Q9LJL3 (PREP1_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Presequence protease 1, chloroplastic/mitochondrial
Short name=AtPreP1
Short name=PreP 1
EC=3.4.24.-

Alternative name(s):
Zinc metalloprotease 1
Short name=AtZnMP1

Gene names

Name:	PREP1
Synonyms:	ZNMP1
Ordered Locus Names:	At3g19170
ORF Names:	MVI11.6, MVI11.7, MVI11_8

Organism

Arabidopsis thaliana (Mouse-ear cress)

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	1080 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	ATP-independent protease that degrades both mitochondrial and chloroplastic transit peptides after their cleavage. Also degrades other unstructured peptides. Specific for peptides in the range of 10 to 65 residues. Shows a preference for cleavage after small polar residues and before basic residues, with a bias for positively charged amino acid residues. Ref.4
Cofactor	Binds 1 zinc ion per subunit. Binds 2 Magnesium ions per subunit.
Enzyme regulation	Inactive in the absence of MgCl2 and CaCl2 and full activation at 10 mM concentrations of either ion. Completely inhibited by the metal chelator orthophenanthroline, but not affected by phenylmethylsulphonylfluoride (PMSF) or N-ethylmaleimide (NEM).
Subunit structure	Homodimer.
Subcellular location	Plastid › chloroplast stroma. Mitochondrion matrix Ref.5 Ref.6.
Tissue specificity	Expressed only in siliques and flowers. Ref.6
Miscellaneous	The 2 enzymes halves enclose a large proteolytic chamber spacious enough to hold peptide substrates, but sufficiently small to exclude larger, folded proteins. Since the active site includes residues from both the N- and C-terminal part of the protein, proteolysis can occur only when the chamber is closed. Covalently locking the 2 halves of the protease with disulfide bonds induces a loss of activity.
Sequence similarities	Belongs to the peptidase M16 family. PreP subfamily.
Biophysicochemical properties	pH dependence: Active from pH 4 to 10. Temperature dependence: Optimum temperature is 28 degrees Celsius. Active from 4 to 40 degrees Celsius.
Sequence caution	The sequence BAB02957.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Cellular component	Chloroplast Mitochondrion Plastid
Coding sequence diversity	Alternative splicing
Domain	Coiled coil Transit peptide
Ligand	Magnesium Metal-binding Zinc
Molecular function	Hydrolase Metalloprotease Protease
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	protein processing Inferred from direct assay Ref.5. Source: TAIR proteolysis Inferred from electronic annotation. Source: UniProtKB-KW response to cadmium ion Inferred from expression pattern. Source: TAIR
Cellular component	apoplast Inferred from direct assay. Source: TAIR chloroplast envelope Inferred from direct assay. Source: TAIR chloroplast stroma Inferred from direct assay. Source: TAIR mitochondrial matrix Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	metalloendopeptidase activity Inferred from direct assay Ref.4. Source: TAIR zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

This entry describes 1 isoform produced by alternative splicing. [Select]

Note: A number of isoforms are produced. According to EST sequences.

Isoform 1 (identifier: Q9LJL3-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Transit peptide

1 – 84

84

Chloroplast and mitochondrion Potential

Chain

85 – 1080

996

Presequence protease 1, chloroplastic/mitochondrial

PRO_0000249938

Regions

Coiled coil

571 – 612

42

Potential

Sites

Active site

165

1

Proton acceptor

Metal binding

162

1

Zinc; catalytic

Metal binding

166

1

Zinc; catalytic

Metal binding

262

1

Zinc; catalytic

Experimental info

Mutagenesis

162

1

H → L: Loss of activity. Ref.5

Mutagenesis

165

1

E → Q: Loss of activity. Ref.5

Mutagenesis

166

1

H → L: Loss of activity. Ref.5

Mutagenesis

179

1

E → Q: Decreased activity toward some substrates. Ref.8

Mutagenesis

194

1

N → A: Reduced activity. Ref.8

Mutagenesis

240

1

E → Q: Decreased activity toward some substrates. Ref.5

Mutagenesis

245

1

E → Q: No loss of activity. Ref.5

Mutagenesis

256

1

K → C: Inactive under oxidizing conditions and fully active under reducing conditions; when associated with C-937. Ref.8

