Q9FUZ2 (DEF1B_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Peptide deformylase 1B, chloroplastic/mitochondrial
Short name=AtDEF2
Short name=AtPDF1B
Short name=PDF 1B
EC=3.5.1.88

Alternative name(s):
Polypeptide deformylase

Gene names

Name:	PDF1B
Synonyms:	DEF2
Ordered Locus Names:	At5g14660
ORF Names:	T15N1_150

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	273 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)

Function	Removes the formyl group from the N-terminal Met of newly synthesized proteins. Has a preferred substrate specificity towards the photosystem II (PS II) D1 polypeptide. Ref.1
Catalytic activity	Formyl-L-methionyl peptide + H2O = formate + methionyl peptide.
Cofactor	Binds 1 Fe2+ ion. Ref.7
Enzyme regulation	Inhibited by actinonin. Ref.6 Ref.7
Subunit structure	Homodimer. Ref.9
Subcellular location	Plastid › chloroplast stroma. Mitochondrion. Note: Reported to be localized to chloroplast and mitochondria based on transient GFP expression in a heterologous system (Ref.1). Ref.1 Ref.6
Tissue specificity	Expressed in leaves and flowers. Ref.1
Disruption phenotype	Albino. Ref.8
Sequence similarities	Belongs to the polypeptide deformylase family.
Biophysicochemical properties	Kinetic parameters: KM=130 µM for N-formyl-Met-Leu-rho-nitroanilide Ref.6 KM=3200 µM for N-formyl-Met-Ala-Ser Vmax=20 µmol/min/mg enzyme toward N-formyl-Met-Leu-rho-nitroanilide Vmax=1.3 µmol/min/mg enzyme toward N-formyl-Met-Ala-Ser

Ontologies

Keywords
Biological process	Protein biosynthesis
Cellular component	Chloroplast Mitochondrion Plastid
Domain	Transit peptide
Ligand	Iron Metal-binding
Molecular function	Hydrolase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	translation Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	chloroplast Inferred from direct assay PubMed 18431481. Source: TAIR chloroplast stroma Inferred from electronic annotation. Source: UniProtKB-SubCell mitochondrion Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	iron ion binding Inferred from electronic annotation. Source: InterPro peptide deformylase activity Inferred from direct assay Ref.9. Source: TAIR
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Transit peptide

1 – 56

56

Chloroplast and mitochondrion Potential

Chain

57 – 273

217

Peptide deformylase 1B, chloroplastic/mitochondrial

PRO_0000006732

Sites

Active site

214

1

By similarity

Metal binding

171

1

Iron

Metal binding

213

1

Iron

Metal binding

217

1

Iron

Experimental info

Mutagenesis

178

1

Y → A: Decrease in substrate affinity. Ref.9

Mutagenesis

178

1

Y → F or R: Increase in substrate affinity. Ref.9

Sequence conflict

48

1

T → N in AAM62644. Ref.5

Sequence conflict

205

1

R → S in AAG33980. Ref.1

Secondary structure

1

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273

Helix Strand Turn

Details...

