EzCatDB: D00251

DB codeD00251
CATH domainDomain 12.40.37.10Catalytic domain
Domain 23.20.20.10Catalytic domain
E.C.4.1.1.17
CSA7odc

CATH domainRelated DB codes (homologues)
2.40.37.10D00271
3.20.20.10D00271

Enzyme Name
Swiss-protKEGG

P11926P00860P07805
Protein nameOrnithine decarboxylaseOrnithine decarboxylaseOrnithine decarboxylaseornithine decarboxylase
SpeC
L-ornithine carboxy-lyase
SynonymsODC
EC 4.1.1.17
ODC
EC 4.1.1.17
ODC
EC 4.1.1.17

KEGG pathways
MAP codePathways
MAP00220Urea cycle and metabolism of amino groups
MAP00480Glutathione metabolism

Swiss-prot:Accession NumberP11926P00860P07805
Entry nameDCOR_HUMANDCOR_MOUSEDCOR_TRYBB
ActivityL-ornithine = putrescine + CO(2).L-ornithine = putrescine + CO(2).L-ornithine = putrescine + CO(2).
SubunitHomodimer.Homodimer.
Subcellular location


CofactorPyridoxal phosphate.Pyridoxal phosphate.Pyridoxal phosphate.


CofactorsSubstratesProductsintermediates
KEGG-idC00018C00077C00134C00011
CompoundPyridoxal phosphateL-OrnithinePutrescineCO2
Typearomatic ring (with nitrogen atoms),phosphate group/phosphate ionamino acids,amine group,lipidamine group,lipidothers
1d7kA01UnboundUnboundUnboundUnboundUnbound
1d7kB01UnboundUnboundUnboundUnboundUnbound
1f3tA01UnboundUnboundUnboundUnboundIntermediate-bound:PLP-PUT
1f3tB01UnboundUnboundUnboundUnboundIntermediate-bound:PLP-PUT
1f3tC01UnboundUnboundUnboundUnboundIntermediate-bound:PLP-PUT
1f3tD01UnboundUnboundUnboundUnboundIntermediate-bound:PLP-PUT
1qu4A01UnboundUnboundUnboundUnboundUnbound
1qu4B01UnboundUnboundUnboundUnboundUnbound
1qu4C01UnboundUnboundUnboundUnboundUnbound
1qu4D01UnboundUnboundUnboundUnboundUnbound
2todA01UnboundUnboundUnboundUnboundIntermediate-analogue:PLP-DMO
2todB01UnboundUnboundUnboundUnboundIntermediate-analogue:PLP-DMO
2todC01UnboundUnboundUnboundUnboundIntermediate-analogue:PLP-DMO
2todD01UnboundUnboundUnboundUnboundIntermediate-analogue:PLP-DMO
7odcA01Bound:PLPUnboundUnboundUnboundUnbound
1d7kA02Bound:LLPUnboundUnboundUnboundUnbound
1d7kB02Bound:LLPUnboundUnboundUnboundUnbound
1f3tA02Bound:PLPUnboundUnboundUnboundUnbound
1f3tB02Bound:PLPUnboundUnboundUnboundUnbound
1f3tC02Bound:PLPUnboundUnboundUnboundUnbound
1f3tD02Bound:PLPUnboundUnboundUnboundUnbound
1qu4A02Bound:PLPUnboundUnboundUnboundUnbound
1qu4B02Bound:PLPUnboundUnboundUnboundUnbound
1qu4C02Bound:PLPUnboundUnboundUnboundUnbound
1qu4D02Bound:PLPUnboundUnboundUnboundUnbound
2todA02Bound:PLPUnboundUnboundUnboundUnbound
2todB02Bound:PLPUnboundUnboundUnboundUnbound
2todC02Bound:PLPUnboundUnboundUnboundUnbound
2todD02Bound:PLPUnboundUnboundUnboundUnbound
7odcA02Bound:PLPUnboundUnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;P11926, P00860, P07805 & PDB;2tod
pdbCatalytic residuesModified residuescomment
1d7kA01CYS 360

invisible S303(phosphorylation)
1d7kB01CYS 360

invisible S303(phosphorylation)
1f3tA01CYS 360


1f3tB01CYS 360


1f3tC01CYS 360


1f3tD01CYS 360


1qu4A01CYS 360


1qu4B01CYS 360


1qu4C01CYS 360


1qu4D01CYS 360


2todA01CYS 360


2todB01CYS 360


2todC01CYS 360


2todD01CYS 360


7odcA01CYS 360

invisible S303(phosphorylation)
1d7kA02       
LLP 69(Pyridoxal-phosphorylation)

