Q9SWE5 (HAL3A_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Phosphopantothenoylcysteine decarboxylase
Short name=PPCDC
EC=4.1.1.36

Alternative name(s):
Halotolerance protein Hal3a
Short name=AtCoaC
Short name=AtHal3a

Gene names

Name:	HAL3A
Ordered Locus Names:	At3g18030
ORF Names:	MBG14.2

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	209 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Involved in plant growth and salt and osmotic tolerance. Catalyzes the decarboxylation of 4'-phosphopantothenoylcysteine to 4'-phosphopantetheine, a key step in coenzyme A biosynthesis. The enzyme is also able to decarboxylate pantothenoylcysteine to pantothenoylcysteamine.
Catalytic activity	N-((R)-4'-phosphopantothenoyl)-L-cysteine = pantotheine 4'-phosphate + CO2.
Cofactor	Binds 1 FMN per subunit.
Pathway	Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-pantothenate: step 3/5.
Subunit structure	Homotrimer.
Tissue specificity	Expressed in roots, shoots, leaves, flowers, developing siliques and seeds with highest expression in seed embryos and phloem. Ref.1
Induction	By salt stress. Ref.1
Sequence similarities	Belongs to the HFCD (homooligomeric flavin containing Cys decarboxylase) superfamily.

Ontologies

Keywords
Biological process	Stress response
Ligand	FMN Flavoprotein
Molecular function	Decarboxylase Lyase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	coenzyme A biosynthetic process Traceable author statement PubMed 16415216. Source: TAIR hyperosmotic salinity response Inferred from expression pattern Ref.1. Source: TAIR
Cellular_component	cytosol Inferred from direct assay PubMed 21166475. Source: TAIR
Molecular_function	phosphopantothenoylcysteine decarboxylase activity Inferred from direct assay PubMed 12860978. Source: TAIR
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 209

209

Phosphopantothenoylcysteine decarboxylase

PRO_0000182032

Regions

Nucleotide binding

106 – 109

4

FMN

Sites

Active site

175

1

Proton donor

Binding site

59

1

FMN

Binding site

142

1

Substrate

Experimental info

Mutagenesis

30

1

V → I: No effect on activity. Ref.7

Mutagenesis

33

1

I → L or V: No effect on activity. Ref.7

Mutagenesis

34

1

K → N or R: No effect on activity. Ref.7

Mutagenesis

34

1

K → Q: Small decrease of activity. Ref.7

Mutagenesis

90

1

H → N: Complete loss of activity. Ref.6

Mutagenesis

95

1

R → Q: Very low activity. Can reduce the oxidied intermediate. Ref.7

Mutagenesis

142

1

N → D: Complete loss of activity. Ref.7

Mutagenesis

145

1

M → L: Complete loss of activity. Ref.7

Mutagenesis

174

1

A → S: Significantly reduced activity. Can reduce the oxidied intermediate. Ref.7

Mutagenesis

174

1

A → V: No effect. Ref.7

Mutagenesis

175

1

C → S: Complete loss of activity. Ref.7

Mutagenesis

177

1

D → N: Very low activity. Can reduce the oxidied intermediate. Ref.7

Mutagenesis

179

1

G → A: Very low activity. Can reduce the oxidied intermediate. Ref.7

Mutagenesis

181

1

G → A: Significantly reduced activity. Ref.7

Secondary structure

1

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209

Helix Strand Turn

Details...

