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Protein

Beta-peptidyl aminopeptidase BapA

Gene

bapA

Organism
Sphingosinicella xenopeptidilytica
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Beta-aminopeptidase that can cleave synthetic beta-peptides which consist of backbone-elongated beta-amino acid residues that are not processed by common proteolytic enzymes. Can cleave the beta-peptides beta-homoVal-beta-homoAla-beta-homoLeu and beta-homoAla-beta-homoLeu. Requires a beta-amino acid at the N-terminus of peptide substrates and cleaves the peptide bond between the N-terminal beta-amino acid and the amino acid at the second position of tripeptidic substrates of the general structure H-betahXaa-Ile-betahTyr-OH according to the following preferences with regard to the side chain of the N-terminal beta-amino acid: aliphatic and aromatic > OH-containing > hydrogen, basic and polar.2 Publications

Catalytic activityi

Cleaves N-terminal beta-homoamino acids from peptides composed of 2 to 6 amino acids.4 Publications

Enzyme regulationi

Inhibited by AEBSF (4-(2-aminoethyl)benzenesulfonyl fluoride, Pefabloc SC), ampicillin and AMP(hyd) (ampillicin-derived penicilloic acid).3 Publications

Kineticsi

  1. KM=9.0 mM for beta-homoVal-beta-homoAla-beta-homoLeu1 Publication
  2. KM=20 mM for beta-homoAla-beta-homoLeu1 Publication
  3. KM=8.2 mM for beta-homoGly-pNA1 Publication
  4. KM=1.2 mM for beta-homoAla-pNA1 Publication
  1. Vmax=3.1 µmol/min/mg enzyme with beta-homoVal-beta-homoAla-beta-homoLeu as substrate1 Publication
  2. Vmax=1.1 µmol/min/mg enzyme with beta-homoAla-beta-homoLeu as substrate1 Publication
  3. Vmax=0.026 µmol/min/mg enzyme with carnosine as substrate1 Publication
  4. Vmax=0.98 µmol/min/mg enzyme with beta-homoVal-Ile-beta-homoTyr as substrate1 Publication
  5. Vmax=1.9 µmol/min/mg enzyme with beta-homoVal-Ile-beta-homoTyr as substrate1 Publication
  6. Vmax=0.68 µmol/min/mg enzyme with beta-homoPhe-Ile-beta-homoTyr as substrate1 Publication
  7. Vmax=0.47 µmol/min/mg enzyme with beta-homoTyr-Ile-beta-homoTyr as substrate1 Publication
  8. Vmax=0.047 µmol/min/mg enzyme with beta-homoTrp-Ile-beta-homoTyr as substrate1 Publication
  9. Vmax=0.095 µmol/min/mg enzyme with beta-homoSer-Ile-beta-homoTyr as substrate1 Publication
  10. Vmax=0.068 µmol/min/mg enzyme with beta-homoThr-Ile-beta-homoTyr as substrate1 Publication
  11. Vmax=0.017 µmol/min/mg enzyme with beta-homoLys-Ile-beta-homoTyr as substrate1 Publication
  12. Vmax=0.028 µmol/min/mg enzyme with D-beta-homoVal-Ile-beta-homoTyr as substrate1 Publication
  13. Vmax=16.4 µmol/min/mg enzyme with beta-homoAla-pNA as substrate1 Publication

pH dependencei

Optimum pH is between 8 and 9.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei279 – 2791Nucleophile1 Publication
Active sitei317 – 3171Proton donor/proton acceptor1 Publication
Active sitei319 – 3191Proton donor/proton acceptor1 Publication

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Aminopeptidase, Hydrolase, Protease

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-16515.
BRENDAi3.4.11.25. 12099.

Protein family/group databases

MEROPSiP01.002.

