Lysine/ornithine decarboxylase - Selenomonas ruminantium

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O50657 (DCLO_SELRU) Reviewed, UniProtKB/Swiss-Prot

Last modified September 21, 2011. Version 62. History...

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

Documents (2) |

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:
Lysine/ornithine decarboxylase
Short name=LDC
EC=4.1.1.17
EC=4.1.1.18

Gene names

Name:

ldc

Organism

Selenomonas ruminantium

Taxonomic identifier

971 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Negativicutes › Selenomonadales › Veillonellaceae › Selenomonas

Protein attributes

Sequence length	393 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Decarboxylates both L-lysine and L-ornithine with similar catalytic efficiency.
Catalytic activity	L-lysine = cadaverine + CO₂. L-ornithine = putrescine + CO₂.
Cofactor	Pyridoxal phosphate.
Enzyme regulation	Inhibited competitively by both alpha-difluoromethyllysine and alpha-difluoromethylornithine.
Pathway	Amine and polyamine biosynthesis; putrescine biosynthesis via L-ornithine pathway; putrescine from L-ornithine: step 1/1.
Subunit structure	Homodimer.
Miscellaneous	Mutagen studies showed that it is possible to convert S.ruminantium LDC to an enzyme with a preference for decarboxylating L-ornithine when five amino acid residues (Ala-44, Gly-45, Val-46, Pro-54 and Ser-322) were replaced with the corresponding ones found in mouse ODC.
Sequence similarities	Belongs to the Orn/Lys/Arg decarboxylase class-II family.
Biophysicochemical properties	Kinetic parameters: K_M=1.5 mM for L-lysine K_M=0.96 mM for L-ornithine

Ontologies

Keywords
Biological process	Polyamine biosynthesis Putrescine biosynthesis Spermidine biosynthesis
Ligand	Pyridoxal phosphate
Molecular function	Decarboxylase Lyase
Technical term	Direct protein sequencing
Gene Ontology (GO)
Biological process	putrescine biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW spermidine biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	lysine decarboxylase activity Inferred from electronic annotation. Source: EC ornithine decarboxylase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 393

393

Lysine/ornithine decarboxylase

PRO_0000149910

Sites

Active site

323

Proton donor; shared with dimeric partner By similarity

Amino acid modifications

Modified residue

N6-(pyridoxal phosphate)lysine By similarity

Experimental info

Mutagenesis

44 – 46

AGV → VTP: 2-fold increase in substrate specificity towards ornithine. 5-fold increase in substrate specificity towards ornithine; when associated with D-54. 70-fold increase in substrate specificity towards ornithine; when associated with D-54 and A-322. 16-fold increase in substrate specificity towards ornithine; when associated with D-54; T-322 and L-326. Ref.1

Mutagenesis

A → C: No change in substrate specificity.

Mutagenesis

P → D: 3-fold increase in substrate specificity towards ornithine. 5-fold increase in substrate specificity towards ornithine; when associated with 44-V--P-46. 70-fold increase in substrate specificity towards ornithine; when associated with 44-V--P-46 and A-322. 16-fold increase in substrate specificity towards ornithine; when associated with 44-V--P-46; T-322 and L-326. Ref.1

Mutagenesis

319

G → W: 7-fold increase in substrate specificity towards ornithine. Ref.1

Mutagenesis

322

S → A: 29-fold increase in substrate specificity towards ornithine. 70-fold increase in substrate specificity towards ornithine; when associated with 44-V--P-46 and D-54. Ref.1

Mutagenesis

322

S → T: 16-fold increase in substrate specificity towards ornithine; when associated with L-326. 16-fold increase in substrate specificity towards ornithine; when associated with 44-V--P-46; D-54 and L-326. Ref.1

Mutagenesis

326

I → L: 16-fold increase in substrate specificity towards ornithine; when associated with T-322. 16-fold increase in substrate specificity towards ornithine; when associated with 44-V--P-46; D-54 and T-322. Ref.1

Mutagenesis

350

G → D: Loss of dimer formation and decarboxylase activity. Ref.1

Sequences

Sequence

Length

Mass (Da)

Tools

O50657 [UniParc].

Last modified June 1, 1998. Version 1.
Checksum: 66249907E2061167
Show »

FASTA

393

43,214

        10         20         30         40         50         60 
MKNFRLSEKE VKTLAKRIPT PFLVASLDKV EENYQFMRRH LPRAGVFYAM KANPTPEILS 

        70         80         90        100        110        120 
LLAGLGSHFD VASAGEMEIL HELGVDGSQM IYANPVKDAR GLKAAADYNV RRFTFDDPSE 

       130        140        150        160        170        180 
IDKMAKAVPG ADVLVRIAVR NNKALVDLNT KFGAPVEEAL DLLKAAQDAG LHAMGICFHV 

       190        200        210        220        230        240 
GSQSLSTAAY EEALLVARRL FDEAEEMGMH LTDLDIGGGF PVPDAKGLNV DLAAMMEAIN 

       250        260        270        280        290        300 
KQIDRLFPDT AVWTEPGRYM CGTAVNLVTS VIGTKTRGEQ PWYILDEGIY GCFSGIMYDH 

       310        320        330        340        350        360 
WTYPLHCFGK GNKKPSTFGG PSCDGIDVLY RDFMAPELKI GDKVLVTEMG SYTSVSATRF 

       370        380        390 
NGFYLAPTII FEDQPEYAAR LTEDDDVKKK AAV

« Hide

References

[1]

"Gene cloning and molecular characterization of lysine decarboxylase from Selenomonas ruminantium delineate its evolutionary relationship to ornithine decarboxylases from eukaryotes."
Takatsuka Y., Yamaguchi Y., Ono M., Kamio Y.
J. Bacteriol. 182:6732-6741(2000) [PubMed: 11073919] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-28; 30-37; 52-64; 153-163; 276-288 AND 344-352, MUTAGENESIS OF 44-ALA--VAL-46; PRO-54; GLY-319; SER-322; ILE-326 AND GLY-350.
Strain: Subsp. lactilytica.

Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AB011029 Genomic DNA. Translation: BAA24923.1. AB104737 Genomic DNA. Translation: BAC57940.1.
3D structure databases
ProteinModelPortal	O50657.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Enzyme and pathway databases
BioCyc	MetaCyc:MONOMER-12423.
BRENDA	4.1.1.18. 5668.
Family and domain databases
InterPro	IPR009006. Ala_racemase/Decarboxylase_C. IPR022643. De-COase2_C. IPR022657. De-COase2_CS. IPR022644. De-COase2_N. IPR022653. De-COase2_pyr-phos_BS. IPR000183. Orn/DAP/Arg_de-COase. IPR002433. Orn_de-COase. [Graphical view]
Gene3D	G3DSA:2.40.37.10. Ala_racemase/Decarboxylase_C. 1 hit.
Pfam	PF02784. Orn_Arg_deC_N. 1 hit. PF00278. Orn_DAP_Arg_deC. 1 hit. [Graphical view]
PRINTS	PR01179. ODADCRBXLASE. PR01182. ORNDCRBXLASE.
SUPFAM	SSF50621. Racem_decarbox_C. 1 hit.
PROSITE	PS00878. ODR_DC_2_1. 1 hit. PS00879. ODR_DC_2_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DCLO_SELRU

Accession

Primary (citable) accession number: O50657
Secondary accession number(s): Q7DFY1

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 21, 2001
Last sequence update:	June 1, 1998
Last modified:	September 21, 2011
This is version 62 of the entry and version 1 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

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

Amino acid modifications

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protocols and materials databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents