PDF1A

Functionⁱ

Removes the formyl group from the N-terminal Met of newly synthesized proteins.

Catalytic activityⁱ

Formyl-L-methionyl peptide + H₂O = formate + methionyl peptide.

Cofactorⁱ

Zn²⁺By similarityNote: Binds 1 Zn²⁺ ion per subunit.By similarity

Enzyme regulationⁱ

Inhibited by actinonin.

Sites

Feature key	Position(s)	DescriptionActions	Length
Binding siteⁱ	178	Substrate; via carbonyl oxygenBy similarity	1
Metal bindingⁱ	179	ZincBy similarity	1
Metal bindingⁱ	221	ZincBy similarity	1
Active siteⁱ	222	By similarity	1
Metal bindingⁱ	225	ZincBy similarity	1

GO - Molecular functionⁱ

metal ion binding Source: UniProtKB-KW
peptide deformylase activity Source: GO_Central

Complete GO annotation...

GO - Biological processⁱ

co-translational protein modification Source: GO_Central
N-terminal protein amino acid modification Source: GO_Central
peptidyl-methionine modification Source: GO_Central
translation Source: UniProtKB-KW

Complete GO annotation...

Keywordsⁱ

Molecular function	Hydrolase
Biological process	Protein biosynthesis
Ligand	Metal-binding, Zinc

Enzyme and pathway databases

BRENDAⁱ	3.5.1.88. 4460.

BRENDAⁱ

3.5.1.88. 4460.

Names & Taxonomyⁱ

Protein namesⁱ	Recommended name: Peptide deformylase 1A, chloroplastic (EC:3.5.1.88) Short name: OsPDF1A Short name: PDF 1A
Gene namesⁱ	Name:PDF1A Ordered Locus Names:Os01g0555800, LOC_Os01g37510 ORF Names:OsJ_002139, OsJ_02204
Organismⁱ	Oryza sativa subsp. japonica (Rice)
Taxonomic identifierⁱ	39947 [NCBI]
Taxonomic lineageⁱ	cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › Mesangiospermae › Liliopsida › Petrosaviidae › commelinids › Poales › Poaceae › BOP clade › Oryzoideae › Oryzeae › Oryzinae › Oryza › Oryza sativa
Proteomesⁱ	UP000059680 Componentⁱ: Chromosome 1

Keywords - Cellular componentⁱ

Chloroplast, Plastid

PTM / Processingⁱ

Molecule processing

Feature key	Position(s)	DescriptionActions	Graphical view	Length
Transit peptideⁱ	1 – 43	ChloroplastSequence analysisAdd BLAST		43
ChainⁱPRO_0000369420	44 – 260	Peptide deformylase 1A, chloroplasticAdd BLAST		217

Proteomic databases

PaxDbⁱ	B6RGY0.
PRIDEⁱ	B6RGY0.

Expressionⁱ

Tissue specificityⁱ

Mainly expressed in roots. Lower expression in shoots, mature panicles at flowering stages and mature leaves.1 Publication

Gene expression databases

Genevisibleⁱ	B6RGY0. OS.

Genevisibleⁱ

B6RGY0. OS.

Interactionⁱ

Subunit structureⁱ

Homodimer.By similarity

Protein-protein interaction databases

STRINGⁱ	39947.LOC_Os01g37510.1.

STRINGⁱ

39947.LOC_Os01g37510.1.

Structureⁱ

3D structure databases

ProteinModelPortalⁱ	B6RGY0.
SMRⁱ	B6RGY0.
ModBaseⁱ	Search...
MobiDBⁱ	Search...

Family & Domainsⁱ

Region

Feature key	Position(s)	DescriptionActions	Length
Regionⁱ	114 – 117	Substrate bindingBy similarity	4
Regionⁱ	182 – 187	DimerizationBy similarity	6
Regionⁱ	227 – 245	DimerizationBy similarityAdd BLAST	19

Compositional bias

Feature key	Position(s)	DescriptionActions	Graphical view	Length
Compositional biasⁱ	47 – 50	Poly-Gly		4
Compositional biasⁱ	57 – 63	Poly-Gly		7

Sequence similaritiesⁱ

Belongs to the polypeptide deformylase family.Curated

Keywords - Domainⁱ

Transit peptide

Phylogenomic databases

eggNOGⁱ	KOG3137. Eukaryota. COG0242. LUCA.
InParanoidⁱ	B6RGY0.
KEGG Orthology (KO) More...KOⁱ	K01462.
Database of Orthologous Groups More...OrthoDBⁱ	EOG09360MKH.