Helix

89 – 91

3

Helix

103 – 118

16

Beta strand

122 – 125

4

Helix

126 – 129

4

Beta strand

133 – 138

6

Beta strand

150 – 160

11

Beta strand

164 – 169

6

Beta strand

179 – 185

7

Beta strand

187 – 192

6

Beta strand

194 – 196

3

Beta strand

198 – 203

6

Helix

205 – 218

14

Helix

223 – 226

4

Helix

229 – 233

5

Helix

236 – 250

15

Helix

258 – 260

3

Sequences

	Sequence		Length	Mass (Da)
	Q9FUZ2 [UniParc]. Last modified December 15, 2003. Version 2. Checksum: 25CDA90ED6D9603E	FASTA	273	30,610
	10 20 30 40 50 60 MAVCNCFLQA PPLSRILLPV LSRRATTLSA GYGRLKSTVT FCSTVNRTSP LTSSVRAEVK 70 80 90 100 110 120 RVSRKDDKVA SATDVQFETP LKIVEYPDPI LRAKNKRIDI FDENLKNLVD AMFDVMYKTD 130 140 150 160 170 180 GIGLSAPQVG LNVQLMVFNP AGEPGEGKEI VLVNPKIKKY SDKLVPFDEG CLSFPGIYAE 190 200 210 220 230 240 VVRPQSVKID ARDITGERFS ISLSRLPARI FQHEYDHLEG VLFFDRMTDQ VLDSIREELE 250 260 270 ALEKKYEEKT GLPSPERVEA RQKRKAGVGF GKR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Identification of eukaryotic peptide deformylases reveals universality of N-terminal protein processing mechanisms." Giglione C., Serero A., Pierre M., Boisson B., Meinnel T. EMBO J. 19:5916-5929(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, SUBCELLULAR LOCATION.
[2]	"Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana." Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E., Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K. , Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L., O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D., Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M., Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L., Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B., Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P., Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M., Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D., Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A., Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I., Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T., Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A., McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U., Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M., Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G., Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W., Bevan M., Fransz P.F. Nature 408:823-826(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]	"Empirical analysis of transcriptional activity in the Arabidopsis genome." Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G. , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R. Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[5]	"Full-length cDNA from Arabidopsis thaliana." Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A. Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[6]	"Eukaryotic peptide deformylases. Nuclear-encoded and chloroplast-targeted enzymes in Arabidopsis." Dirk L.M., Williams M.A., Houtz R.L. Plant Physiol. 127:97-107(2001) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES.
[7]	"Distinctive features of the two classes of eukaryotic peptide deformylases." Serero A., Giglione C., Meinnel T. J. Mol. Biol. 314:695-708(2001) [PubMed] [Europe PMC] [Abstract] Cited for: COFACTOR, ENZYME REGULATION.
[8]	"Control of protein life-span by N-terminal methionine excision." Giglione C., Vallon O., Meinnel T. EMBO J. 22:13-23(2003) [PubMed] [Europe PMC] [Abstract] Cited for: DISRUPTION PHENOTYPE.
[9]	"Insights into the substrate specificity of plant peptide deformylase, an essential enzyme with potential for the development of novel biotechnology applications in agriculture." Dirk L.M., Schmidt J.J., Cai Y., Barnes J.C., Hanger K.M., Nayak N.R., Williams M.A., Grossman R.B., Houtz R.L., Rodgers D.W. Biochem. J. 413:417-427(2008) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 65-257, HOMODIMERIZATION, MUTAGENESIS OF TYR-178.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AF269165 mRNA. Translation: AAG33980.1.
AL163792 Genomic DNA. Translation: CAB87633.1.
CP002688 Genomic DNA. Translation: AED92059.1.
CP002688 Genomic DNA. Translation: AED92060.1.
AY050879 mRNA. Translation: AAK92816.1.
AY096673 mRNA. Translation: AAM20307.1.
AY085417 mRNA. Translation: AAM62644.1.

IPI

IPI00542984.

PIR

T48639.

RefSeq

NP_196970.1. NM_121470.3.
NP_850821.1. NM_180490.1.

UniGene

At.5087.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3CPM	X-ray	2.40	A	65-257	[»]
3M6O	X-ray	2.00	A/B	83-273	[»]
3M6P	X-ray	2.00	A/B	83-273	[»]
3M6Q	X-ray	2.40	A	83-273	[»]
3M6R	X-ray	2.40	A/B/C/D	83-273	[»]
3O3J	X-ray	3.00	A	83-273	[»]
3PN2	X-ray	2.00	A	83-273	[»]
3PN3	X-ray	1.30	A/B	83-273	[»]
3PN4	X-ray	1.90	A	83-273	[»]
3PN5	X-ray	2.30	A	83-273	[»]
3PN6	X-ray	2.10	A/B	83-273	[»]

ProteinModelPortal

Q9FUZ2.

SMR

Q9FUZ2. Positions 74-257.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q9FUZ2. 2 interactions.

Proteomic databases

PaxDb

Q9FUZ2.

PRIDE

Q9FUZ2.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblPlants

AT5G14660.1; AT5G14660.1; AT5G14660.
AT5G14660.2; AT5G14660.2; AT5G14660.

GeneID

831318.

KEGG

ath:AT5G14660.

Organism-specific databases

TAIR

At5g14660.

Phylogenomic databases

eggNOG

COG0242.

HOGENOM

HOG000243509.

InParanoid

Q9FUZ2.

KO

K01462.

OMA

PEQSHEI.

PhylomeDB

Q9FUZ2.

ProtClustDB

CLSN2687238.

Enzyme and pathway databases

SABIO-RK

Q9FUZ2.

Gene expression databases

ArrayExpress

Q9FUZ2.

Genevestigator

Q9FUZ2.

GermOnline

AT5G14660. Arabidopsis thaliana.

Family and domain databases

Gene3D

3.90.45.10. 1 hit.

InterPro

IPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]

PANTHER

PTHR10458. PTHR10458. 1 hit.

Pfam

PF01327. Pep_deformylase. 1 hit.
[Graphical view]

PRINTS

PR01576. PDEFORMYLASE.

SUPFAM

SSF56420. Fmet_deformylase. 1 hit.

TIGRFAMs

TIGR00079. pept_deformyl. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

Q9FUZ2.

Entry information

Entry name

DEF1B_ARATH

Accession

Primary (citable) accession number: Q9FUZ2
Secondary accession number(s): Q8LEH0, Q949U8, Q9LYJ4

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 5, 2001
Last sequence update:	December 15, 2003
Last modified:	May 1, 2013
This is version 93 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program