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Q9ZFE7

- MTND_KLEOX

UniProt

Q9ZFE7 - MTND_KLEOX

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Protein

Acireductone dioxygenase

Gene

mtnD

Organism
Klebsiella oxytoca
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

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.1 Publication

Catalytic activityi

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

Cofactori

Binds 1 iron ion per monomer. Can be replaced by magnesium ion, but with lower activity.
Binds 1 nickel ion per monomer. Can be replaced by manganese or cobalt ions.

Kineticsi

  1. KM=50 µM for 1,2-dihydroxy-3-keto-1-hexene (with Ni-ARD)1 Publication
  2. KM=52 µM for 1,2-dihydroxy-3-keto-1-hexene (with Fe-ARD)1 Publication
  3. KM=47 µM for oxygene (with Fe-ARD)1 Publication
  4. KM=110 µM for oxygene (with Ni-ARD)1 Publication

Pathwayi

Sites

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

GO - Molecular functioni

  1. acireductone dioxygenase (Ni2+-requiring) activity Source: UniProtKB-HAMAP
  2. acireductone dioxygenase [iron(II)-requiring] activity Source: UniProtKB-HAMAP
  3. iron ion binding Source: UniProtKB-HAMAP
  4. nickel cation binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. L-methionine biosynthetic process from methylthioadenosine Source: UniProtKB-UniPathway
  2. L-methionine biosynthetic process from S-adenosylmethionine Source: UniProtKB-HAMAP
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

BioCyciMetaCyc:MONOMER-1323.
BRENDAi1.13.11.54. 2811.
UniPathwayiUPA00904; UER00878.

Names & Taxonomyi

Protein namesi
Recommended name:
Acireductone dioxygenase
Alternative name(s):
1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase
Short name:
DHK-MTPene dioxygenase
Acireductone dioxygenase (Fe(2+)-requiring) (EC:1.13.11.54)
Short name:
ARD'
Short name:
Fe-ARD
Acireductone dioxygenase (Ni(2+)-requiring) (EC:1.13.11.53)
Short name:
ARD
Short name:
Ni-ARD
Gene namesi
Name:mtnD
Synonyms:masB
OrganismiKlebsiella oxytoca
Taxonomic identifieri571 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeKlebsiella

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi96 – 961E → A: Loss of dioxygenase activity and decrease in expression of soluble protein. 1 Publication
Mutagenesisi97 – 971H → A: Loss of dioxygenase activity and strong decrease in expression of soluble protein. 1 Publication
Mutagenesisi99 – 991H → A: Loss of dioxygenase activity and decrease in expression of soluble protein. 1 Publication
Mutagenesisi99 – 991H → S: Loss of dioxygenase activity, and little affinity for either Ni(2+) or Fe(3+) ions. 1 Publication
Mutagenesisi101 – 1011E → A: Strong decrease in dioxygenase activity. Exhibits high affinity for both Ni(2+) and Fe(3+) ions, but the activities of both Ni(2+)- and Fe(3+)-reconstituted mutant are considerably lower than wild-type enzymes. 1 Publication
Mutagenesisi102 – 1021D → A: Shows a slight decrease in dioxygenase activity and high affinity for both Ni(2+) and Fe(3+) ions. 1 Publication
Mutagenesisi103 – 1031E → A: Loss of dioxygenase activity and strong decrease in expression of soluble protein. 1 Publication
Mutagenesisi141 – 1411H → A: No expression of soluble protein. 1 Publication
Mutagenesisi141 – 1411H → F: Strong decrease in expression of soluble protein. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 180180Acireductone dioxygenasePRO_0000359200Add
BLAST

Interactioni

Subunit structurei

Monomer.3 Publications

Structurei

Secondary structure

1
180
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 75
Beta strandi12 – 143
Beta strandi15 – 195
Helixi23 – 319
Beta strandi35 – 373
Helixi51 – 6919
Beta strandi72 – 776
Helixi85 – 9410
Beta strandi97 – 1015
Beta strandi103 – 1108
Beta strandi122 – 1265
Beta strandi132 – 1354
Beta strandi141 – 1444
Beta strandi152 – 1576
Helixi160 – 1623
Beta strandi163 – 1653
Helixi173 – 1753

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1ZRRNMR-A2-180[»]
2HJINMR-A2-180[»]
ProteinModelPortaliQ9ZFE7.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9ZFE7.

Family & Domainsi

Sequence similaritiesi

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.

