DEF1B_ARATH
ID DEF1B_ARATH Reviewed; 273 AA.
AC Q9FUZ2; Q8LEH0; Q949U8; Q9LYJ4;
DT 05-DEC-2001, integrated into UniProtKB/Swiss-Prot.
DT 15-DEC-2003, sequence version 2.
DT 03-AUG-2022, entry version 146.
DE RecName: Full=Peptide deformylase 1B, chloroplastic/mitochondrial;
DE Short=AtDEF2;
DE Short=AtPDF1B;
DE Short=PDF 1B;
DE EC=3.5.1.88 {ECO:0000269|PubMed:11553738, ECO:0000269|PubMed:18412546};
DE AltName: Full=Polypeptide deformylase;
DE Flags: Precursor;
GN Name=PDF1B; Synonyms=DEF2; OrderedLocusNames=At5g14660; ORFNames=T15N1_150;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, AND SUBCELLULAR
RP LOCATION.
RX PubMed=11060042; DOI=10.1093/emboj/19.21.5916;
RA Giglione C., Serero A., Pierre M., Boisson B., Meinnel T.;
RT "Identification of eukaryotic peptide deformylases reveals universality of
RT N-terminal protein processing mechanisms.";
RL EMBO J. 19:5916-5929(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP SUBCELLULAR LOCATION, ACTIVITY REGULATION, BIOPHYSICOCHEMICAL PROPERTIES,
RP CATALYTIC ACTIVITY, AND FUNCTION.
RX PubMed=11553738; DOI=10.1104/pp.127.1.97;
RA Dirk L.M., Williams M.A., Houtz R.L.;
RT "Eukaryotic peptide deformylases. Nuclear-encoded and chloroplast-targeted
RT enzymes in Arabidopsis.";
RL Plant Physiol. 127:97-107(2001).
RN [7]
RP COFACTOR, AND ACTIVITY REGULATION.
RX PubMed=11733990; DOI=10.1006/jmbi.2001.5175;
RA Serero A., Giglione C., Meinnel T.;
RT "Distinctive features of the two classes of eukaryotic peptide
RT deformylases.";
RL J. Mol. Biol. 314:695-708(2001).
RN [8]
RP DISRUPTION PHENOTYPE.
RX PubMed=12505980; DOI=10.1093/emboj/cdg007;
RA Giglione C., Vallon O., Meinnel T.;
RT "Control of protein life-span by N-terminal methionine excision.";
RL EMBO J. 22:13-23(2003).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 65-257, HOMODIMERIZATION,
RP MUTAGENESIS OF TYR-178, FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=18412546; DOI=10.1042/bj20071641;
RA Dirk L.M., Schmidt J.J., Cai Y., Barnes J.C., Hanger K.M., Nayak N.R.,
RA Williams M.A., Grossman R.B., Houtz R.L., Rodgers D.W.;
RT "Insights into the substrate specificity of plant peptide deformylase, an
RT essential enzyme with potential for the development of novel biotechnology
RT applications in agriculture.";
RL Biochem. J. 413:417-427(2008).
CC -!- FUNCTION: Removes the formyl group from the N-terminal Met of newly
CC synthesized proteins. Has a preferred substrate specificity towards the
CC photosystem II (PS II) D1 polypeptide. {ECO:0000269|PubMed:11060042,
CC ECO:0000269|PubMed:11553738, ECO:0000269|PubMed:18412546}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N-terminal N-formyl-L-methionyl-[peptide] = formate + N-
CC terminal L-methionyl-[peptide]; Xref=Rhea:RHEA:24420, Rhea:RHEA-
CC COMP:10639, Rhea:RHEA-COMP:10640, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15740, ChEBI:CHEBI:49298, ChEBI:CHEBI:64731; EC=3.5.1.88;
CC Evidence={ECO:0000269|PubMed:11553738, ECO:0000269|PubMed:18412546};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:24421;
CC Evidence={ECO:0000305|PubMed:18412546};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000269|PubMed:11733990};
CC Note=Binds 1 Fe(2+) ion. {ECO:0000269|PubMed:11733990};
CC -!- ACTIVITY REGULATION: Inhibited by actinonin.
CC {ECO:0000269|PubMed:11553738, ECO:0000269|PubMed:11733990}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=130 uM for N-formyl-Met-Leu-rho-nitroanilide
CC {ECO:0000269|PubMed:11553738};
CC KM=3200 uM for N-formyl-Met-Ala-Ser {ECO:0000269|PubMed:11553738};
CC Vmax=20 umol/min/mg enzyme toward N-formyl-Met-Leu-rho-nitroanilide
CC {ECO:0000269|PubMed:11553738};
CC Vmax=1.3 umol/min/mg enzyme toward N-formyl-Met-Ala-Ser
CC {ECO:0000269|PubMed:11553738};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:18412546}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma. Mitochondrion.
