P10507 (MPPB_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Mitochondrial-processing peptidase subunit beta
EC=3.4.24.64

Alternative name(s):
Beta-MPP
PEP

Gene names

Name:	MAS1
Synonyms:	MIF1
Ordered Locus Names:	YLR163C
ORF Names:	L9632.10

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	462 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	Cleaves presequences (transit peptides) from mitochondrial protein precursors.
Catalytic activity	Release of N-terminal transit peptides from precursor proteins imported into the mitochondrion, typically with Arg in position P2.
Cofactor	Binds 1 zinc ion per subunit.
Subunit structure	Heterodimer of alpha and beta subunits.
Subcellular location	Mitochondrion matrix.
Miscellaneous	Present with 1360 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the peptidase M16 family.

Ontologies

Keywords
Cellular component	Mitochondrion
Domain	Transit peptide
Ligand	Metal-binding Zinc
Molecular function	Hydrolase Metalloprotease Protease
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	protein processing involved in protein targeting to mitochondrion Inferred from direct assay Ref.5. Source: SGD proteolysis Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	mitochondrial processing peptidase complex Inferred from direct assay PubMed 2905264. Source: SGD
Molecular_function	metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW metalloendopeptidase activity Traceable author statement. Source: Reactome
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
MAS2	P11914	5	EBI-11212,EBI-11205

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Transit peptide

1 – 20

20

Mitochondrion Ref.5

Chain

21 – 462

442

Mitochondrial-processing peptidase subunit beta

PRO_0000026784

Sites

Active site

73

1

Proton acceptor

Metal binding

70

1

Zinc

Metal binding

74

1

Zinc

Metal binding

150

1

Zinc

Amino acid modifications

Modified residue

243

1

Phosphoserine Ref.7

Experimental info

Mutagenesis

73

1

E → Q: Loss of activity. Ref.8

Secondary structure

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462

Helix Strand Turn

Details...

Beta strand

27 – 30

4

Beta strand

36 – 41

6

Beta strand

46 – 55

10

Helix

58 – 60

3

Turn

63 – 67

5

Helix

68 – 75

8

Beta strand

78 – 82

5

Helix

85 – 94

10

Beta strand

98 – 103

6

Beta strand

105 – 115

11

Helix

116 – 118

3

Helix

119 – 131

13

Helix

137 – 154

18

Helix

158 – 170

13

Turn

171 – 173

3

Helix

175 – 177

3

Helix

184 – 189

6

Helix

192 – 202

11

Helix

205 – 207

3

Beta strand

208 – 215

8

Helix

218 – 229

12

Beta strand

254 – 259

6

Beta strand

264 – 273

10

Helix

282 – 292

11

Beta strand

294 – 296

3

Turn

297 – 299

3

Beta strand

302 – 305

4

Helix

308 – 314

7

Beta strand

321 – 329

9

Beta strand

334 – 343

10

Turn

344 – 346

3

Helix

349 – 364

16

Helix

370 – 385

16

Helix

391 – 405

15

Helix

411 – 419

9

Helix

423 – 433

11

Beta strand

434 – 436

3

Beta strand

439 – 445

7

Helix

447 – 449

3

Helix

453 – 461

9

Sequences

	Sequence		Length	Mass (Da)
	P10507 [UniParc]. Last modified July 1, 1989. Version 1. Checksum: 084CE63C495EDFC4	FASTA	462	51,084
	10 20 30 40 50 60 MFSRTASKFR NTRRLLSTIS SQIPGTRTSK LPNGLTIATE YIPNTSSATV GIFVDAGSRA 70 80 90 100 110 120 ENVKNNGTAH FLEHLAFKGT QNRSQQGIEL EIENIGSHLN AYTSRENTVY YAKSLQEDIP 130 140 150 160 170 180 KAVDILSDIL TKSVLDNSAI ERERDVIIRE SEEVDKMYDE VVFDHLHEIT YKDQPLGRTI 190 200 210 220 230 240 LGPIKNIKSI TRTDLKDYIT KNYKGDRMVL AGAGAVDHEK LVQYAQKYFG HVPKSESPVP 250 260 270 280 290 300 LGSPRGPLPV FCRGERFIKE NTLPTTHIAI ALEGVSWSAP DYFVALATQA IVGNWDRAIG 310 320 330 340 350 360 TGTNSPSPLA VAASQNGSLA NSYMSFSTSY ADSGLWGMYI VTDSNEHNVQ LIVNEILKEW 370 380 390 400 410 420 KRIKSGKISD AEVNRAKAQL KAALLLSLDG STAIVEDIGR QVVTTGKRLS PEEVFEQVDK 430 440 450 460 ITKDDIIMWA NYRLQNKPVS MVALGNTSTV PNVSYIEEKL NQ