Q9ZFE7-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSALTIFSVK DPQNSLWHST NAEEIQQQLN AKGVRFERWQ ADRDLGAAPT
60 70 80 90 100
AETVIAAYQH AIDKLVAEKG YQSWDVISLR ADNPQKEALR EKFLNEHTHG
110 120 130 140 150
EDEVRFFVEG AGLFCLHIGD EVFQVLCEKN DLISVPAHTP HWFDMGSEPN
160 170 180
FTAIRIFDNP EGWIAQFTGD DIASAYPRLA
Length:180
Mass (Da):20,329
Last modified:January 20, 2009 - v2
Checksum:i7EC4B7E668C91F14
GO

Mass spectrometryi

Molecular mass is 20252 Da from positions 2 - 180. Determined by ESI. Ni-ARD.2 Publications
Molecular mass is 20238 Da from positions 2 - 180. Determined by ESI. Fe-ARD.1 Publication
Molecular mass is 20236 Da from positions 2 - 180. Determined by ESI. Fe-ARD.1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U00148 Genomic DNA. Translation: AAC43184.1.
AF102514 Genomic DNA. Translation: AAD11793.1.
PIRiA59159.
RefSeqiWP_004135399.1. NZ_JNFT01000001.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U00148 Genomic DNA. Translation: AAC43184.1 .
AF102514 Genomic DNA. Translation: AAD11793.1 .
PIRi A59159.
RefSeqi WP_004135399.1. NZ_JNFT01000001.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1ZRR NMR - A 2-180 [» ]
2HJI NMR - A 2-180 [» ]
ProteinModelPortali Q9ZFE7.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Enzyme and pathway databases

UniPathwayi UPA00904 ; UER00878 .
BioCyci MetaCyc:MONOMER-1323.
BRENDAi 1.13.11.54. 2811.

Miscellaneous databases

EvolutionaryTracei Q9ZFE7.

Family and domain databases

Gene3Di 2.60.120.10. 1 hit.
HAMAPi MF_01682. Salvage_MtnD.
InterProi IPR023956. Acireductn_d0ase.
IPR004313. Acireductn_dOase_family.
IPR014710. RmlC-like_jellyroll.
IPR011051. RmlC_Cupin.
[Graphical view ]
PANTHERi PTHR23418. PTHR23418. 1 hit.
Pfami PF03079. ARD. 1 hit.
[Graphical view ]
SUPFAMi SSF51182. SSF51182. 1 hit.
ProtoNeti Search...

Publicationsi

  1. "Appendix. Cloning and sequence of the gene encoding enzyme E-1 from the methionine salvage pathway of Klebsiella oxytoca."
    Balakrishnan R., Frohlich M., Rahaim P.T., Backman K., Yocum R.R.
    J. Biol. Chem. 268:24792-24795(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-82.
    Strain: M5a1.
  2. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 2-180, PROTEIN SEQUENCE OF N-TERMINUS, MASS SPECTROMETRY, COFACTOR.
    Strain: UNF932.
  3. "A bacterial enzyme that catalyzes formation of carbon monoxide."
    Wray J.W., Abeles R.H.
    J. Biol. Chem. 268:21466-21469(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY.
  4. "Mechanistic studies of two dioxygenases in the methionine salvage pathway of Klebsiella pneumoniae."
    Dai Y., Pochapsky T.C., Abeles R.H.
    Biochemistry 40:6379-6387(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: MASS SPECTROMETRY, SUBUNIT, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES.
  5. "Characterization of metal binding in the active sites of acireductone dioxygenase isoforms from Klebsiella ATCC 8724."
    Chai S.C., Ju T., Dang M., Goldsmith R.B., Maroney M.J., Pochapsky T.C.
    Biochemistry 47:2428-2438(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF GLU-96; HIS-97; HIS-99; GLU-101; ASP-102; GLU-103 AND HIS-141, COFACTOR.
  6. "Modeling and experiment yields the structure of acireductone dioxygenase from Klebsiella pneumoniae."
    Pochapsky T.C., Pochapsky S.S., Ju T., Mo H., Al-Mjeni F., Maroney M.J.
    Nat. Struct. Biol. 9:966-972(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR, SUBUNIT, COFACTOR.
  7. "A refined model for the structure of acireductone dioxygenase from Klebsiella ATCC 8724 incorporating residual dipolar couplings."
    Pochapsky T.C., Pochapsky S.S., Ju T., Hoefler C., Liang J.
    J. Biomol. NMR 34:117-127(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR.
  8. "One protein, two enzymes revisited: a structural entropy switch interconverts the two isoforms of acireductone dioxygenase."
    Ju T., Goldsmith R.B., Chai S.C., Maroney M.J., Pochapsky S.S., Pochapsky T.C.
    J. Mol. Biol. 363:823-834(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR, SUBUNIT.

Entry informationi

Entry nameiMTND_KLEOX
AccessioniPrimary (citable) accession number: Q9ZFE7
Secondary accession number(s): Q48390
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 20, 2009
Last sequence update: January 20, 2009
Last modified: October 29, 2014
This is version 67 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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

External Data

Dasty 3