PEPB_ECOLI
ID PEPB_ECOLI Reviewed; 427 AA.
AC P37095; P76580; P76989; P76991; Q47131;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 2.
DT 03-AUG-2022, entry version 177.
DE RecName: Full=Peptidase B {ECO:0000255|HAMAP-Rule:MF_00504};
DE EC=3.4.11.23 {ECO:0000255|HAMAP-Rule:MF_00504};
DE AltName: Full=Aminopeptidase B {ECO:0000255|HAMAP-Rule:MF_00504};
GN Name=pepB {ECO:0000255|HAMAP-Rule:MF_00504}; Synonyms=yfhI;
GN OrderedLocusNames=b2523, JW2507;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RA Suzuki H., Kim E., Yamamoto N., Hashimoto W., Yamamoto K., Kumagai H.;
RT "Mapping, cloning, and DNA sequencing of pepB gene which encodes peptidase
RT B of Escherichia coli K-12.";
RL J. Ferment. Bioeng. 82:392-397(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9205837; DOI=10.1093/dnares/4.2.91;
RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K.,
RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S.,
RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H.,
RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12
RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of
RT its sequence features.";
RL DNA Res. 4:91-113(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-42.
RC STRAIN=K12;
RX PubMed=8300516; DOI=10.1128/jb.176.3.610-619.1994;
RA Kawula T.H., Lelivelt M.J.;
RT "Mutations in a gene encoding a new Hsp70 suppress rapid DNA inversion and
RT bgl activation, but not proU derepression, in hns-1 mutant Escherichia
RT coli.";
RL J. Bacteriol. 176:610-619(1994).
RN [6]
RP FUNCTION IN PEPTIDE DEGRADATION, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / JM101 / ATCC 33876 / DSM 3948 / NCIMB 11926;
RX PubMed=20067529; DOI=10.1111/j.1574-6968.2009.01879.x;
RA Hayashi M., Tabata K., Yagasaki M., Yonetani Y.;
RT "Effect of multidrug-efflux transporter genes on dipeptide resistance and
RT overproduction in Escherichia coli.";
RL FEMS Microbiol. Lett. 304:12-19(2010).
CC -!- FUNCTION: Probably plays an important role in intracellular peptide
CC degradation (PubMed:20067529). {ECO:0000255|HAMAP-Rule:MF_00504,
CC ECO:0000305|PubMed:20067529}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Release of an N-terminal amino acid, Xaa, from a peptide or
CC arylamide. Xaa is preferably Glu or Asp but may be other amino acids,
CC including Leu, Met, His, Cys and Gln.; EC=3.4.11.23;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00504};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00504};
CC Note=Binds 2 manganese ions per subunit. {ECO:0000255|HAMAP-
CC Rule:MF_00504};
CC -!- SUBUNIT: Homohexamer. {ECO:0000255|HAMAP-Rule:MF_00504}.
CC -!- INTERACTION:
CC P37095; P0A7C6: pepE; NbExp=2; IntAct=EBI-549539, EBI-555623;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00504}.
CC -!- DISRUPTION PHENOTYPE: A quadruple peptidase disruption (pepA, pepB,
CC pepD and pepN) does not grow in M9 minimal medium, grows better when
CC supplemented with casamino acids (PubMed:20067529).
CC {ECO:0000269|PubMed:20067529}.
CC -!- SIMILARITY: Belongs to the peptidase M17 family. {ECO:0000255|HAMAP-
CC Rule:MF_00504}.
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DR EMBL; D84499; BAA12689.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75576.2; -; Genomic_DNA.
DR EMBL; AP009048; BAA16413.1; -; Genomic_DNA.
DR EMBL; U01827; -; NOT_ANNOTATED_CDS; Unassigned_DNA.
DR PIR; B65029; B65029.
DR RefSeq; NP_417018.4; NC_000913.3.
DR RefSeq; WP_000133592.1; NZ_LN832404.1.
DR PDB; 6OAD; X-ray; 2.05 A; A/B/C/D/E/F/G/H/I/J/K/L=1-427.
DR PDB; 6OV8; X-ray; 2.61 A; A/B/C/D/E/F=2-427.
DR PDBsum; 6OAD; -.