Mutagenesis

262

1

E → Q: Loss of activity. Ref.8

Mutagenesis

264

1

K → C: Inactive under oxidizing conditions and fully active under reducing conditions; when associated with C-895. Ref.8

Mutagenesis

416

1

A → C: Little or no effect; when associated with C-700. Ref.8

Mutagenesis

430

1

E → C: Inactive under oxidizing conditions and fully active under reducing conditions; when associated with C-767. Ref.8

Mutagenesis

700

1

N → C: Little or no effect; when associated with C-416. Ref.8

Mutagenesis

767

1

S → C: Inactive under oxidizing conditions and fully active under reducing conditions; when associated with C-430. Ref.8

Mutagenesis

895

1

Q → C: Inactive under oxidizing conditions and fully active under reducing conditions; when associated with C-264. Ref.8

Mutagenesis

933

1

R → A or K: Loss of activity. Ref.8

Mutagenesis

937

1

G → C: Inactive under oxidizing conditions and fully active under reducing conditions; when associated with C-256. Ref.8

Mutagenesis

939

1

Y → F: Loss of activity. Ref.8

Secondary structure

1

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1080

Helix Strand Turn

Details...

Helix

101 – 104

4

Beta strand

107 – 115

9

Turn

116 – 119

4

Beta strand

120 – 127

8

Turn

128 – 130

3

Beta strand

133 – 138

6

Beta strand

142 – 151

10

Beta strand

155 – 158

4

Helix

160 – 167

8

Helix

180 – 187

8

Beta strand

190 – 193

4

Beta strand

199 – 210

12

Helix

211 – 226

16

Helix

229 – 231

3

Helix

235 – 240

6

Beta strand

243 – 245

3

Beta strand

254 – 256

3

Helix

258 – 266

9

Helix

270 – 282

13

Helix

287 – 289

3

Turn

296 – 298

3

Helix

299 – 301

3

Helix

304 – 314

11

Helix

317 – 319

3

Beta strand

320 – 328

9

Helix

330 – 341

12

Helix

349 – 352

4

Beta strand

365 – 372

8

Beta strand

375 – 377

3

Helix

379 – 381

3

Beta strand

383 – 390

8

Helix

398 – 412

15

Helix

418 – 425

8

Beta strand

430 – 432

3

Beta strand

436 – 438

3

Beta strand

440 – 443

4

Beta strand

445 – 453

9

Helix

455 – 457

3

Helix

458 – 475

18

Helix

479 – 495

17

Helix

503 – 515

13

Turn

516 – 518

3

Helix

523 – 525

3

Helix

528 – 541

14

Helix

543 – 554

12

Turn

555 – 557

3

Beta strand

561 – 569

9

Helix

572 – 589

18

Helix

593 – 610

18

Helix

616 – 619

4

Helix

627 – 629

3

Beta strand

640 – 653

14

Beta strand

657 – 667

11

Turn

673 – 675

3

Helix

676 – 678

3

Helix

679 – 688

10

Beta strand

692 – 694

3

Helix

696 – 706

11

Beta strand

707 – 719

13

Beta strand

722 – 736

15

Helix

737 – 739

3

Helix

740 – 753

14

Helix

759 – 779

21

Helix

781 – 791

11

Helix

795 – 804

10

Helix

806 – 821

16

Helix

823 – 837

15

Beta strand

844 – 849

6

Helix

851 – 866

16

Beta strand

888 – 891

4

Beta strand

895 – 904

10

Helix

905 – 908

4

Helix

915 – 925

11

Helix

927 – 931

5

Turn

932 – 936

5

Beta strand

939 – 946

8

Turn

947 – 950

4

Beta strand

951 – 960

10

Helix

963 – 970

8

Helix

972 – 977

6

Helix

983 – 997

15

Helix

1003 – 1015

13

Helix

1020 – 1031

12

Helix

1035 – 1051

17

Beta strand

1053 – 1058

6

Helix

1060 – 1069

10

Turn

1070 – 1072

3

Beta strand

1074 – 1077

4

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified September 19, 2006. Version 2. Checksum: 9FD259970195B9FC	FASTA	1,080	121,015