Family and domain databases

Conserved Domains Database More...CDDⁱ	cd00487. Pep_deformylase. 1 hit.
Gene3Dⁱ	3.90.45.10. 1 hit.
HAMAPⁱ	MF_00163. Pep_deformylase. 1 hit.
InterProⁱ	View protein in InterPro IPR023635. Peptide_deformylase.
PANTHERⁱ	PTHR10458. PTHR10458. 1 hit.
Pfam protein domain database More...Pfamⁱ	View protein in Pfam PF01327. Pep_deformylase. 1 hit.
PRINTSⁱ	PR01576. PDEFORMYLASE.
SUPFAMⁱ	SSF56420. SSF56420. 1 hit.
TIGRFAMsⁱ	TIGR00079. pept_deformyl. 1 hit.

Sequenceⁱ

Sequence statusⁱ: Complete.

Sequence processingⁱ: The displayed sequence is further processed into a mature form.

B6RGY0-1 [UniParc]FASTA Add to basket

« Hide

        10         20         30         40         50
MEAHLRPLSA AALLLSPAAP LPTAVAASAR RASPGGRRWS SVRASAGGGG 
        60         70         80         90        100
WLSGLLGGKG GGGAPTAMTV TPGTVKAGDP VLHEPAQDVA PGDIPSEKVQ 
       110        120        130        140        150
GVIDRMVAVM RKAPGVGLAA PQIGVPLKII VLEDTQEYIS YAPKKDIEAQ 
       160        170        180        190        200
DRRPFDLLVI INPKLKTTSK RTALFFEGCL SVDGYRALVE RHLDVEVSGL 
       210        220        230        240        250
DRNGRPIKVE ASGWQARILQ HECDHLEGTL YVDTMVPRTF RIVDNLDLPL 
       260
PVGCPPIGAR

Length:260

Mass (Da):27,493

Last modified:December 16, 2008 - v1

Checksum:ⁱA0CEB3C83E884CCE

GO

Sequence cautionⁱ

The sequence BAF05237 differs from that shown. Reason: Erroneous gene model prediction.Curated

The sequence EEE54799 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Sequence databases

Select the link destinations: EMBLⁱ GenBankⁱ DDBJⁱ Links Updated	EU213045 mRNA. Translation: ABY64739.1. AP008207 Genomic DNA. Translation: BAF05237.1. Sequence problems. AP014957 Genomic DNA. No translation available. CM000138 Genomic DNA. Translation: EEE54799.1. Different initiation.
NCBI Reference Sequences More...RefSeqⁱ	XP_015621038.1. XM_015765552.1.
UniGeneⁱ	Os.14593.

Genome annotation databases

GeneIDⁱ	4324565.
KEGGⁱ	osa:4324565.

Similar proteinsⁱ

Protein	Similar proteins	Organisms	Length	Cluster ID	Cluster name	Size
B6RGY0	B8AA31 A0A0P0V402	Oryza sativa subsp. japonica (Rice) Oryza sativa subsp. indica (Rice)	260	UniRef100_B6RGY0	Cluster: Peptide deformylase 1A, chloroplastic	3

Protein	Similar proteins	Organisms	Length	Cluster ID	Cluster name	Size
B6RGY0	B8AA31 A0A0P0V402 A0A0D9YAF8 A0A0D3EQ32	Oryza sativa subsp. japonica (Rice) Oryza sativa subsp. indica (Rice) Oryza glumipatula Oryza barthii	260	UniRef90_B6RGY0	Cluster: Peptide deformylase 1A, chloroplastic	5

Protein	Similar proteins	Organisms	Length	Cluster ID	Cluster name	Size
B6RGY0	B8AA31 A0A0P0V402 A0A0D9YAF8 A0A0D3EQ32 I1KVC5 A0A0B2SSE5 F2E2L8 M0Z9W7 M7YV25 A0A1D5V5L8 +66	Oryza sativa subsp. japonica (Rice) Oryza sativa subsp. indica (Rice) Oryza glumipatula Oryza barthii Glycine max (Soybean) (Glycine hispida) Glycine soja (Wild soybean) Hordeum vulgare subsp. vulgare (Domesticated barley) Triticum urartu (Red wild einkorn) (Crithodium urartu) Triticum aestivum (Wheat) Brassica napus (Rape) And more	260	UniRef50_B6RGY0	Cluster: Peptide deformylase 1A, chloroplastic	77

Cross-referencesⁱ

Sequence databases

Select the link destinations: EMBLⁱ GenBankⁱ DDBJⁱ Links Updated	EU213045 mRNA. Translation: ABY64739.1. AP008207 Genomic DNA. Translation: BAF05237.1. Sequence problems. AP014957 Genomic DNA. No translation available. CM000138 Genomic DNA. Translation: EEE54799.1. Different initiation.
NCBI Reference Sequences More...RefSeqⁱ	XP_015621038.1. XM_015765552.1.
UniGeneⁱ	Os.14593.