1d7kB02       
LLP 69(Pyridoxal-phosphorylation)

1f3tA02       
                                 

1f3tB02       
                                 

1f3tC02       
                                 

1f3tD02       
                                 

1qu4A02       
                                 

1qu4B02       
                                 

1qu4C02       
                                 

1qu4D02       
                                 

2todA02       
                                 
mutant K69A
2todB02       
                                 
mutant K69A
2todC02       
                                 
mutant K69A
2todD02       
                                 
mutant K69A
7odcA02       
                                 


References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[9]Fig.97
[18]Fig.1, Fig.95
[19]Fig.1
[22]Scheme 55
[24]Fig.7
[26]Fig. 14

references
[1]
PubMed ID6781187
JournalActa Chem Scand B
Year1980
Volume34
Pages457-8
AuthorsOredsson S, Anehus S, Heby O
TitleInhibition of cell proliferation by DL-alpha-difluoromethylornithine, a catalytic irreversible inhibitor of ornithine decarboxylase.
[2]
PubMed ID6631913
JournalJ Med Chem
Year1983
Volume26
Pages1551-6
AuthorsBey P, Gerhart F, Van Dorsselaer V, Danzin C
Titlealpha-(Fluoromethyl)dehydroornithine and alpha-(fluoromethyl)dehydroputrescine analogues as irreversible inhibitors of ornithine decarboxylase.
[3]
PubMed ID3930296
JournalFEBS Lett
Year1985
Volume190
Pages324-8
AuthorsSolano F, Penafiel R, Solano ME, Lozano JA
TitleEquilibrium between active and inactive forms of rat liver ornithine decarboxylase mediated by L-ornithine and salts.
[4]
PubMed ID3822048
JournalNeurochem Res
Year1986
Volume11
Pages1653-62
AuthorsBondy SC
TitleOrnithine decarboxylase activity associated with a particulate fraction of brain.
[5]
PubMed ID3612691
JournalJ Med Chem
Year1987
Volume30
Pages1474-82
AuthorsSpruce LW, Rajadhyaksha SN, Berlin KD, Gale JB, Miranda ET, Ford WT, Blossey EC, Verma AK, Hossain MB, van der Helm D, et al
TitleHeteroarotinoids. Synthesis, characterization, and biological activity in terms of an assessment of these systems to inhibit the induction of ornithine decarboxylase activity and to induce terminal differentiation of HL-60 cells.
[6]
PubMed ID3480519
JournalProc Natl Acad Sci U S A
Year1987
Volume84
Pages8927-31
AuthorsO'Brien TG, Hietala O, O'Donnell K, Holmes M
TitleActivation of mouse epidermal tumor ornithine decarboxylase by GTP: evidence for different catalytic forms of the enzyme.
[7]
PubMed ID3392002
JournalJ Biochem (Tokyo)
Year1988
Volume103
Pages547-53
AuthorsKitani T, Fujisawa H
TitleMolecular properties of ornithine decarboxylase from mouse kidney: detailed comparison with those of the enzyme from rat liver.
[8]
PubMed ID1577163
JournalFEBS Lett
Year1992
Volume301
Pages261-4
AuthorsCeriani C, Gonzalez NS, Algranati ID
TitleOrnithine decarboxylase from Crithidia fasciculata is metabolically unstable and resistant to polyamine down-regulation.
[9]
CommentsACTIVE SITE, AND PYRIDOXAL-PHOSPHATE BINDING SITE.
Medline ID92112641
PubMed ID1730582
JournalJ Biol Chem
Year1992
Volume267
Pages150-8
AuthorsPoulin R, Lu L, Ackermann B, Bey P, Pegg AE
TitleMechanism of the irreversible inactivation of mouse ornithine decarboxylase by alpha-difluoromethylornithine. Characterization of sequences at the inhibitor and coenzyme binding sites.
