Reviewed, UniProtKB/Swiss-Prot Q57764 (PDAD_METJA)

Names and origin

Protein names

Recommended name:
    Pyruvoyl-dependent arginine decarboxylase
      Short name=PvlArgDC
    EC=4.1.1.19
Cleaved into the following 2 chains:
    1- Recommended name:
            Pyruvoyl-dependent arginine decarboxylase subunit beta
    2- Recommended name:
            Pyruvoyl-dependent arginine decarboxylase subunit alpha

Gene names

Name:	pdaD
Ordered Locus Names:	MJ0316

Organism

Methanocaldococcus jannaschii (Methanococcus jannaschii) [Complete proteome] [HAMAP]

Taxonomic identifier

2190 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Methanococci › Methanococcales › Methanocaldococcaceae › Methanocaldococcus

Protein attributes

Sequence length	165 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Catalytic activity	L-arginine = agmatine + CO2. HAMAP MF_01404
Cofactor	Pyruvoyl group. HAMAP MF_01404
Subunit structure	Trimer of an alpha-beta dimer. HAMAP MF_01404
Sequence similarities	Belongs to the pdaD family.
Biophysicochemical properties	Temperature dependence: Thermostable. HAMAP MF_01404
Mass spectrometry	Molecular mass is 5436±11 Da from positions 1 - 52. Determined by MALDI. Ref.2 Molecular mass is 12356±57 Da from positions 53 - 165. Determined by MALDI. Ref.2

Ontologies

Keywords
Ligand	Pyruvate
Molecular function	Decarboxylase Lyase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	arginine catabolic process Inferred from electronic annotation. Source: InterPro
Molecular function	arginine decarboxylase activity 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 – 52

52

Pyruvoyl-dependent arginine decarboxylase subunit beta HAMAP MF_01404

PRO_0000023314

Chain

53 – 165

113

Pyruvoyl-dependent arginine decarboxylase subunit alpha HAMAP MF_01404

PRO_0000023315

Sites

Site

52 – 53

2

Cleavage (non-hydrolytic) HAMAP MF_01404

Amino acid modifications

Modified residue

53

1

Pyruvic acid (Ser) HAMAP MF_01404

Secondary structure

1

.

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165

Helix Strand Turn

Details...

Beta strand

17 – 26

10

Helix

30 – 41

12

Beta strand

46 – 51

6

Beta strand

72 – 82

11

Beta strand

88 – 100

13

Beta strand

105 – 114

10

Helix

116 – 134

19

Beta strand

138 – 149

12

Beta strand

151 – 163

13

Sequences

	Sequence		Length	Mass (Da)
	Q57764-1 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: 04C7F8AB3AEC2342	FASTA	165	17,708
	10 20 30 40 50 60 MNAEINPLHA YFKLPNTVSL VAGSSEGETP LNAFDGALLN AGIGNVNLIR ISSIMPPEAE 70 80 90 100 110 120 IVPLPKLPMG ALVPTAYGYI ISDVPGETIS AAISVAIPKD KSLCGLIMEY EGKCSKKEAE 130 140 150 160 KTVREMAKIG FEMRGWELDR IESIAVEHTV EKLGCAFAAA ALWYK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii." Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G., Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R., Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R., Kirkness E.F., Weinstock K.G. , Merrick J.M., Glodek A., Scott J.L., Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R., Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D., Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P., Fraser C.M., Smith H.O., Woese C.R., Venter J.C. Science 273:1058-1073(1996) [PubMed: 8688087] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.
[2]	"Methanococcus jannaschii uses a pyruvoyl-dependent arginine decarboxylase in polyamine biosynthesis." Graham D.E., Xu H., White R.H. J. Biol. Chem. 277:23500-23507(2002) [PubMed: 11980912] [Abstract] Cited for: CHARACTERIZATION, MASS SPECTROMETRY. Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

L77117 Genomic DNA. Translation: AAB98302.1.

PIR

E64339.

RefSeq

NP_247289.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1MT1	X-ray	2.20	A/C/E/G/I/K	1-52	[»]
			B/D/F/H/J/L	54-165	[»]
1N13	X-ray	1.40	A/C/E/G/I/K	1-52	[»]
			B/D/F/H/J/L	54-165	[»]
1N2M	X-ray	1.90	A/B/C/D/E/F	1-165	[»]
2QQC	X-ray	2.00	A/C/E/G/I/K	1-52	[»]
			B/D/F/H/J/L	54-165	[»]
2QQD	X-ray	2.00	A/D	1-52	[»]
			B/E	54-165	[»]
			C/F/G/H	1-165	[»]

ModBase

Search...

Genome annotation databases

GeneID

1451171.

GenomeReviews

Gene locus MJ0316 in contig L77117_GR.

KEGG

mja:MJ0316.

NMPDR

fig|243232.1.peg.326.

TIGR

MJ0316.

Phylogenomic databases

HOGENOM

HBG539680.

OMA

LVPTAYG.

Enzyme and pathway databases

BRENDA

4.1.1.19. 256362.

Family and domain databases

HAMAP

MF_01404. PvlArgDC.
[Tree]

InterPro

IPR016104. Pyr-dep_his/arg-deCO2ase.
IPR016105. Pyr-dep_his/arg-deCO2ase_sand.
IPR002724. Pyruvoyl-dep_arg_deCO2ase.
[Graphical view]

Gene3D

G3DSA:3.50.20.10. Pyr-dep_his/arg-deCO2ase_sand. 1 hit.

Pfam

PF01862. PvlArgDC. 1 hit.
[Graphical view]

PIRSF

PIRSF005216. Pyruvoyl-dep_arg_deCO2ase. 1 hit.

ProDom

PD010449. Pyruvoyl-dep_arg_deCO2ase. 1 hit.
[Graphical view] [Entries sharing at least one domain]

TIGRFAMs

TIGR00286. PvlArgDC. 1 hit.

ProtoNet

Search...

Entry information

Entry name

PDAD_METJA

Accession

Primary (citable) accession number: Q57764

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1996
Last modified:	February 9, 2010
This is version 82 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)