	10 20 30 40 50 60 MLRTVSCLAS RSSSSLFFRF FRQFPRSYMS LTSSTAALRV PSRNLRRISS PSVAGRRLLL 70 80 90 100 110 120 RRGLRIPSAA VRSVNGQFSR LSVRAVATQP APLYPDVGQD EAEKLGFEKV SEEFISECKS 130 140 150 160 170 180 KAILFKHKKT GCEVMSVSNE DENKVFGVVF RTPPKDSTGI PHILEHSVLC GSRKYPVKEP 190 200 210 220 230 240 FVELLKGSLH TFLNAFTYPD RTCYPVASTN TKDFYNLVDV YLDAVFFPKC VDDAHTFQQE 250 260 270 280 290 300 GWHYELNDPS EDISYKGVVF NEMKGVYSQP DNILGRIAQQ ALSPENTYGV DSGGDPKDIP 310 320 330 340 350 360 NLTFEEFKEF HRQYYHPSNA RIWFYGDDDP VHRLRVLSEY LDMFEASPSP NSSKIKFQKL 370 380 390 400 410 420 FSEPVRLVEK YPAGRDGDLK KKHMLCVNWL LSEKPLDLQT QLALGFLDHL MLGTPASPLR 430 440 450 460 470 480 KILLESGLGE ALVSSGLSDE LLQPQFGIGL KGVSEENVQK VEELIMDTLK KLAEEGFDND 490 500 510 520 530 540 AVEASMNTIE FSLRENNTGS FPRGLSLMLQ SISKWIYDMD PFEPLKYTEP LKALKTRIAE 550 560 570 580 590 600 EGSKAVFSPL IEKLILNNSH RVTIEMQPDP EKATQEEVEE KNILEKVKAA MTEEDLAELA 610 620 630 640 650 660 RATEELKLKQ ETPDPPEALR CVPSLNLGDI PKEPTYVPTE VGDINGVKVL RHDLFTNDII 670 680 690 700 710 720 YTEVVFDIGS LKHELLPLVP LFCQSLLEMG TKDLTFVQLN QLIGRKTGGI SVYPLTSSVR 730 740 750 760 770 780 GKDEPCSKII VRGKSMAGRA DDLFNLMNCL LQEVQFTDQQ RFKQFVSQSR ARMENRLRGS 790 800 810 820 830 840 GHGIAAARMD AMLNIAGWMS EQMGGLSYLE FLHTLEKKVD EDWEGISSSL EEIRRSLLAR 850 860 870 880 890 900 NGCIVNMTAD GKSLTNVEKS VAKFLDLLPE NPSGGLVTWD GRLPLRNEAI VIPTQVNYVG 910 920 930 940 950 960 KAGNIYSTGY ELDGSAYVIS KHISNTWLWD RVRVSGGAYG GFCDFDSHSG VFSYLSYRDP 970 980 990 1000 1010 1020 NLLKTLDIYD GTGDFLRGLD VDQETLTKAI IGTIGDVDSY QLPDAKGYSS LLRHLLGVTD 1030 1040 1050 1060 1070 1080 EERQRKREEI LTTSLKDFKD FAQAIDVVRD KGVAVAVASA EDIDAANNER SNFFEVKKAL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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: 10907853] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[2]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[3]	"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: 14593172] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[4]	"Isolation and identification of a novel mitochondrial metalloprotease (PreP) that degrades targeting presequences in plants." Staahl A., Moberg P., Ytterberg J., Panfilov O., Brockenhuus Von Lowenhielm H., Nilsson F., Glaser E. J. Biol. Chem. 277:41931-41939(2002) [PubMed: 12138166] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION.
[5]	"Characterization of a novel zinc metalloprotease involved in degrading targeting peptides in mitochondria and chloroplasts." Moberg P., Staahl A., Bhushan S., Wright S.J., Eriksson A., Bruce B.D., Glaser E. Plant J. 36:616-628(2003) [PubMed: 14617063] [Abstract] Cited for: CHARACTERIZATION, MUTAGENESIS OF HIS-162; GLU-165; HIS-166; GLU-240 AND GLU-245, SUBCELLULAR LOCATION.
[6]	"Catalysis, subcellular localization, expression and evolution of the targeting peptides degrading protease, AtPreP2." Bhushan S., Staahl A., Nilsson S., Lefebvre B., Seki M., Roth C., McWilliam D., Wright S.J., Liberles D.A., Shinozaki K., Bruce B.D., Boutry M., Glaser E. Plant Cell Physiol. 46:985-996(2005) [PubMed: 15827031] [Abstract] Cited for: CHARACTERIZATION, IDENTIFICATION BY MASS SPECTROMETRY, TISSUE SPECIFICITY, SUBCELLULAR LOCATION.
[7]	"Two novel targeting peptide degrading proteases, PrePs, in mitochondria and chloroplasts, so similar and still different." Staahl A., Nilsson S., Lundberg P., Bhushan S., Biverstaahl H., Moberg P., Morisset M., Vener A., Maeler L., Langel U., Glaser E. J. Mol. Biol. 349:847-860(2005) [PubMed: 15893767] [Abstract] Cited for: CLEAVAGE SPECIFICITY.
[8]	"The closed structure of presequence protease PreP forms a unique 10,000 Angstroms3 chamber for proteolysis." Johnson K.A., Bhushan S., Staahl A., Hallberg B.M., Frohn A., Glaser E., Eneqvist T. EMBO J. 25:1977-1986(2006) [PubMed: 16601675] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 86-1080, MUTAGENESIS OF GLU-179; ASN-194; LYS-256; GLU-262; LYS-264; ALA-416; GLU-430; ASN-700; SER-767; GLN-895; ARG-933; GLY-937 AND TYR-939.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AP000419 Genomic DNA. Translation: BAB02957.1. Different initiation.
CP002686 Genomic DNA. Translation: AEE76201.1.
AY090240 mRNA. Translation: AAL90904.1.
AY091051 mRNA. Translation: AAM13872.1.
BT006362 mRNA. Translation: AAP21170.1.
BT002372 mRNA. Translation: AAN86205.1.