Beta strand

21 – 26

6

Helix

30 – 34

5

Helix

35 – 43

9

Beta strand

46 – 52

7

Helix

55 – 58

4

Helix

62 – 64

3

Beta strand

70 – 72

3

Helix

76 – 80

5

Helix

89 – 96

8

Beta strand

98 – 105

8

Helix

107 – 115

9

Helix

121 – 127

7

Beta strand

135 – 139

5

Helix

143 – 147

5

Helix

149 – 161

13

Beta strand

169 – 172

4

Beta strand

178 – 182

5

Helix

186 – 199

14

Sequences

	Sequence		Length	Mass (Da)
	Q9SWE5 [UniParc]. Last modified May 1, 2000. Version 1. Checksum: 3AB1BB364F8E40DE	FASTA	209	23,355
	10 20 30 40 50 60 MENGKRDRQD MEVNTTPRKP RVLLAASGSV AAIKFGNLCH CFTEWAEVRA VVTKSSLHFL 70 80 90 100 110 120 DKLSLPQEVT LYTDEDEWSS WNKIGDPVLH IELRRWADVL VIAPLSANTL GKIAGGLCDN 130 140 150 160 170 180 LLTCIIRAWD YTKPLFVAPA MNTLMWNNPF TERHLLSLDE LGITLIPPIK KRLACGDYGN 190 200 GAMAEPSLIY STVRLFWESQ AHQQTGGTS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Arabidopsis thaliana AtHAL3: a flavoprotein related to salt and osmotic tolerance and plant growth." Espinosa-Ruiz A., Belles J.M., Serrano R., Culianez-Macia F.A. Plant J. 20:529-539(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], TISSUE SPECIFICITY, INDUCTION. Strain: cv. Columbia.
[2]	"Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC clones." Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Tabata S. DNA Res. 7:217-221(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[3]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[4]	"Arabidopsis ORF clones." Shinn P., Chen H., Cheuk R.F., Kim C.J., Ecker J.R. Submitted (SEP-2004) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[5]	"Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs." Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K. , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K. Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[6]	"Arabidopsis thaliana flavoprotein AtHAL3a catalyzes the decarboxylation of 4'-Phosphopantothenoylcysteine to 4'-phosphopantetheine, a key step in coenzyme A biosynthesis." Kupke T., Hernandez-Acosta P., Steinbacher S., Culianez-Macia F.A. J. Biol. Chem. 276:19190-19196(2001) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION OF ACTIVITY, MUTAGENESIS OF HIS-90.
[7]	"Molecular characterization of the Arabidopsis thaliana flavoprotein AtHAL3a reveals the general reaction mechanism of 4'-phosphopantothenoylcysteine decarboxylases." Hernandez-Acosta P., Schmid D.G., Jung G., Culianez-Macia F.A., Kupke T. J. Biol. Chem. 277:20490-20498(2002) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION OF ACTIVITY, MUTAGENESIS OF VAL-30; ILE-33; LYS-34; ARG-95; ASN-142; MET-145; ALA-174; CYS-175; ASP-177; GLY-179 AND GLY-181.
[8]	"The X-ray structure of the FMN-binding protein AtHal3 provides the structural basis for the activity of a regulatory subunit involved in signal transduction." Albert A., Martinez-Ripoll M., Espinosa-Ruiz A., Yenush L., Culianez-Macia F.A., Serrano R. Structure 8:961-969(2000) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH FMN.
[9]	"Crystal structure of the plant PPC decarboxylase AtHAL3a complexed with an ene-thiol reaction intermediate." Steinbacher S., Hernandez-Acosta P., Bieseler B., Blaesse M., Huber R., Culianez-Macia F.A., Kupke T. J. Mol. Biol. 327:193-202(2003) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.21 ANGSTROMS) OF MUTANT SER-175 IN COMPLEX WITH SUBSTRATE AND FMN.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AF166262 Genomic DNA. Translation: AAD51616.1.
AB026641 Genomic DNA. Translation: BAB01331.1.
CP002686 Genomic DNA. Translation: AEE76036.1.
BT014781 mRNA. Translation: AAT41764.1.
BT015689 mRNA. Translation: AAU29466.1.
AK228559 mRNA. Translation: BAF00478.1.

IPI

IPI00536622.

RefSeq

NP_188430.1. NM_112684.4.

UniGene

At.24652.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1E20	X-ray	2.02	A	1-209	[»]
1MVL	X-ray	2.00	A	1-209	[»]
1MVN	X-ray	2.21	A	1-209	[»]

ProteinModelPortal

Q9SWE5.

SMR

Q9SWE5. Positions 18-202.

ModBase

Search...

Proteomic databases

PaxDb

Q9SWE5.

PRIDE

Q9SWE5.

Protocols and materials databases

DNASU

821327.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblPlants

AT3G18030.1; AT3G18030.1; AT3G18030.

GeneID

821327.

KEGG

ath:AT3G18030.

Organism-specific databases

TAIR

At3g18030.

Phylogenomic databases

eggNOG

COG0452.

HOGENOM

HOG000187629.

InParanoid

Q9SWE5.

KO

K01598.

OMA

PQDIPVT.

PhylomeDB

Q9SWE5.

ProtClustDB

PLN02496.

Enzyme and pathway databases

UniPathway

UPA00241; UER00354.

Gene expression databases

Genevestigator

Q9SWE5.

GermOnline

AT3G18030. Arabidopsis thaliana.

Family and domain databases

Gene3D

3.40.50.1950. 1 hit.

InterPro

IPR003382. Flavoprotein.
[Graphical view]

Pfam

PF02441. Flavoprotein. 1 hit.
[Graphical view]

SUPFAM

SSF52507. Flavoprotein. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

Q9SWE5.

Entry information

Entry name

HAL3A_ARATH

Accession

Primary (citable) accession number: Q9SWE5
Secondary accession number(s): Q6ID92

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 21, 2001
Last sequence update:	May 1, 2000
Last modified:	May 1, 2013
This is version 102 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program