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Protein

Acireductone dioxygenase

Gene

mtnD

Organism
Parvibaculum lavamentivorans (strain DS-1 / DSM 13023 / NCIMB 13966)
Status
Reviewed-Annotation score: Annotation score: 4 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

Pathway: 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

BioCyciPLAV402881:GHQA-1879-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:Plav_1853
OrganismiParvibaculum lavamentivorans (strain DS-1 / DSM 13023 / NCIMB 13966)
Taxonomic identifieri402881 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhodobiaceaeParvibaculum
ProteomesiUP000006377 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 184184Acireductone dioxygenasePRO_0000359214Add
BLAST

Interactioni

Subunit structurei

Monomer.UniRule annotation

Protein-protein interaction databases

STRINGi402881.Plav_1853.

Structurei

3D structure databases

ProteinModelPortaliA7HU87.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG1791.
HOGENOMiHOG000201072.
KOiK08967.
OMAiVLCEKND.
OrthoDBiEOG6ZPT06.

Family and domain databases

Gene3Di2.60.120.10. 1 hit.
HAMAPiMF_01682. Salvage_MtnD.
InterProiIPR023956. Acireductn_d0ase.
IPR004313. Acireductn_dOase_family.
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.

A7HU87-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTHLTVYPDT DPATVLLDTR DGAEIAASLS GIGVVFERWD APHALGEDAD
60 70 80 90 100
QTAVLAAYEA DVKRLMDEGG YKSVDVVRVK PDNPNRAEMR QKFLAEHTHD
110 120 130 140 150
DDEVRFFVEG AGAFYLRKDG RVYRVVCERN DLISVPAGTT HWFDTGAAPH
160 170 180
FCAIRIFTSP EGWVGHFTGD DIATRFPKFE SEPQ
Length:184
Mass (Da):20,487
Last modified:September 11, 2007 - v1
Checksum:iDDCA09AEF14BD9AD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000774 Genomic DNA. Translation: ABS63470.1.
RefSeqiWP_012110763.1. NC_009719.1.
YP_001413127.1. NC_009719.1.

Genome annotation databases

EnsemblBacteriaiABS63470; ABS63470; Plav_1853.
KEGGipla:Plav_1853.
PATRICi22865357. VBIParLav90819_1905.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000774 Genomic DNA. Translation: ABS63470.1.
RefSeqiWP_012110763.1. NC_009719.1.
YP_001413127.1. NC_009719.1.

3D structure databases

ProteinModelPortaliA7HU87.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi402881.Plav_1853.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABS63470; ABS63470; Plav_1853.
KEGGipla:Plav_1853.
PATRICi22865357. VBIParLav90819_1905.

Phylogenomic databases

eggNOGiCOG1791.
HOGENOMiHOG000201072.
KOiK08967.
OMAiVLCEKND.
OrthoDBiEOG6ZPT06.

Enzyme and pathway databases

UniPathwayiUPA00904; UER00878.
BioCyciPLAV402881:GHQA-1879-MONOMER.

Family and domain databases

Gene3Di2.60.120.10. 1 hit.
HAMAPiMF_01682. Salvage_MtnD.
InterProiIPR023956. Acireductn_d0ase.
IPR004313. Acireductn_dOase_family.
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. "Complete genome sequence and annotation of Parvibaculum lavamentivorans DS-1."
    Copeland A., Lucas S., Lapidus A., Barry K., Glavina del Rio T., Dalin E., Tice H., Pitluck S., Saunders E., Brettin T., Bruce D., Detter J.C., Han C., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Richardson P.
    Submitted (JUL-2007) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: DS-1 / DSM 13023 / NCIMB 13966.

Entry informationi

Entry nameiMTND_PARL1
AccessioniPrimary (citable) accession number: A7HU87
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 20, 2009
Last sequence update: September 11, 2007
Last modified: April 1, 2015
This is version 53 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.