DR PDBsum; 6OV8; -.
DR AlphaFoldDB; P37095; -.
DR SMR; P37095; -.
DR BioGRID; 4261583; 32.
DR DIP; DIP-10455N; -.
DR IntAct; P37095; 16.
DR STRING; 511145.b2523; -.
DR MEROPS; M17.004; -.
DR jPOST; P37095; -.
DR PaxDb; P37095; -.
DR PRIDE; P37095; -.
DR EnsemblBacteria; AAC75576; AAC75576; b2523.
DR EnsemblBacteria; BAA16413; BAA16413; BAA16413.
DR GeneID; 948766; -.
DR KEGG; ecj:JW2507; -.
DR KEGG; eco:b2523; -.
DR PATRIC; fig|1411691.4.peg.4211; -.
DR EchoBASE; EB2216; -.
DR eggNOG; COG0260; Bacteria.
DR HOGENOM; CLU_013734_7_1_6; -.
DR InParanoid; P37095; -.
DR OMA; EKSWAFW; -.
DR PhylomeDB; P37095; -.
DR BioCyc; EcoCyc:EG12310-MON; -.
DR BioCyc; MetaCyc:EG12310-MON; -.
DR BRENDA; 3.4.11.23; 2026.
DR SABIO-RK; P37095; -.
DR PRO; PR:P37095; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0004177; F:aminopeptidase activity; IDA:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR GO; GO:0030145; F:manganese ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0070006; F:metalloaminopeptidase activity; IEA:InterPro.
DR GO; GO:0008233; F:peptidase activity; IBA:GO_Central.
DR GO; GO:0000976; F:transcription cis-regulatory region binding; IEA:InterPro.
DR GO; GO:0043171; P:peptide catabolic process; IGI:EcoliWiki.
DR GO; GO:0006508; P:proteolysis; IDA:EcoCyc.
DR CDD; cd00433; Peptidase_M17; 1.
DR HAMAP; MF_00504; Aminopeptidase_M17; 1.
DR InterPro; IPR011356; Leucine_aapep/pepB.
DR InterPro; IPR008330; Pept_M17_PepB.
DR InterPro; IPR000819; Peptidase_M17_C.
DR PANTHER; PTHR11963; PTHR11963; 1.
DR Pfam; PF12404; DUF3663; 1.
DR Pfam; PF00883; Peptidase_M17; 1.
DR PIRSF; PIRSF036388; Ctsl_amnpptdse_B; 1.
DR PRINTS; PR00481; LAMNOPPTDASE.
DR PROSITE; PS00631; CYTOSOL_AP; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Aminopeptidase; Cytoplasm; Hydrolase; Manganese;
KW Metal-binding; Protease; Reference proteome.
FT CHAIN 1..427
FT /note="Peptidase B"
FT /id="PRO_0000165833"
FT ACT_SITE 207
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00504"
FT ACT_SITE 281
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00504"
FT BINDING 195
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00504"
FT BINDING 200
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00504"
FT BINDING 200
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00504"
FT BINDING 218
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00504"
FT BINDING 277
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00504"
FT BINDING 279
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00504"
FT BINDING 279
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00504"
FT CONFLICT 41
FT /note="L -> P (in Ref. 5; U01827)"
FT /evidence="ECO:0000305"
FT CONFLICT 155
FT /note="Q -> P (in Ref. 1; BAA12689)"
FT /evidence="ECO:0000305"
FT CONFLICT 375..427