Related Swiss-protP00860
[10]
PubMed ID1737994
JournalJ Neurochem
Year1992
Volume58
Pages831-6
AuthorsKauppinen RA, Halmekyto M, Alhonen L, Janne J
TitleNuclear magnetic resonance spectroscopy study on energy metabolism, intracellular pH, and free Mg2+ concentration in the brain of transgenic mice overexpressing human ornithine decarboxylase gene.
[11]
CommentsACTIVE SITE.
Medline ID93277871
PubMed ID8504104
JournalBiochemistry
Year1993
Volume32
Pages5842-7
AuthorsTobias KE, Kahana C
TitleIntersubunit location of the active site of mammalian ornithine decarboxylase as determined by hybridization of site-directed mutants.
Related Swiss-protP00860
[12]
PubMed ID8221660
JournalCancer Res
Year1993
Volume53
Pages5262-8
AuthorsAsk A, Persson L, Rehnholm A, Frostesjo L, Holm I, Heby O
TitleDevelopment of resistance to hydroxyurea during treatment of human myelogenous leukemia K562 cells with alpha-difluoromethylornithine as a result of coamplification of genes for ornithine decarboxylase and ribonucleotide reductase R2 subunit.
[13]
PubMed ID7626053
JournalBiochem Biophys Res Commun
Year1995
Volume212
Pages396-403
AuthorsSanchez CP, Sidrauski C, Freire SM, Gonzalez NS, Algranati ID
TitleOrnithine decarboxylase from Leishmania mexicana promastigotes: interaction with pyridoxal 5'-phosphate and alpha-difluoromethylornithine.
[14]
PubMed ID8528457
JournalEur J Neurosci
Year1995
Volume7
Pages1840-9
AuthorsLukkarainen J, Kauppinen RA, Koistinaho J, Halmekyto, Alhonen LM, Janne J
TitleCerebral energy metabolism and immediate early gene induction following severe incomplete ischaemia in transgenic mice overexpressing the human ornithine decarboxylase gene: evidence that putrescine is not neurotoxic in vivo.
[15]
PubMed ID8798774
JournalJ Biol Chem
Year1996
Volume271
Pages24945-53
AuthorsReddy SG, Mcllheran SM, Cochran BJ, Worth LL, Bishop LA, Brown PJ, Knutson VP, Haddox MK
TitleMultisite phosphorylation of ornithine decarboxylase in transformed macrophages results in increased intracellular enzyme stability and catalytic efficiency.
[16]
PubMed ID8820496
JournalProteins
Year1996
Volume24
Pages272-3
AuthorsGrishin NV, Osterman AL, Goldsmith EJ, Phillips MA
TitleCrystallization and preliminary X-ray studies of ornithine decarboxylase from Trypanosoma brucei.
[17]
PubMed ID8820494
JournalProteins
Year1996
Volume24
Pages266-8
AuthorsKern A, Oliveira MA, Chang NL, Ernst SR, Carroll DW, Momany C, Minard K, Coffino P, Hackert ML
TitleCrystallization of a mammalian ornithine decarboxylase.
[18]
PubMed ID9398243
JournalBiochemistry
Year1997
Volume36
Pages15147-55
AuthorsBrooks HB, Phillips MA
TitleCharacterization of the reaction mechanism for Trypanosoma brucei ornithine decarboxylase by multiwavelength stopped-flow spectroscopy.
[19]
PubMed ID9109665
JournalBiochemistry
Year1997
Volume36
Pages4558-67
AuthorsOsterman AL, Brooks HB, Rizo J, Phillips MA
TitleRole of Arg-277 in the binding of pyridoxal 5'-phosphate to Trypanosoma brucei ornithine decarboxylase.
[20]
PubMed ID10462479
JournalBiochem Biophys Res Commun
Year1999
Volume262
Pages355-8
AuthorsBauer PM, Fukuto JM, Buga GM, Pegg AE, Ignarro LJ
TitleNitric oxide inhibits ornithine decarboxylase by S-nitrosylation.
[21]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID20031512
PubMed ID10563800
JournalBiochemistry
