorporation in vivoUniRule annotation
Metal bindingi97 – 971Iron; alternateUniRule annotation
Metal bindingi97 – 971Nickel; alternateUniRule annotation
Metal bindingi99 – 991Iron; alternateUniRule annotation
Metal bindingi99 – 991Nickel; alternateUniRule annotation
Sitei102 – 1021May play a role in transmitting local conformational changesUniRule annotation
Metal bindingi103 – 1031Iron; alternateUniRule annotation
Metal bindingi103 – 1031Nickel; alternateUniRule annotation
Sitei105 – 1051Important to generate the dianionUniRule annotation
Metal bindingi141 – 1411Iron; alternateUniRule annotation
Metal bindingi141 – 1411Nickel; alternateUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Dioxygenase, Oxidoreductase

Keywords - Biological processi

Amino-acid biosynthesis, Methionine biosynthesis

Keywords - Ligandi

Iron, Metal-binding, Nickel

Enzyme and pathway databases

BioCyciYPES386656:GKD7-2939-MONOMER.
UniPathwayiUPA00904; UER00878.

Names & Taxonomyi

Protein namesi
Recommended name:
Acireductone dioxygenaseUniRule annotation
Alternative name(s):
1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenaseUniRule annotation
Short name:
DHK-MTPene dioxygenaseUniRule annotation
Acireductone dioxygenase (Fe(2+)-requiring)UniRule annotation (EC:1.13.11.54UniRule annotation)
Short name:
ARD'UniRule annotation
Short name:
Fe-ARDUniRule annotation
Acireductone dioxygenase (Ni(2+)-requiring)UniRule annotation (EC:1.13.11.53UniRule annotation)
Short name:
ARDUniRule annotation
Short name:
Ni-ARDUniRule annotation
Gene namesi
Name:mtnDUniRule annotation
Ordered Locus Names:YPDSF_2880
OrganismiYersinia pestis (strain Pestoides F)
Taxonomic identifieri386656 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeYersinia

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 180180Acireductone dioxygenasePRO_0000359259Add
BLAST

Interactioni

Subunit structurei

Monomer.UniRule annotation

Structurei

3D structure databases

ProteinModelPortaliA4TPN0.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the acireductone dioxygenase (ARD) family.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000201072.
KOiK08967.
OMAiWFDMGSE.
OrthoDBiEOG6ZPT06.

Family and domain databases

Gene3Di2.60.120.10. 1 hit.
HAMAPiMF_01682. Salvage_MtnD.
InterProiIPR004313. ARD.
IPR023956. ARD_bac.
IPR014710. RmlC-like_jellyroll.
IPR011051. RmlC_Cupin.
[Graphical view]
PANTHERiPTHR23418. PTHR23418. 1 hit.
PfamiPF03079. ARD. 1 hit.
[Graphical view]
SUPFAMiSSF51182. SSF51182. 1 hit.

Sequencei

Sequence statusi: Complete.

A4TPN0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSGLTIFSDQ QPEKPLWQSH NAEEIQQQLT AIGVRFERWQ ADCELGENPQ
60 70 80 90 100
PEAVIAAYQH EIDRLVAENG YKSWDVISMR PDNPQREALR EKFLSEHTHG
110 120 130 140 150
EDEVRFFVEG SGLFCLHLNE KVYQILCEKN DLLSVPADIP HWFDMGSAPN
160 170 180
FTAIRVFDNP EGWIARSTGD NIADGYPRLA
Length:180
Mass (Da):20,585
Last modified:May 15, 2007 - v1
Checksum:iD25D6F3FDDBD957F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000668 Genomic DNA. Translation: ABP41242.1.
RefSeqiWP_011191833.1. NZ_CP009715.1.

Genome annotation databases

EnsemblBacteriaiABP41242; ABP41242; YPDSF_2880.
KEGGiypp:YPDSF_2880.
PATRICi18615534. VBIYerPes122972_3650.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000668 Genomic DNA. Translation: ABP41242.1.
RefSeqiWP_011191833.1. NZ_CP009715.1.

3D structure databases

ProteinModelPortaliA4TPN0.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABP41242; ABP41242; YPDSF_2880.
KEGGiypp:YPDSF_2880.
PATRICi18615534. VBIYerPes122972_3650.

Phylogenomic databases

HOGENOMiHOG000201072.
KOiK08967.
OMAiWFDMGSE.
OrthoDBiEOG6ZPT06.

Enzyme and pathway databases

UniPathwayiUPA00904; UER00878.
BioCyciYPES386656:GKD7-2939-MONOMER.

Family and domain databases

Gene3Di2.60.120.10. 1 hit.
HAMAPiMF_01682. Salvage_MtnD.
InterProiIPR004313. ARD.
IPR023956. ARD_bac.
IPR014710. RmlC-like_jellyroll.
IPR011051. RmlC_Cupin.
[Graphical view]
PANTHERiPTHR23418. PTHR23418. 1 hit.
PfamiPF03079. ARD. 1 hit.
[Graphical view]
SUPFAMiSSF51182. SSF51182. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Pestoides F.

Entry informationi

Entry nameiMTND_YERPP
AccessioniPrimary (citable) accession number: A4TPN0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 20, 2009
Last sequence update: May 15, 2007
Last modified: November 11, 2015
This is version 60 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.