FT /note="STAAGFLSHFVENYQQGWLHIDCSATYRKAPVEQWSAGATGLGVRTIANLLT
FT A -> TRRRASCRTLLRTISKAGCISTARRLTVKRRLNSGLRALRDLVCAR (in
FT Ref. 1; BAA12689)"
FT /evidence="ECO:0000305"
FT STRAND 5..12
FT /evidence="ECO:0007829|PDB:6OAD"
FT TURN 16..18
FT /evidence="ECO:0007829|PDB:6OAD"
FT STRAND 23..27
FT /evidence="ECO:0007829|PDB:6OAD"
FT STRAND 30..34
FT /evidence="ECO:0007829|PDB:6OAD"
FT HELIX 40..53
FT /evidence="ECO:0007829|PDB:6OAD"
FT STRAND 58..61
FT /evidence="ECO:0007829|PDB:6OAD"
FT HELIX 68..78
FT /evidence="ECO:0007829|PDB:6OAD"
FT STRAND 81..83
FT /evidence="ECO:0007829|PDB:6OAD"
FT STRAND 86..88
FT /evidence="ECO:0007829|PDB:6OAD"
FT HELIX 94..115
FT /evidence="ECO:0007829|PDB:6OAD"
FT TURN 118..120
FT /evidence="ECO:0007829|PDB:6OAD"
FT HELIX 123..138
FT /evidence="ECO:0007829|PDB:6OAD"
FT HELIX 139..141
FT /evidence="ECO:0007829|PDB:6OAD"
FT STRAND 142..148
FT /evidence="ECO:0007829|PDB:6OAD"
FT HELIX 150..154
FT /evidence="ECO:0007829|PDB:6OAD"
FT HELIX 158..164
FT /evidence="ECO:0007829|PDB:6OAD"
FT STRAND 167..169
FT /evidence="ECO:0007829|PDB:6OAD"
FT STRAND 172..178
FT /evidence="ECO:0007829|PDB:6OAD"
FT STRAND 188..200
FT /evidence="ECO:0007829|PDB:6OAD"
FT HELIX 209..212
FT /evidence="ECO:0007829|PDB:6OAD"
FT HELIX 215..217
FT /evidence="ECO:0007829|PDB:6OAD"
FT HELIX 220..235
FT /evidence="ECO:0007829|PDB:6OAD"
FT STRAND 239..250
FT /evidence="ECO:0007829|PDB:6OAD"
FT STRAND 262..264
FT /evidence="ECO:0007829|PDB:6OAD"
FT STRAND 270..272
FT /evidence="ECO:0007829|PDB:6OAD"
FT HELIX 280..293
FT /evidence="ECO:0007829|PDB:6OAD"
FT STRAND 297..303
FT /evidence="ECO:0007829|PDB:6OAD"
FT HELIX 307..313
FT /evidence="ECO:0007829|PDB:6OAD"
FT STRAND 316..321
FT /evidence="ECO:0007829|PDB:6OAD"
FT HELIX 325..337
FT /evidence="ECO:0007829|PDB:6OAD"
FT STRAND 342..344
FT /evidence="ECO:0007829|PDB:6OAD"
FT HELIX 349..353
FT /evidence="ECO:0007829|PDB:6OAD"
FT STRAND 358..365
FT /evidence="ECO:0007829|PDB:6OAD"
FT HELIX 373..382
FT /evidence="ECO:0007829|PDB:6OAD"
FT TURN 386..389
FT /evidence="ECO:0007829|PDB:6OAD"
FT STRAND 390..396
FT /evidence="ECO:0007829|PDB:6OAD"
FT STRAND 400..404
FT /evidence="ECO:0007829|PDB:6OAD"
FT STRAND 411..413
FT /evidence="ECO:0007829|PDB:6OAD"
FT HELIX 418..426
FT /evidence="ECO:0007829|PDB:6OAD"
SQ SEQUENCE 427 AA; 46180 MW; 8299E7D440F5732E CRC64;
MTEAMKITLS TQPADARWGE KATYSINNDG ITLHLNGADD LGLIQRAARK IDGLGIKHVQ
LSGEGWDADR CWAFWQGYKA PKGTRKVVWP DLDDAQRQEL DNRLMIIDWV RDTINAPAEE
LGPSQLAQRA VDLISNVAGD RVTYRITKGE DLREQGYMGL HTVGRGSERS PVLLALDYNP
TGDKEAPVYA CLVGKGITFD SGGYSIKQTA FMDSMKSDMG GAATVTGALA FAITRGLNKR
VKLFLCCADN LISGNAFKLG DIITYRNGKK VEVMNTDAEG RLVLADGLID ASAQKPEMII
DAATLTGAAK TALGNDYHAL FSFDDALAGR LLASAAQENE PFWRLPLAEF HRSQLPSNFA
ELNNTGSAAY PAGASTAAGF LSHFVENYQQ GWLHIDCSAT YRKAPVEQWS AGATGLGVRT
IANLLTA