3D structure databases

ProteinModelPortalⁱ	B6RGY0.
SMRⁱ	B6RGY0.
ModBaseⁱ	Search...
MobiDBⁱ	Search...

Protein-protein interaction databases

STRINGⁱ	39947.LOC_Os01g37510.1.

STRINGⁱ

39947.LOC_Os01g37510.1.

Proteomic databases

PaxDbⁱ	B6RGY0.
PRIDEⁱ	B6RGY0.

Protocols and materials databases

Structural Biology Knowledgebase	Search...

Structural Biology Knowledgebase

Search...

Genome annotation databases

GeneIDⁱ	4324565.
KEGGⁱ	osa:4324565.

Phylogenomic databases

eggNOGⁱ	KOG3137. Eukaryota. COG0242. LUCA.
InParanoidⁱ	B6RGY0.
KEGG Orthology (KO) More...KOⁱ	K01462.
Database of Orthologous Groups More...OrthoDBⁱ	EOG09360MKH.

Enzyme and pathway databases

BRENDAⁱ	3.5.1.88. 4460.

BRENDAⁱ

3.5.1.88. 4460.

Gene expression databases

Genevisibleⁱ	B6RGY0. OS.

Genevisibleⁱ

B6RGY0. OS.

Family and domain databases

Conserved Domains Database More...CDDⁱ	cd00487. Pep_deformylase. 1 hit.
Gene3Dⁱ	3.90.45.10. 1 hit.
HAMAPⁱ	MF_00163. Pep_deformylase. 1 hit.
InterProⁱ	View protein in InterPro IPR023635. Peptide_deformylase.
PANTHERⁱ	PTHR10458. PTHR10458. 1 hit.
Pfam protein domain database More...Pfamⁱ	View protein in Pfam PF01327. Pep_deformylase. 1 hit.
PRINTSⁱ	PR01576. PDEFORMYLASE.
SUPFAMⁱ	SSF56420. SSF56420. 1 hit.
TIGRFAMsⁱ	TIGR00079. pept_deformyl. 1 hit.
ProtoNetⁱ	Search...

Entry informationⁱ

Entry nameⁱ	DEF1A_ORYSJ
Accessionⁱ	B6RGY0Primary (citable) accession number: B6RGY0 Secondary accession number(s): A2ZUB7, B9EXI6, Q0JLZ1
Entry historyⁱ	Integrated into UniProtKB/Swiss-Prot:	April 14, 2009
	Last sequence update:	December 16, 2008
	Last modified:	August 30, 2017
	This is version 58 of the entry and version 1 of the sequence. See complete history.
Entry statusⁱ	Reviewed (UniProtKB/Swiss-Prot)
Annotation program	Plant Protein Annotation Program

Miscellaneousⁱ

Keywords - Technical termⁱ

Complete proteome, Reference proteome

Documents

Oryza sativa (rice)
Index of Oryza sativa entries and their corresponding gene designations
SIMILARITY comments
Index of protein domains and families

UniProtKB

UniParc

Help

UniRef

Proteomes

Annotation systems

Supporting data

UniProtKB - B6RGY0 (DEF1A_ORYSJ)

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Peptide deformylase 1A, chloroplastic

Select a section on the left to see content.

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

<p>This subsection of the ‘Function’ section describes an enzyme regulatory mechanism and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/enzyme_regulation' target='_top'>More...</a></p>Enzyme regulationi

Sites

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Biological processi

Enzyme and pathway databases

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Chloroplast

Chloroplast

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Proteomic databases

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

Gene expression databases

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

Protein-protein interaction databases

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Region

Compositional bias

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Phylogenomic databases

Family and domain databases

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including length and molecular weight.<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the ‘Sequence’ section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

Sequence databases

Genome annotation databases

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Documents

Functionⁱ

Enzyme regulationⁱ

GO - Molecular functionⁱ

GO - Biological processⁱ

Names & Taxonomyⁱ

Subcellular locationⁱ

PTM / Processingⁱ

Expressionⁱ

Interactionⁱ

Structureⁱ

Family & Domainsⁱ

Sequence similaritiesⁱ

Sequenceⁱ

Sequence cautionⁱ

Cross-referencesⁱ

Entry informationⁱ

Miscellaneousⁱ