DB code: D00251

CATH domain 2.40.37.10 : Lyase, Ornithine Decarboxylase; Chain A, domain 1 Catalytic domain
3.20.20.10 : TIM Barrel Catalytic domain
E.C. 4.1.1.17
CSA 7odc
M-CSA 7odc
MACiE

CATH domain Related DB codes (homologues)
2.40.37.10 : Lyase, Ornithine Decarboxylase; Chain A, domain 1 D00271
3.20.20.10 : TIM Barrel D00271

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P11926 Ornithine decarboxylase
ODC
EC 4.1.1.17
NP_002530.1 (Protein)
NM_002539.1 (DNA/RNA sequence)
PF02784 (Orn_Arg_deC_N)
PF00278 (Orn_DAP_Arg_deC)
[Graphical View]
P00860 Ornithine decarboxylase
ODC
EC 4.1.1.17
NP_038642.2 (Protein)
NM_013614.2 (DNA/RNA sequence)
PF02784 (Orn_Arg_deC_N)
PF00278 (Orn_DAP_Arg_deC)
[Graphical View]
P07805 Ornithine decarboxylase
ODC
EC 4.1.1.17
PF02784 (Orn_Arg_deC_N)
PF00278 (Orn_DAP_Arg_deC)
[Graphical View]

KEGG enzyme name
ornithine decarboxylase
SpeC
L-ornithine carboxy-lyase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P11926 DCOR_HUMAN L-ornithine = putrescine + CO(2). Homodimer. Pyridoxal phosphate.
P00860 DCOR_MOUSE L-ornithine = putrescine + CO(2). Homodimer. Pyridoxal phosphate.
P07805 DCOR_TRYBB L-ornithine = putrescine + CO(2). Pyridoxal phosphate.

KEGG Pathways
Map code Pathways E.C.
MAP00220 Urea cycle and metabolism of amino groups
MAP00480 Glutathione metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00018 C00077 C00134 C00011
E.C.
Compound Pyridoxal phosphate L-Ornithine Putrescine CO2
Type aromatic ring (with nitrogen atoms),phosphate group/phosphate ion amino acids,amine group,lipid amine group,lipid others
ChEBI 18405
15729
17148
16526
PubChem 1051
6262
88747248
1045
280
1d7kA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1d7kB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1f3tA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Intermediate-bound:PLP-PUT
1f3tB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Intermediate-bound:PLP-PUT
1f3tC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Intermediate-bound:PLP-PUT
1f3tD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Intermediate-bound:PLP-PUT
1qu4A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1qu4B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1qu4C01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1qu4D01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
2todA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Intermediate-analogue:PLP-DMO
2todB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Intermediate-analogue:PLP-DMO
2todC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Intermediate-analogue:PLP-DMO
2todD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Intermediate-analogue:PLP-DMO
7odcA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound
1d7kA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:LLP Unbound Unbound Unbound Unbound
1d7kB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:LLP Unbound Unbound Unbound Unbound
1f3tA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound
1f3tB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound
1f3tC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound
1f3tD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound
1qu4A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound
1qu4B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound
1qu4C02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound
1qu4D02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound
2todA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound
2todB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound
2todC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound
2todD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound
7odcA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PLP Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P11926, P00860, P07805 & PDB;2tod

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1d7kA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 360 invisible S303(phosphorylation)
1d7kB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 360 invisible S303(phosphorylation)
1f3tA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 360
1f3tB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 360
1f3tC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 360
1f3tD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 360
1qu4A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 360
1qu4B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 360
1qu4C01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 360
1qu4D01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 360
2todA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 360
2todB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 360
2todC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 360
2todD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 360
7odcA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 360 invisible S303(phosphorylation)
1d7kA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LLP 69(Pyridoxal-phosphorylation)
1d7kB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LLP 69(Pyridoxal-phosphorylation)
1f3tA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1f3tB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1f3tC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1f3tD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qu4A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qu4B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qu4C02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qu4D02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2todA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain mutant K69A
2todB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain mutant K69A
2todC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain mutant K69A
2todD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain mutant K69A
7odcA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[9]
Fig.9 7
[18]
Fig.1, Fig.9 5
[19]
Fig.1
[22]
Scheme 5 5
[24]
Fig.7
[26]
Fig. 1 4