CC Note=Reported to be localized to chloroplast and mitochondria based on
CC transient GFP expression in a heterologous system.
CC {ECO:0000269|PubMed:11060042}.
CC -!- TISSUE SPECIFICITY: Expressed in leaves and flowers.
CC {ECO:0000269|PubMed:11060042}.
CC -!- DISRUPTION PHENOTYPE: Albino. {ECO:0000269|PubMed:12505980}.
CC -!- SIMILARITY: Belongs to the polypeptide deformylase family.
CC {ECO:0000305}.
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DR EMBL; AF269165; AAG33980.1; -; mRNA.
DR EMBL; AL163792; CAB87633.1; -; Genomic_DNA.
DR EMBL; CP002688; AED92059.1; -; Genomic_DNA.
DR EMBL; CP002688; AED92060.1; -; Genomic_DNA.
DR EMBL; CP002688; ANM71170.1; -; Genomic_DNA.
DR EMBL; AY050879; AAK92816.1; -; mRNA.
DR EMBL; AY096673; AAM20307.1; -; mRNA.
DR EMBL; AY085417; AAM62644.1; -; mRNA.
DR PIR; T48639; T48639.
DR RefSeq; NP_001332718.1; NM_001343352.1.
DR RefSeq; NP_196970.1; NM_121470.3.
DR RefSeq; NP_850821.1; NM_180490.1.
DR PDB; 3CPM; X-ray; 2.40 A; A=65-257.
DR PDB; 3M6O; X-ray; 2.00 A; A/B=83-273.
DR PDB; 3M6P; X-ray; 2.00 A; A/B=83-273.
DR PDB; 3M6Q; X-ray; 2.40 A; A=83-273.
DR PDB; 3M6R; X-ray; 2.40 A; A/B/C/D=83-273.
DR PDB; 3O3J; X-ray; 3.00 A; A=83-273.
DR PDB; 3PN2; X-ray; 2.00 A; A=83-273.
DR PDB; 3PN3; X-ray; 1.30 A; A/B=83-273.
DR PDB; 3PN4; X-ray; 1.90 A; A=83-273.
DR PDB; 3PN5; X-ray; 2.30 A; A=83-273.
DR PDB; 3PN6; X-ray; 2.10 A; A/B=83-273.
DR PDBsum; 3CPM; -.
DR PDBsum; 3M6O; -.
DR PDBsum; 3M6P; -.
DR PDBsum; 3M6Q; -.
DR PDBsum; 3M6R; -.
DR PDBsum; 3O3J; -.
DR PDBsum; 3PN2; -.
DR PDBsum; 3PN3; -.
DR PDBsum; 3PN4; -.
DR PDBsum; 3PN5; -.
DR PDBsum; 3PN6; -.
DR AlphaFoldDB; Q9FUZ2; -.
DR SMR; Q9FUZ2; -.
DR BioGRID; 16595; 3.
DR IntAct; Q9FUZ2; 2.
DR STRING; 3702.AT5G14660.1; -.
DR iPTMnet; Q9FUZ2; -.
DR PaxDb; Q9FUZ2; -.
DR PRIDE; Q9FUZ2; -.
DR ProteomicsDB; 224073; -.
DR EnsemblPlants; AT5G14660.1; AT5G14660.1; AT5G14660.
DR EnsemblPlants; AT5G14660.2; AT5G14660.2; AT5G14660.
DR EnsemblPlants; AT5G14660.3; AT5G14660.3; AT5G14660.
DR GeneID; 831318; -.
DR Gramene; AT5G14660.1; AT5G14660.1; AT5G14660.
DR Gramene; AT5G14660.2; AT5G14660.2; AT5G14660.
DR Gramene; AT5G14660.3; AT5G14660.3; AT5G14660.
DR KEGG; ath:AT5G14660; -.
DR Araport; AT5G14660; -.
DR TAIR; locus:2222667; AT5G14660.
DR eggNOG; KOG3137; Eukaryota.
DR HOGENOM; CLU_061901_0_1_1; -.
DR InParanoid; Q9FUZ2; -.
DR OMA; CAAWLQP; -.
DR OrthoDB; 1532656at2759; -.
DR PhylomeDB; Q9FUZ2; -.
DR BRENDA; 3.5.1.88; 399.
DR SABIO-RK; Q9FUZ2; -.