Names & Taxonomyi

Protein namesi
Recommended name:
Beta-peptidyl aminopeptidase BapA1 Publication (EC:3.4.11.254 Publications)
Cleaved into the following 2 chains:
Beta-peptidyl aminopeptidase BapA alpha subunit1 Publication
Beta-peptidyl aminopeptidase BapA beta subunit1 Publication
Gene namesi
Name:bapA1 Publication
OrganismiSphingosinicella xenopeptidilyticaImported
Taxonomic identifieri364098 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaSphingomonadalesSphingomonadaceaeSphingosinicella

Subcellular locationi

  • Periplasm 1 Publication

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Periplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi162 – 1621E → A: Delays precursor cleavage and abolishes enzymatic activity. 1 Publication
Mutagenesisi277 – 2771K → A: Delays precursor cleavage. 1 Publication
Mutagenesisi278 – 2781N → A: Delays precursor cleavage. 1 Publication
Mutagenesisi279 – 2791S → A: Abolishes precursor cleavage and enzymatic activity. 1 Publication
Mutagenesisi317 – 3171S → A: Abolishes precursor cleavage and enzymatic activity. 1 Publication
Mutagenesisi319 – 3191E → A: Abolishes precursor cleavage and reduces enzymatic activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 29291 PublicationAdd
BLAST
Chaini30 – 278249Beta-peptidyl aminopeptidase BapA alpha subunit1 PublicationPRO_0000430763Add
BLAST
Chaini279 – 402124Beta-peptidyl aminopeptidase BapA beta subunit1 PublicationPRO_0000430764Add
BLAST

Post-translational modificationi

Autoproteolytic processing to generate the alpha and beta subunit is required for self-activation and is proposed to use a similar mechanism as substrate cleavage.1 Publication

Interactioni

Subunit structurei

Heterooctamer of 4 heterodimers ((alpha:beta)4); each heterodimer is composed of an alpha subunit and a beta subunit processed from the same precursor.3 Publications

Protein-protein interaction databases

DIPiDIP-59978N.

Structurei

Secondary structure

1
402
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi33 – 364Combined sources
Beta strandi46 – 494Combined sources
Helixi50 – 523Combined sources
Beta strandi57 – 659Combined sources
Turni72 – 743Combined sources
Beta strandi77 – 859Combined sources
Beta strandi94 – 10310Combined sources
Helixi111 – 1177Combined sources
Beta strandi118 – 1225Combined sources
Beta strandi124 – 1285Combined sources
Helixi129 – 1313Combined sources
Helixi132 – 14615Combined sources
Helixi149 – 1557Combined sources
Beta strandi159 – 1635Combined sources
Turni166 – 1683Combined sources
Helixi178 – 18710Combined sources
Beta strandi189 – 1924Combined sources
Helixi199 – 2013Combined sources
Beta strandi212 – 22211Combined sources
Beta strandi225 – 23511Combined sources
Turni240 – 2423Combined sources
Turni251 – 2533Combined sources
Turni269 – 2724Combined sources
Beta strandi280 – 2867Combined sources
Helixi292 – 3009Combined sources
Helixi302 – 3087Combined sources
Beta strandi319 – 33012Combined sources
Helixi347 – 37125Combined sources
Helixi378 – 3803Combined sources
Beta strandi381 – 3833Combined sources
Helixi388 – 39811Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3N2WX-ray1.45A/B/C/D30-402[»]
3N33X-ray1.80A/B/C/D30-402[»]
3N5IX-ray1.80A/B/C/D30-402[»]
3NDVX-ray1.70A/B/C/D30-402[»]
3NFBX-ray1.85A/B/C/D30-402[»]
ProteinModelPortaliQ52VH2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the peptidase S58 family.Curated

Keywords - Domaini

Signal

Family and domain databases

Gene3Di3.60.70.12. 1 hit.
InterProiIPR016117. ArgJ-like_dom.
IPR005321. Peptidase_S58_DmpA.
[Graphical view]
PfamiPF03576. Peptidase_S58. 1 hit.
[Graphical view]
SUPFAMiSSF56266. SSF56266. 1 hit.

Sequencei

Sequence statusi: Complete.