IPI

IPI00547030.

RefSeq

NP_188548.2. NM_112804.4.

UniGene

At.27915.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2FGE	X-ray	2.10	A/B	86-1080	[»]

ProteinModelPortal

Q9LJL3.

SMR

Q9LJL3. Positions 100-1078.

ModBase

Search...

Protein-protein interaction databases

MINT

MINT-7231907.

STRING

Q9LJL3.

Protein family/group databases

MEROPS

M16.012.

Proteomic databases

PRIDE

Q9LJL3.

ProMEX

Q9LJL3.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblPlants

AT3G19170.1; AT3G19170.1; AT3G19170.

GeneID

821451.

GenomeReviews

Gene locus AT3G19170 in contig BA000014_GR.

KEGG

ath:AT3G19170.

NMPDR

fig|3702.1.peg.14130.

Organism-specific databases

GeneFarm

2137. 225.

TAIR

At3g19170.

Phylogenomic databases

eggNOG

KOG2019.

GeneTree

EPGT00070000030705.

HOGENOM

HBG413876.

InParanoid

Q9LJL3.

OMA

IAFKTIP.

PhylomeDB

Q9LJL3.

ProtClustDB

CLSN2690450.

Gene expression databases

Genevestigator

Q9LJL3.

GermOnline

AT3G19170. Arabidopsis thaliana.

Family and domain databases

InterPro

IPR011249. Metalloenz_metal-bd.
IPR011237. Pept_M16_core.
IPR011765. Pept_M16_N.
IPR007863. Peptidase_M16_C.
IPR013578. Peptidase_M16C_assoc.
[Graphical view]

Gene3D

G3DSA:3.30.830.10. Pept_M16_core. 1 hit.

KO

K06972.

Pfam

PF08367. M16C_assoc. 1 hit.
PF00675. Peptidase_M16. 1 hit.
PF05193. Peptidase_M16_C. 1 hit.
[Graphical view]

SUPFAM

SSF63411. Metalloenz_metal-bd. 4 hits.

PROSITE

PS00143. INSULINASE. False negative.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

PREP1_ARATH

Accession

Primary (citable) accession number: Q9LJL3
Secondary accession number(s): Q8RUN6

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 19, 2006
Last sequence update:	September 19, 2006
Last modified:	November 16, 2011
This is version 73 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program