Year1999
Volume38
Pages15174-84
AuthorsGrishin NV, Osterman AL, Brooks HB, Phillips MA, Goldsmith EJ
TitleX-ray structure of ornithine decarboxylase from Trypanosoma brucei: the native structure and the structure in complex with alpha-difluoromethylornithine.
Related PDB1qu4,2tod
Related Swiss-protP07805
[22]
PubMed ID10512638
JournalBiochemistry
Year1999
Volume38
Pages11814-26
AuthorsOsterman AL, Brooks HB, Jackson L, Abbott JJ, Phillips MA
TitleLysine-69 plays a key role in catalysis by ornithine decarboxylase through acceleration of the Schiff base formation, decarboxylation, and product release steps.
[23]
PubMed ID10218900
JournalNeurosci Lett
Year1999
Volume263
Pages17-20
AuthorsYatin SM, Yatin M, Aulick T, Ain KB, Butterfield DA
TitleAlzheimer's amyloid beta-peptide associated free radicals increase rat embryonic neuronal polyamine uptake and ornithine decarboxylase activity: protective effect of vitamin E.
[24]
CommentsX-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
Medline ID99306039
PubMed ID10378276
JournalStructure Fold Des
Year1999
Volume7
Pages567-81
AuthorsKern AD, Oliveira MA, Coffino P, Hackert ML
TitleStructure of mammalian ornithine decarboxylase at 1.6 A resolution: stereochemical implications of PLP-dependent amino acid decarboxylases.
Related PDB7odc
Related Swiss-protP00860
[25]
PubMed ID11085920
JournalBiochem J
Year2000
Volume352 Pt 2
Pages287-92
AuthorsKrause T, Luersen K, Wrenger C, Gilberger TW, Muller S, Walter RD
TitleThe ornithine decarboxylase domain of the bifunctional ornithine decarboxylase/S-adenosylmethionine decarboxylase of Plasmodium falciparum: recombinant expression and catalytic properties of two different constructs.
[26]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID20442076
PubMed ID10985770
JournalBiochemistry
Year2000
Volume39
Pages11247-57
AuthorsJackson LK, Brooks HB, Osterman AL, Goldsmith EJ, Phillips MA
TitleAltering the reaction specificity of eukaryotic ornithine decarboxylase.
Related PDB1f3t
Related Swiss-protP07805
[27]
CommentsX-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
Medline ID20090911
PubMed ID10623504
JournalJ Mol Biol
Year2000
Volume295
Pages7-16
AuthorsAlmrud JJ, Oliveira MA, Kern AD, Grishin NV, Phillips MA, Hackert ML
TitleCrystal structure of human ornithine decarboxylase at 2.1 A resolution: structural insights to antizyme binding.
Related PDB1d7k
Related Swiss-protP11926
[28]
PubMed ID11736657
JournalBiochem J
Year2001
Volume360
Pages657-65
AuthorsLee YS, Cho YD
TitleIdentification of essential active-site residues in ornithine decarboxylase of Nicotiana glutinosa decarboxylating both L-ornithine and L-lysine.
[29]
PubMed ID11683631
JournalBiochemistry
Year2001
Volume40
Pages13230-6
AuthorsMyers DP, Jackson LK, Ipe VG, Murphy GE, Phillips MA
TitleLong-range interactions in the dimer interface of ornithine decarboxylase are important for enzyme function.
[30]
PubMed ID11390378
JournalJ Biol Chem
Year2001
Volume276
Pages29651-6
AuthorsWrenger C, Luersen K, Krause T, Muller S, Walter RD
TitleThe Plasmodium falciparum bifunctional ornithine decarboxylase, S-adenosyl-L-methionine decarboxylase, enables a well balanced polyamine synthesis without domain-domain interaction.


createdupdated
2004-05-202009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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