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Q9ZBA9 (DAP_OCHAN) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 50. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
D-aminopeptidase
EC=3.4.11.19
Gene names
Name:dap
OrganismOchrobactrum anthropi
Taxonomic identifier529 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Alphaproteobacteria › Rhizobiales › Brucellaceae › Ochrobactrum

Protein attributes

Sequence length520 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Hydrolyzes N-terminal residues in D-amino acid-containing peptides. HAMAP-Rule MF_01960

Catalytic activity

Release of an N-terminal D-amino acid from a peptide, Xaa-|-Yaa-, in which Xaa is preferably D-Ala, D-Ser or D-Thr. D-amino acid amides and methyl esters also are hydrolyzed, as is glycine amide. Ref.2 Ref.3

Enzyme regulation

Inhibited by beta-lactam compounds such as 6-aminopenicillic acid, 7-aminocephalosporanic acid, benzylpenicillin and ampicillin. Inhibited by p-chloromercuribenzoate. Ref.1

Subunit structure

Homodimer. Ref.2

Sequence similarities

Belongs to the peptidase S12 family.

Biophysicochemical properties

Absorption:

Abs(max)=281 nm Ref.2

Kinetic parameters:

KM=0.65 mM for D-alanine amide (at 30 degrees Celsius)

pH dependence:

Optimum pH is 8.5.

Temperature dependence:

Optimum temperature is 45 degrees Celsius.

Ontologies

Keywords
   Molecular functionAminopeptidase
Hydrolase
Protease
   Technical term3D-structure
Direct protein sequencing
Gene Ontology (GO)
   Biological_processproteolysis

Inferred from electronic annotation. Source: UniProtKB-KW

   Molecular_functionaminopeptidase activity

Inferred from electronic annotation. Source: HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.2
Chain2 – 520519D-aminopeptidase HAMAP-Rule MF_01960
PRO_0000250696

Regions

Region477 – 48711Important for specificity HAMAP-Rule MF_01960

Sites

Active site621Nucleophile Probable
Active site651Proton donor/acceptor Probable
Binding site4811Substrate

Experimental info

Mutagenesis581M → F: No effect on enzymatic activity. Ref.1
Mutagenesis611C → S: Alters sensitivity to p-chloromercuribenzoate. Ref.1
Mutagenesis621S → G: Abolishes enzymatic activity. Ref.1
Mutagenesis651K → N: Abolishes enzymatic activity. Ref.1
Mutagenesis691C → S: No effect on enzymatic activity. Ref.1

Secondary structure

1 .................................................................................................. 520
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q9ZBA9 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: CB364A8061DFBF4A

FASTA52057,392
        10         20         30         40         50         60 
MSKFDTSALE AFVRHIPQNY KGPGGVVAVV KDGEVVLQHA WGFADLRTRT PMTLDTRMPI 

        70         80         90        100        110        120 
CSVSKQFTCA VLLDAVGEPE LLDDALEAYL DKFEDERPAV RDLCNNQSGL RDYWALSVLC 

       130        140        150        160        170        180 
GADPEGVFLP AQAQSLLRRL KTTHFEPGSH YSYCNGNFRI LADLIEAHTG RTLVDILSER 

       190        200        210        220        230        240 
IFAPAGMKRA ELISDTALFD ECTGYEGDTV RGFLPATNRI QWMGDAGICA SLNDMIAWEQ 

       250        260        270        280        290        300 
FIDATRDDES GLYRRLSGPQ TFKDGVAAPY GFGLNLHETG GKRLTGHGGA LRGWRCQRWH 

       310        320        330        340        350        360 
CADERLSTIA MFNFEGGASE VAFKLMNIAL GVSSSEVSRV EADSAWFGSW LDDETGLVLS 

       370        380        390        400        410        420 
LEDAGHGRMK ARFGTSPEMM DVVSANEARS AVTTIRRDGE TIELVRASEN LRLSMKRVKG 

       430        440        450        460        470        480 
EAKHDIIGRY HSDELDADLL LVSEGGAIYG AFEGFLGKSD MYPLYSVGSD VWLLPVQRSM 

       490        500        510        520 
DAPSPGEWKL VFRRDDKGEI TGLSVGCWLA RGVEYRRVQP

« Hide

References

[1]"Structural similarity of D-aminopeptidase carboxypeptidase DD and beta-lactamases."
Asano Y., Kato Y., Yamada A., Kondo K.
Biochemistry 31:2316-2328(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], MUTAGENESIS OF MET-58; CYS-61; SER-62; LYS-65 AND CYS-69, ENZYME REGULATION.
Strain: ATCC 49237 / SCRC C1-38.
[2]"Properties of a novel D-stereospecific aminopeptidase from Ochrobactrum anthropi."
Asano Y., Nakazawa A., Kato Y., Kondo K.
J. Biol. Chem. 264:14233-14239(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 2-26, SUBUNIT, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES.
Strain: ATCC 49237 / SCRC C1-38.
[3]"Specificity inversion of Ochrobactrum anthropi D-aminopeptidase to a D,D-carboxypeptidase with new penicillin binding activity by directed mutagenesis."
Delmarcelle M., Boursoit M.-C., Filee P., Baurin S.L., Frere J.-M., Joris B.
Protein Sci. 14:2296-2303(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: CATALYTIC ACTIVITY.
[4]"Crystal structure of a D-aminopeptidase from Ochrobactrum anthropi, a new member of the 'penicillin-recognizing enzyme' family."
Bompard-Gilles C., Remaut H., Villeret V., Prange T., Fanuel L., Delmarcelle M., Joris B., Frere J.-M., Van Beeumen J.
Structure 8:971-980(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 1-520, PROBABLE ACTIVE SITE.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		M84523 Genomic DNA. Translation: AAA25519.1.
PIRA42209.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1EI5X-ray1.90A1-520[»]
ProteinModelPortalQ9ZBA9.
SMRQ9ZBA9. Positions 3-520.
ModBaseSearch...

Protein family/group databases

MEROPSS12.002.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Enzyme and pathway databases

SABIO-RKQ9ZBA9.

Family and domain databases

Gene3D2.40.128.50. 2 hits.
3.40.710.10. 1 hit.
HAMAPMF_01960. D_aminopeptidase.
InterProIPR001466. Beta-lactam-related.
IPR012338. Beta-lactam/transpept-like.
IPR027279. D_amino_pept/lipop.
IPR009090. D_amino_pept_B/C.
IPR023645. Pept_S12_aminopept_DmpB.
IPR012856. Pept_S12_DmpB_dom-B.
IPR012857. Pept_S12_DmpB_dom-C.
[Graphical view]
PfamPF00144. Beta-lactamase. 1 hit.
PF07930. DAP_B. 1 hit.
PF07932. DAP_C. 1 hit.
[Graphical view]
SUPFAMSSF50886. D_amino_pept_C. 2 hits.
SSF56601. PBP_transp_fold. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceQ9ZBA9.

Entry information

Entry nameDAP_OCHAN
AccessionPrimary (citable) accession number: Q9ZBA9
Entry history
Integrated into UniProtKB/Swiss-Prot: October 3, 2006
Last sequence update: January 23, 2007
Last modified: May 1, 2013
This is version 50 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

Peptidase families

Classification of peptidase families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

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