References
[1]
Resource
Comments
Medline ID
PubMed ID 6781187
Journal Acta Chem Scand B
Year 1980
Volume 34
Pages 457-8
Authors Oredsson S, Anehus S, Heby O
Title Inhibition of cell proliferation by DL-alpha-difluoromethylornithine, a catalytic irreversible inhibitor of ornithine decarboxylase.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 6631913
Journal J Med Chem
Year 1983
Volume 26
Pages 1551-6
Authors Bey P, Gerhart F, Van Dorsselaer V, Danzin C
Title alpha-(Fluoromethyl)dehydroornithine and alpha-(fluoromethyl)dehydroputrescine analogues as irreversible inhibitors of ornithine decarboxylase.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 3930296
Journal FEBS Lett
Year 1985
Volume 190
Pages 324-8
Authors Solano F, Penafiel R, Solano ME, Lozano JA
Title Equilibrium between active and inactive forms of rat liver ornithine decarboxylase mediated by L-ornithine and salts.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 3822048
Journal Neurochem Res
Year 1986
Volume 11
Pages 1653-62
Authors Bondy SC
Title Ornithine decarboxylase activity associated with a particulate fraction of brain.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 3612691
Journal J Med Chem
Year 1987
Volume 30
Pages 1474-82
Authors Spruce LW, Rajadhyaksha SN, Berlin KD, Gale JB, Miranda ET, Ford WT, Blossey EC, Verma AK, Hossain MB, van der Helm D, et al
Title Heteroarotinoids. 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.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 3480519
Journal Proc Natl Acad Sci U S A
Year 1987
Volume 84
Pages 8927-31
Authors O'Brien TG, Hietala O, O'Donnell K, Holmes M
Title Activation of mouse epidermal tumor ornithine decarboxylase by GTP: evidence for different catalytic forms of the enzyme.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 3392002
Journal J Biochem (Tokyo)
Year 1988
Volume 103
Pages 547-53
Authors Kitani T, Fujisawa H
Title Molecular properties of ornithine decarboxylase from mouse kidney: detailed comparison with those of the enzyme from rat liver.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 1577163
Journal FEBS Lett
Year 1992
Volume 301
Pages 261-4
Authors Ceriani C, Gonzalez NS, Algranati ID
Title Ornithine decarboxylase from Crithidia fasciculata is metabolically unstable and resistant to polyamine down-regulation.
Related PDB
Related UniProtKB
[9]
Resource
Comments ACTIVE SITE, AND PYRIDOXAL-PHOSPHATE BINDING SITE.
Medline ID 92112641
PubMed ID 1730582
Journal J Biol Chem
Year 1992
Volume 267
Pages 150-8
Authors Poulin R, Lu L, Ackermann B, Bey P, Pegg AE
Title Mechanism of the irreversible inactivation of mouse ornithine decarboxylase by alpha-difluoromethylornithine. Characterization of sequences at the inhibitor and coenzyme binding sites.
Related PDB
Related UniProtKB P00860
[10]
Resource
Comments
Medline ID
PubMed ID 1737994
Journal J Neurochem
Year 1992
Volume 58
Pages 831-6
Authors Kauppinen RA, Halmekyto M, Alhonen L, Janne J
Title Nuclear magnetic resonance spectroscopy study on energy metabolism, intracellular pH, and free Mg2+ concentration in the brain of transgenic mice overexpressing human ornithine decarboxylase gene.
Related PDB
Related UniProtKB
[11]
Resource
Comments ACTIVE SITE.
Medline ID 93277871
PubMed ID 8504104
Journal Biochemistry
Year 1993
Volume 32
Pages 5842-7
Authors Tobias KE, Kahana C
Title Intersubunit location of the active site of mammalian ornithine decarboxylase as determined by hybridization of site-directed mutants.
Related PDB
Related UniProtKB P00860
[12]
Resource
Comments
Medline ID
PubMed ID 8221660
Journal Cancer Res
Year 1993
Volume 53
Pages 5262-8
Authors Ask A, Persson L, Rehnholm A, Frostesjo L, Holm I, Heby O
Title Development 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.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 7626053
Journal Biochem Biophys Res Commun
Year 1995
Volume 212
Pages 396-403
Authors Sanchez CP, Sidrauski C, Freire SM, Gonzalez NS, Algranati ID
Title Ornithine decarboxylase from Leishmania mexicana promastigotes: interaction with pyridoxal 5'-phosphate and alpha-difluoromethylornithine.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 8528457
Journal Eur J Neurosci
Year 1995
Volume 7
Pages 1840-9
Authors Lukkarainen J, Kauppinen RA, Koistinaho J, Halmekyto, Alhonen LM, Janne J
Title Cerebral 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.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 8798774
Journal J Biol Chem
Year 1996
Volume 271
Pages 24945-53
Authors Reddy SG, Mcllheran SM, Cochran BJ, Worth LL, Bishop LA, Brown PJ, Knutson VP, Haddox MK
Title Multisite phosphorylation of ornithine decarboxylase in transformed macrophages results in increased intracellular enzyme stability and catalytic efficiency.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 8820496
Journal Proteins
Year 1996
Volume 24
Pages 272-3
Authors Grishin NV, Osterman AL, Goldsmith EJ, Phillips MA
