Acireductone dioxygenase - Klebsiella oxytoca

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Q9ZFE7 (MTND_KLEOX) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 63. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

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)
Short name=ARD'
Short name=Fe-ARD
EC=1.13.11.54
Acireductone dioxygenase (Ni(2+)-requiring)
Short name=ARD
Short name=Ni-ARD
EC=1.13.11.53

Gene names

Name:	mtnD
Synonyms:	masB

Organism

Klebsiella oxytoca

Taxonomic identifier

571 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Klebsiella

Protein attributes

Sequence length	180 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.3
Catalytic activity	1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O₂ = 3-(methylthio)propanoate + formate + CO. Ref.3 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O₂ = 4-(methylthio)-2-oxobutanoate + formate.
Cofactor	Binds 1 iron ion per monomer. Can be replaced by magnesium ion, but with lower activity. Ref.2 Ref.4 Ref.5 Ref.6 Binds 1 nickel ion per monomer. Can be replaced by manganese or cobalt ions. Ref.2 Ref.4 Ref.5 Ref.6
Pathway	Amino-acid biosynthesis; L-methionine biosynthesis via salvage pathway; L-methionine from S-methyl-5-thio-alpha-D-ribose 1-phosphate: step 5/6. HAMAP-Rule MF_01682
Subunit structure	Monomer. Ref.4 Ref.6 Ref.8
Sequence similarities	Belongs to the acireductone dioxygenase (ARD) family.
Biophysicochemical properties	Kinetic parameters: K_M=50 µM for 1,2-dihydroxy-3-keto-1-hexene (with Ni-ARD) Ref.4 K_M=52 µM for 1,2-dihydroxy-3-keto-1-hexene (with Fe-ARD) K_M=47 µM for oxygene (with Fe-ARD) K_M=110 µM for oxygene (with Ni-ARD)
Mass spectrometry	Molecular mass is 20252 Da from positions 2 - 180. Determined by ESI. Ni-ARD. Ref.2 Ref.4 Molecular mass is 20238 Da from positions 2 - 180. Determined by ESI. Fe-ARD. Ref.2 Molecular mass is 20236 Da from positions 2 - 180. Determined by ESI. Fe-ARD. Ref.4

Ontologies

Keywords
Biological process	Amino-acid biosynthesis Methionine biosynthesis
Ligand	Iron Metal-binding Nickel
Molecular function	Dioxygenase Oxidoreductase
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological_process	L-methionine biosynthetic process from S-adenosylmethionine Inferred from electronic annotation. Source: HAMAP L-methionine salvage from methylthioadenosine Inferred from electronic annotation. Source: UniProtKB-UniPathway
Molecular_function	acireductone dioxygenase (Ni2+-requiring) activity Inferred from electronic annotation. Source: HAMAP acireductone dioxygenase [iron(II)-requiring] activity Inferred from electronic annotation. Source: HAMAP iron ion binding Inferred from electronic annotation. Source: HAMAP nickel cation binding Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 180

180

Acireductone dioxygenase HAMAP-Rule MF_01682

PRO_0000359200

Sites

Metal binding

Iron; alternate

Metal binding

Nickel; alternate

Metal binding

Iron; alternate

Metal binding

Nickel; alternate

Metal binding

103

Iron; alternate

Metal binding

103

Nickel; alternate

Metal binding

141

Iron; alternate

Metal binding

141

Nickel; alternate

Site

May play a role in metal incorporation in vivo

Site

102

May play a role in transmitting local conformational changes

Site

105

Important to generate the dianion

Experimental info

Mutagenesis

E → A: Loss of dioxygenase activity and decrease in expression of soluble protein. Ref.5

Mutagenesis

H → A: Loss of dioxygenase activity and strong decrease in expression of soluble protein. Ref.5

Mutagenesis

H → A: Loss of dioxygenase activity and decrease in expression of soluble protein. Ref.5

Mutagenesis

H → S: Loss of dioxygenase activity, and little affinity for either Ni(2+) or Fe(3+) ions. Ref.5

Mutagenesis

101

E → 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. Ref.5

Mutagenesis

102

D → A: Shows a slight decrease in dioxygenase activity and high affinity for both Ni(2+) and Fe(3+) ions. Ref.5

Mutagenesis

103

E → A: Loss of dioxygenase activity and strong decrease in expression of soluble protein. Ref.5

Mutagenesis

141

H → A: No expression of soluble protein. Ref.5

Mutagenesis

141

H → F: Strong decrease in expression of soluble protein. Ref.5

Secondary structure

180

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

Q9ZFE7 [UniParc].

Last modified January 20, 2009. Version 2.
Checksum: 7EC4B7E668C91F14
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FASTA

180

20,329

        10         20         30         40         50         60 
MSALTIFSVK DPQNSLWHST NAEEIQQQLN AKGVRFERWQ ADRDLGAAPT AETVIAAYQH 

        70         80         90        100        110        120 
AIDKLVAEKG YQSWDVISLR ADNPQKEALR EKFLNEHTHG EDEVRFFVEG AGLFCLHIGD 

       130        140        150        160        170        180 
EVFQVLCEKN DLISVPAHTP HWFDMGSEPN FTAIRIFDNP EGWIAQFTGD DIASAYPRLA

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References

[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]	"One protein, two enzymes." Dai Y., Wensink P.C., Abeles R.H. J. Biol. Chem. 274:1193-1195(1999) [PubMed] [Europe PMC] [Abstract] 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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U00148 Genomic DNA. Translation: AAC43184.1.
AF102514 Genomic DNA. Translation: AAD11793.1.

PIR

A59159.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1ZRR	NMR	-	A	2-180	[»]
2HJI	NMR	-	A	2-180	[»]

ProteinModelPortal

Q9ZFE7.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Enzyme and pathway databases

BioCyc

MetaCyc:MONOMER-1323.

BRENDA

1.13.11.54. 2811.

UniPathway

UPA00904; UER00878.

Family and domain databases

Gene3D

2.60.120.10. 1 hit.

HAMAP

MF_01682. Salvage_MtnD.

InterPro

IPR023956. Acireductn_d0ase.
IPR004313. Acireductn_dOase_family.
IPR014710. RmlC-like_jellyroll.
IPR011051. RmlC_Cupin.
[Graphical view]

PANTHER

PTHR23418. PTHR23418. 1 hit.

Pfam

PF03079. ARD. 1 hit.
[Graphical view]

SUPFAM

SSF51182. RmlC_like_cupin. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

Q9ZFE7.

Entry information

Entry name

MTND_KLEOX

Accession

Primary (citable) accession number: Q9ZFE7
Secondary accession number(s): Q48390

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 20, 2009
Last sequence update:	January 20, 2009
Last modified:	April 3, 2013
This is version 63 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protocols and materials databases

Enzyme and pathway databases

Family and domain databases

Other

Entry information

Relevant documents