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

Q52VH2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTSTQRLWSG ALPLLTALIV SIAATASLAG PRARDLGVPF EGTPGALNAI
60 70 80 90 100
TDVAGVEVGH TTVISGDGAM VIGKGPYRTG VTIIHPLGKT SLDGVAAGRA
110 120 130 140 150
VINGTGEWTG MHLVDEVGQF LGPIALTGTG NVGLVHQSMM DWSVGKVPEE
160 170 180 190 200
ALFSRLLPVV AETLDNRLND VFGHGLTRDH VFAALDGAKG GPVAEGNVGG
210 220 230 240 250
GTGMIAYTFK GGIGTSSRVV SAGDTRYTVG VLVQANHGDR NDLRIAGVQI
260 270 280 290 300
GKEIKGAWPE VNGIVAAGPD AGKPQDKNSL LIVIATDAPL MPHQLERMAR
310 320 330 340 350
RAALGVGRNG STAGALSGEF ALAFSTSHVI PLGGKPRLPA IINDTDSETM
360 370 380 390 400
NALFRGVVQA TEEALVNQLV ASETMTGANN AKVYGIPHDQ LARIMKARFP

RR
Length:402
Mass (Da):41,531
Last modified:May 24, 2005 - v1
Checksum:i83A755254EA30436
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY897555 Genomic DNA. Translation: AAX93858.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY897555 Genomic DNA. Translation: AAX93858.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3N2WX-ray1.45A/B/C/D30-402[»]
3N33X-ray1.80A/B/C/D30-402[»]
3N5IX-ray1.80A/B/C/D30-402[»]
3NDVX-ray1.70A/B/C/D30-402[»]
3NFBX-ray1.85A/B/C/D30-402[»]
ProteinModelPortaliQ52VH2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-59978N.

Protein family/group databases

MEROPSiP01.002.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-16515.
BRENDAi3.4.11.25. 12099.

Family and domain databases

Gene3Di3.60.70.12. 1 hit.
InterProiIPR016117. ArgJ-like_dom.
IPR005321. Peptidase_S58_DmpA.
[Graphical view]
PfamiPF03576. Peptidase_S58. 1 hit.
[Graphical view]
SUPFAMiSSF56266. SSF56266. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "A novel beta-peptidyl aminopeptidase (BapA) from strain 3-2W4 cleaves peptide bonds of synthetic beta-tri- and beta-dipeptides."
    Geueke B., Namoto K., Seebach D., Kohler H.P.
    J. Bacteriol. 187:5910-5917(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 30-49 AND 279-291, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, SUBCELLULAR LOCATION.
    Strain: DSM 17130 / CCUG 52537 / 3-2W4Imported.
  2. "Bacterial beta-peptidyl aminopeptidases with unique substrate specificities for beta-oligopeptides and mixed beta,alpha-oligopeptides."
    Geueke B., Heck T., Limbach M., Nesatyy V., Seebach D., Kohler H.P.
    FEBS J. 273:5261-5272(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: CATALYTIC ACTIVITY, FUNCTION, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES.
  3. "Autoproteolytic and catalytic mechanisms for the beta-aminopeptidase BapA--a member of the Ntn hydrolase family."
    Merz T., Heck T., Geueke B., Mittl P.R., Briand C., Seebach D., Kohler H.P., Gruetter M.G.
    Structure 20:1850-1860(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS), X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH INHIBITOR AEBSF, CATALYTIC ACTIVITY, ACTIVE SITE, AUTOPROTEOLYTIC PROCESSING, SUBUNIT, MUTAGENESIS OF GLU-162; LYS-277; ASN-278; SER-279; SER-317 AND GLU-319.
  4. "Crystal structures of BapA complexes with beta-lactam-derived inhibitors illustrate substrate specificity and enantioselectivity of beta-aminopeptidases."
    Heck T., Merz T., Reimer A., Seebach D., Rentsch D., Briand C., Gruetter M.G., Kohler H.P., Geueke B.
    ChemBioChem 13:2137-2145(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS)IN COMPLEX WITH INHIBITOR AMPICILLIN, X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) IN COMPLEX WITH INHIBITOR AMP(HYD), CATALYTIC ACTIVITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.

Entry informationi

Entry nameiBAPA_SPHXN
AccessioniPrimary (citable) accession number: Q52VH2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 29, 2014
Last sequence update: May 24, 2005
Last modified: December 9, 2015
This is version 47 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Peptidase families
    Classification of peptidase families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families

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 one 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.