DR EvolutionaryTrace; Q9FUZ2; -.
DR PRO; PR:Q9FUZ2; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9FUZ2; baseline and differential.
DR Genevisible; Q9FUZ2; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; IEA:UniProtKB-SubCell.
DR GO; GO:0005739; C:mitochondrion; IBA:GO_Central.
DR GO; GO:0009536; C:plastid; HDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0042586; F:peptide deformylase activity; IDA:TAIR.
DR GO; GO:0018206; P:peptidyl-methionine modification; IBA:GO_Central.
DR GO; GO:0006412; P:translation; IEA:UniProtKB-KW.
DR CDD; cd00487; Pep_deformylase; 1.
DR Gene3D; 3.90.45.10; -; 1.
DR HAMAP; MF_00163; Pep_deformylase; 1.
DR InterPro; IPR023635; Peptide_deformylase.
DR InterPro; IPR036821; Peptide_deformylase_sf.
DR PANTHER; PTHR10458; PTHR10458; 1.
DR Pfam; PF01327; Pep_deformylase; 1.
DR PRINTS; PR01576; PDEFORMYLASE.
DR SUPFAM; SSF56420; SSF56420; 1.
DR TIGRFAMs; TIGR00079; pept_deformyl; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Chloroplast; Hydrolase; Iron; Metal-binding; Mitochondrion;
KW Plastid; Protein biosynthesis; Reference proteome; Transit peptide.
FT TRANSIT 1..56
FT /note="Chloroplast and mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN 57..273
FT /note="Peptide deformylase 1B, chloroplastic/mitochondrial"
FT /id="PRO_0000006732"
FT REGION 246..273
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 246..266
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 214
FT /evidence="ECO:0000250"
FT BINDING 171
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT BINDING 213
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT BINDING 217
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT MUTAGEN 178
FT /note="Y->A: Decrease in substrate affinity."
FT /evidence="ECO:0000269|PubMed:18412546"
FT MUTAGEN 178
FT /note="Y->F,R: Increase in substrate affinity."
FT /evidence="ECO:0000269|PubMed:18412546"
FT CONFLICT 48
FT /note="T -> N (in Ref. 5; AAM62644)"
FT /evidence="ECO:0000305"
FT CONFLICT 205
FT /note="R -> S (in Ref. 1; AAG33980)"
FT /evidence="ECO:0000305"
FT HELIX 89..91
FT /evidence="ECO:0007829|PDB:3PN3"
FT HELIX 103..118
FT /evidence="ECO:0007829|PDB:3PN3"
FT STRAND 122..125
FT /evidence="ECO:0007829|PDB:3PN3"
FT HELIX 126..129
FT /evidence="ECO:0007829|PDB:3PN3"
FT STRAND 133..138
FT /evidence="ECO:0007829|PDB:3PN3"
FT STRAND 150..160
FT /evidence="ECO:0007829|PDB:3PN3"
FT STRAND 164..169
FT /evidence="ECO:0007829|PDB:3PN3"
FT STRAND 179..185
FT /evidence="ECO:0007829|PDB:3PN3"
FT STRAND 187..192
FT /evidence="ECO:0007829|PDB:3PN3"
FT STRAND 194..196
FT /evidence="ECO:0007829|PDB:3M6O"
FT STRAND 198..203
FT /evidence="ECO:0007829|PDB:3PN3"
FT HELIX 205..218
FT /evidence="ECO:0007829|PDB:3PN3"
FT HELIX 223..226
FT /evidence="ECO:0007829|PDB:3PN3"
FT HELIX 229..233
FT /evidence="ECO:0007829|PDB:3PN3"
FT HELIX 236..250
FT /evidence="ECO:0007829|PDB:3PN3"
FT HELIX 258..260
FT /evidence="ECO:0007829|PDB:3PN3"
SQ SEQUENCE 273 AA; 30610 MW; 25CDA90ED6D9603E CRC64;
MAVCNCFLQA PPLSRILLPV LSRRATTLSA GYGRLKSTVT FCSTVNRTSP LTSSVRAEVK
RVSRKDDKVA SATDVQFETP LKIVEYPDPI LRAKNKRIDI FDENLKNLVD AMFDVMYKTD
GIGLSAPQVG LNVQLMVFNP AGEPGEGKEI VLVNPKIKKY SDKLVPFDEG CLSFPGIYAE
VVRPQSVKID ARDITGERFS ISLSRLPARI FQHEYDHLEG VLFFDRMTDQ VLDSIREELE
ALEKKYEEKT GLPSPERVEA RQKRKAGVGF GKR