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"MAS1, a gene essential for yeast mitochondrial assembly, encodes a subunit of the mitochondrial processing protease." Witte C., Jensen R.E., Yaffe M.P., Schatz G. EMBO J. 7:1439-1447(1988) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XII." Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W., Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K., Heuss-Neitzel D., Hilbert H. , Hilger F., Kleine K., Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A., Hani J., Hoheisel J.D. Nature 387:87-90(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J. Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[5]	"The MAS-encoded processing protease of yeast mitochondria. Interaction of the purified enzyme with signal peptides and a purified precursor protein." Yang M., Geli V., Oppliger W., Suda K., James P., Schatz G. J. Biol. Chem. 266:6416-6423(1991) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 21-32.
[6]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[7]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-243, MASS SPECTROMETRY.
[8]	"Crystal structures of mitochondrial processing peptidase reveal the mode for specific cleavage of import signal sequences." Taylor A.B., Smith B.S., Kitada S., Kojima K., Miyaura H., Otwinowski Z., Ito A., Deisenhofer J. Structure 9:615-625(2001) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 21-462 IN COMPLEX WITH ZINC AND SUBSTRATES, MUTAGENESIS OF GLU-73.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X07649 Genomic DNA. Translation: CAA30489.1.
U51921 Genomic DNA. Translation: AAB67487.1.
AY693198 Genomic DNA. Translation: AAT93217.1.
BK006945 Genomic DNA. Translation: DAA09485.1.

PIR

S00552.

RefSeq

NP_013264.1. NM_001182050.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1HR6	X-ray	2.50	B/D/F/H	21-462	[»]
1HR7	X-ray	2.55	B/D/F/H	21-462	[»]
1HR8	X-ray	2.70	B/D/F/H	21-462	[»]
1HR9	X-ray	3.01	B/D/F/H	21-462	[»]

ProteinModelPortal

P10507.

SMR

P10507. Positions 23-462.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-2402N.

IntAct

P10507. 16 interactions.

MINT

MINT-614379.

STRING

4932.YLR163C.

Protein family/group databases

MEROPS

M16.980.

Proteomic databases

PaxDb

P10507.

PeptideAtlas

P10507.

PRIDE

P10507.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YLR163C; YLR163C; YLR163C.

GeneID

850860.

KEGG

sce:YLR163C.

Organism-specific databases

CYGD

YLR163c.

SGD

S000004153. MAS1.

Phylogenomic databases

eggNOG

COG0612.

GeneTree

ENSGT00550000074701.

HOGENOM

HOG000242450.

KO

K01412.

OMA

QAIVGNW.

OrthoDB

EOG4J6W09.

Enzyme and pathway databases

BioCyc

MetaCyc:MONOMER-16673.

Reactome

REACT_118590. Mitochondrial Protein Import (yeast).
REACT_85873. Metabolism of proteins.

SABIO-RK

P10507.

Gene expression databases

Genevestigator

P10507.

GermOnline

YLR163C. Saccharomyces cerevisiae.

Family and domain databases

Gene3D

3.30.830.10. 2 hits.

InterPro

IPR011249. Metalloenz_LuxS/M16.
IPR011237. Pept_M16_dom.
IPR011765. Pept_M16_N.
IPR001431. Pept_M16_Zn_BS.
IPR007863. Peptidase_M16_C.
[Graphical view]

Pfam

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

SUPFAM

SSF63411. Metalloenz_metal-bd. 2 hits.

PROSITE

PS00143. INSULINASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P10507.

NextBio

967179.

Entry information

Entry name

MPPB_YEAST

Accession

Primary (citable) accession number: P10507
Secondary accession number(s): D6VYG9

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 1989
Last sequence update:	July 1, 1989
Last modified:	May 1, 2013
This is version 139 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program