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Protein

Peptide deformylase 1B, chloroplastic

Gene

PDF1B

Organism
Solanum lycopersicum (Tomato) (Lycopersicon esculentum)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at transcript leveli

Functioni

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

Catalytic activityi

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

Cofactori

Fe2+By similarityNote: Binds 1 Fe2+ ion.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi177 – 1771IronBy similarity
Metal bindingi219 – 2191IronBy similarity
Active sitei220 – 2201By similarity
Metal bindingi223 – 2231IronBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

SABIO-RKQ9FV54.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase 1B, chloroplastic (EC:3.5.1.88)
Short name:
PDF 1B
Alternative name(s):
Polypeptide deformylase
Gene namesi
Name:PDF1B
OrganismiSolanum lycopersicum (Tomato) (Lycopersicon esculentum)
Taxonomic identifieri4081 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaeasteridslamiidsSolanalesSolanaceaeSolanoideaeSolaneaeSolanumLycopersicon
ProteomesiUP000004994 Componenti: Chromosome 2

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Plastid

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini? – 279Peptide deformylase 1B, chloroplasticPRO_0000006733
Transit peptidei1 – ?ChloroplastSequence Analysis

Interactioni

Protein-protein interaction databases

STRINGi4081.Solyc02g086680.2.1.

Structurei

3D structure databases

ProteinModelPortaliQ9FV54.
SMRiQ9FV54. Positions 80-262.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

InParanoidiQ9FV54.
KOiK01462.
OMAiHEFDHLL.

Family and domain databases

Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase.
InterProiIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
PANTHERiPTHR10458. PTHR10458. 1 hit.
PfamiPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PRINTSiPR01576. PDEFORMYLASE.
SUPFAMiSSF56420. SSF56420. 1 hit.
TIGRFAMsiTIGR00079. pept_deformyl. 1 hit.

Sequencei

Sequence statusi: Complete.

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

Q9FV54-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAMAAASWAS SSSFTRFLRP LLSRNSSPSP ISYSLHRYKS ANCLFFSASS
60 70 80 90 100
NKPPKLAVYA QARRVLSSKT KGDEIATPAD LSFVVPLKIV EYPDPILRAK
110 120 130 140 150
NKRIDNFDAN LKKLVDEMFD IMYKTDGIGL SAPQVGMNVQ LMVFNAAGER
160 170 180 190 200
GEGEEIVLVN PRVSRYSRRI IPYEEGCLSF PMIHGDVKRP ESVKVDAQDI
210 220 230 240 250
NGTRFEISLS ALPARVFQHE FDHLQGVLFF DKMTDEVLDT IREKLVALEK
260 270
KYEDRTGLPT PESINTRKIK KAAVGFGKS
Length:279
Mass (Da):31,197
Last modified:March 1, 2001 - v1
Checksum:i750F6406FDAC4233
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF250958 mRNA. Translation: AAG33972.1.
RefSeqiNP_001234441.1. NM_001247512.1.
UniGeneiLes.3729.

Genome annotation databases

EnsemblPlantsiSolyc02g086680.2.1; Solyc02g086680.2.1; Solyc02g086680.2.
GeneIDi543648.
KEGGisly:543648.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF250958 mRNA. Translation: AAG33972.1.
RefSeqiNP_001234441.1. NM_001247512.1.
UniGeneiLes.3729.

3D structure databases

ProteinModelPortaliQ9FV54.
SMRiQ9FV54. Positions 80-262.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi4081.Solyc02g086680.2.1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiSolyc02g086680.2.1; Solyc02g086680.2.1; Solyc02g086680.2.
GeneIDi543648.
KEGGisly:543648.

Phylogenomic databases

InParanoidiQ9FV54.
KOiK01462.
OMAiHEFDHLL.

Enzyme and pathway databases

SABIO-RKQ9FV54.

Family and domain databases

Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase.
InterProiIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
PANTHERiPTHR10458. PTHR10458. 1 hit.
PfamiPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PRINTSiPR01576. PDEFORMYLASE.
SUPFAMiSSF56420. SSF56420. 1 hit.
TIGRFAMsiTIGR00079. pept_deformyl. 1 hit.
ProtoNetiSearch...

Publicationsi

  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].

Entry informationi

Entry nameiDEF1B_SOLLC
AccessioniPrimary (citable) accession number: Q9FV54
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 5, 2001
Last sequence update: March 1, 2001
Last modified: June 24, 2015
This is version 75 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.