Title Crystallization and preliminary X-ray studies of ornithine decarboxylase from Trypanosoma brucei.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 8820494
Journal Proteins
Year 1996
Volume 24
Pages 266-8
Authors Kern A, Oliveira MA, Chang NL, Ernst SR, Carroll DW, Momany C, Minard K, Coffino P, Hackert ML
Title Crystallization of a mammalian ornithine decarboxylase.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 9398243
Journal Biochemistry
Year 1997
Volume 36
Pages 15147-55
Authors Brooks HB, Phillips MA
Title Characterization of the reaction mechanism for Trypanosoma brucei ornithine decarboxylase by multiwavelength stopped-flow spectroscopy.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 9109665
Journal Biochemistry
Year 1997
Volume 36
Pages 4558-67
Authors Osterman AL, Brooks HB, Rizo J, Phillips MA
Title Role of Arg-277 in the binding of pyridoxal 5'-phosphate to Trypanosoma brucei ornithine decarboxylase.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 10462479
Journal Biochem Biophys Res Commun
Year 1999
Volume 262
Pages 355-8
Authors Bauer PM, Fukuto JM, Buga GM, Pegg AE, Ignarro LJ
Title Nitric oxide inhibits ornithine decarboxylase by S-nitrosylation.
Related PDB
Related UniProtKB
[21]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID 20031512
PubMed ID 10563800
Journal Biochemistry
Year 1999
Volume 38
Pages 15174-84
Authors Grishin NV, Osterman AL, Brooks HB, Phillips MA, Goldsmith EJ
Title X-ray structure of ornithine decarboxylase from Trypanosoma brucei: the native structure and the structure in complex with alpha-difluoromethylornithine.
Related PDB 1qu4 2tod
Related UniProtKB P07805
[22]
Resource
Comments
Medline ID
PubMed ID 10512638
Journal Biochemistry
Year 1999
Volume 38
Pages 11814-26
Authors Osterman AL, Brooks HB, Jackson L, Abbott JJ, Phillips MA
Title Lysine-69 plays a key role in catalysis by ornithine decarboxylase through acceleration of the Schiff base formation, decarboxylation, and product release steps.
Related PDB
Related UniProtKB
[23]
Resource
Comments
Medline ID
PubMed ID 10218900
Journal Neurosci Lett
Year 1999
Volume 263
Pages 17-20
Authors Yatin SM, Yatin M, Aulick T, Ain KB, Butterfield DA
Title Alzheimer's amyloid beta-peptide associated free radicals increase rat embryonic neuronal polyamine uptake and ornithine decarboxylase activity: protective effect of vitamin E.
Related PDB
Related UniProtKB
[24]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
Medline ID 99306039
PubMed ID 10378276
Journal Structure Fold Des
Year 1999
Volume 7
Pages 567-81
Authors Kern AD, Oliveira MA, Coffino P, Hackert ML
Title Structure of mammalian ornithine decarboxylase at 1.6 A resolution: stereochemical implications of PLP-dependent amino acid decarboxylases.
Related PDB 7odc
Related UniProtKB P00860
[25]
Resource
Comments
Medline ID
PubMed ID 11085920
Journal Biochem J
Year 2000
Volume 352 Pt 2
Pages 287-92
Authors Krause T, Luersen K, Wrenger C, Gilberger TW, Muller S, Walter RD
Title The ornithine decarboxylase domain of the bifunctional ornithine decarboxylase/S-adenosylmethionine decarboxylase of Plasmodium falciparum: recombinant expression and catalytic properties of two different constructs.
Related PDB
Related UniProtKB
[26]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID 20442076
PubMed ID 10985770
Journal Biochemistry
Year 2000
Volume 39
Pages 11247-57
Authors Jackson LK, Brooks HB, Osterman AL, Goldsmith EJ, Phillips MA
Title Altering the reaction specificity of eukaryotic ornithine decarboxylase.
Related PDB 1f3t
Related UniProtKB P07805
[27]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
Medline ID 20090911
PubMed ID 10623504
Journal J Mol Biol
Year 2000
Volume 295
Pages 7-16
Authors Almrud JJ, Oliveira MA, Kern AD, Grishin NV, Phillips MA, Hackert ML
Title Crystal structure of human ornithine decarboxylase at 2.1 A resolution: structural insights to antizyme binding.
Related PDB 1d7k
Related UniProtKB P11926
[28]
Resource
Comments
Medline ID
PubMed ID 11736657
Journal Biochem J
Year 2001
Volume 360
Pages 657-65
Authors Lee YS, Cho YD
Title Identification of essential active-site residues in ornithine decarboxylase of Nicotiana glutinosa decarboxylating both L-ornithine and L-lysine.
Related PDB
Related UniProtKB
[29]
Resource
Comments
Medline ID
PubMed ID 11683631
Journal Biochemistry
Year 2001
Volume 40
Pages 13230-6
Authors Myers DP, Jackson LK, Ipe VG, Murphy GE, Phillips MA
Title Long-range interactions in the dimer interface of ornithine decarboxylase are important for enzyme function.
Related PDB
Related UniProtKB
[30]
Resource
Comments
Medline ID
PubMed ID 11390378
Journal J Biol Chem
Year 2001
Volume 276
Pages 29651-6
Authors Wrenger C, Luersen K, Krause T, Muller S, Walter RD
Title The Plasmodium falciparum bifunctional ornithine decarboxylase, S-adenosyl-L-methionine decarboxylase, enables a well balanced polyamine synthesis without domain-domain interaction.
Related PDB
Related UniProtKB

Comments

Created Updated
2004-05-20 2009-02-26