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Protein

D-alanyl-D-alanine carboxypeptidase DacB

Gene

dacB

Organism
Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Not involved in transpeptidation but exclusively catalyzes a DD-carboxypeptidase and DD-endopeptidase reaction.By similarity

Catalytic activityi

Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.

Pathway: peptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.
View all proteins of this organism that are known to be involved in the pathway peptidoglycan biosynthesis and in Cell wall biogenesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei69 – 691Acyl-ester intermediateBy similarity
Active sitei72 – 721Proton acceptorBy similarity
Active sitei310 – 3101By similarity
Binding sitei420 – 4201SubstrateBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Antibiotic resistance, Cell cycle, Cell division, Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis

Enzyme and pathway databases

UniPathwayiUPA00219.

Protein family/group databases

MEROPSiS13.001.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanyl-D-alanine carboxypeptidase DacB (EC:3.4.16.4)
Short name:
DD-carboxypeptidase
Short name:
DD-peptidase
Alternative name(s):
D-alanyl-D-alanine endopeptidase (EC:3.4.21.-)
Short name:
DD-endopeptidase
Penicillin-binding protein 4
Short name:
PBP-4
Gene namesi
Name:dacB
Ordered Locus Names:HI_1330
OrganismiHaemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Taxonomic identifieri71421 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPasteurellalesPasteurellaceaeHaemophilus
ProteomesiUP000000579 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2626Sequence AnalysisAdd
BLAST
Chaini27 – 479453D-alanyl-D-alanine carboxypeptidase DacBPRO_0000027242Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi71421.HI1330.

Structurei

Secondary structure

1
479
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi30 – 345Combined sources
Beta strandi42 – 498Combined sources
Turni50 – 534Combined sources
Beta strandi54 – 607Combined sources
Helixi68 – 714Combined sources
Helixi72 – 8211Combined sources
Beta strandi90 – 978Combined sources
Beta strandi108 – 1114Combined sources
Helixi120 – 13213Combined sources
Beta strandi142 – 1454Combined sources
Helixi160 – 1623Combined sources
Helixi166 – 1683Combined sources
Helixi177 – 1793Combined sources
Beta strandi180 – 1867Combined sources
Beta strandi196 – 1983Combined sources
Beta strandi206 – 2083Combined sources
Beta strandi212 – 2143Combined sources
Turni216 – 2183Combined sources
Helixi219 – 2213Combined sources
Beta strandi224 – 2296Combined sources
Turni230 – 2323Combined sources
Beta strandi233 – 2419Combined sources
Beta strandi247 – 2526Combined sources
Helixi256 – 27015Combined sources
Beta strandi289 – 2957Combined sources
Helixi299 – 30911Combined sources
Helixi312 – 32716Combined sources
Helixi333 – 34614Combined sources
Beta strandi359 – 3613Combined sources
Helixi370 – 38213Combined sources
Helixi384 – 3874Combined sources
Helixi390 – 3923Combined sources
Turni396 – 3983Combined sources
Helixi400 – 4023Combined sources
Helixi406 – 4083Combined sources
Turni411 – 4166Combined sources
Beta strandi418 – 4247Combined sources
Beta strandi427 – 4359Combined sources
Beta strandi441 – 45010Combined sources
Helixi463 – 47816Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3A3DX-ray1.60A/B28-479[»]
3A3EX-ray2.40A/B28-479[»]
3A3FX-ray2.10A/B28-479[»]
3A3IX-ray2.00A/B28-479[»]
ProteinModelPortaliP45161.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP45161.

Family & Domainsi

Sequence similaritiesi

Belongs to the peptidase S13 family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiCOG2027.
KOiK07259.
OMAiFRTIGHE.
OrthoDBiEOG6NGVQ4.
PhylomeDBiP45161.

Family and domain databases

Gene3Di3.40.710.10. 1 hit.
InterProiIPR012338. Beta-lactam/transpept-like.
IPR000667. Peptidase_S13.
[Graphical view]
PfamiPF02113. Peptidase_S13. 1 hit.
[Graphical view]
PRINTSiPR00922. DADACBPTASE3.
SUPFAMiSSF56601. SSF56601. 1 hit.
TIGRFAMsiTIGR00666. PBP4. 1 hit.

Sequencei

Sequence statusi: Complete.

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

P45161-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKLSSISTA LGSFLLSVSF SLPTFANINV SDLTQKLPEG SNVGFIAKNI
60 70 80 90 100
NQNQIIADYN GSTFMLSAST QKVFTAVAAK LALDDQFQFE TALLSNGKIQ
110 120 130 140 150
NGNLDGNLIV RFTGDPDLTR GQLYSLLAEL KKQGIKKING DLVLDTSVFS
160 170 180 190 200
SHDRGLGWIW NDLTMCFNSP PAAANIDNNC FYAELDANKN PGEIVKINVP
210 220 230 240 250
AQFPIQVFGQ VYVADSNEAP YCQLDVVVHD NNRYQVKGCL ARQYKPFGLS
260 270 280 290 300
FAVQNTDAYA AEIIQRQLRQ LGIEFNGKVL LPQKPQQGQL LAKHLSKPLP
310 320 330 340 350
DLLKKMMKKS DNQIADSLFR AVAFNYYKRP ASFQLGTLAV KSILQKQGIR
360 370 380 390 400
FGNSILADGS GLSRHNLVAP KTMLSVLEYI AKNEDKLHLM ETFPIAGVDG
410 420 430 440 450
TISGRGGLIS PPLVKNVIAK TGSLKGVYNL AGFMTNARGE KVAFVQFING
460 470
YSTGDLESKT KRAPLVQFER NLYNELYKY
Length:479
Mass (Da):52,686
Last modified:November 1, 1995 - v1
Checksum:i632868C61206CB48
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L42023 Genomic DNA. Translation: AAC22975.1.
PIRiA64117.
RefSeqiNP_439482.1. NC_000907.1.
WP_005694445.1. NC_000907.1.

Genome annotation databases

EnsemblBacteriaiAAC22975; AAC22975; HI_1330.
GeneIDi950252.
KEGGihin:HI1330.
PATRICi20191345. VBIHaeInf48452_1383.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L42023 Genomic DNA. Translation: AAC22975.1.
PIRiA64117.
RefSeqiNP_439482.1. NC_000907.1.
WP_005694445.1. NC_000907.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3A3DX-ray1.60A/B28-479[»]
3A3EX-ray2.40A/B28-479[»]
3A3FX-ray2.10A/B28-479[»]
3A3IX-ray2.00A/B28-479[»]
ProteinModelPortaliP45161.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi71421.HI1330.

Protein family/group databases

MEROPSiS13.001.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC22975; AAC22975; HI_1330.
GeneIDi950252.
KEGGihin:HI1330.
PATRICi20191345. VBIHaeInf48452_1383.

Phylogenomic databases

eggNOGiCOG2027.
KOiK07259.
OMAiFRTIGHE.
OrthoDBiEOG6NGVQ4.
PhylomeDBiP45161.

Enzyme and pathway databases

UniPathwayiUPA00219.

Miscellaneous databases

EvolutionaryTraceiP45161.

Family and domain databases

Gene3Di3.40.710.10. 1 hit.
InterProiIPR012338. Beta-lactam/transpept-like.
IPR000667. Peptidase_S13.
[Graphical view]
PfamiPF02113. Peptidase_S13. 1 hit.
[Graphical view]
PRINTSiPR00922. DADACBPTASE3.
SUPFAMiSSF56601. SSF56601. 1 hit.
TIGRFAMsiTIGR00666. PBP4. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 51907 / DSM 11121 / KW20 / Rd.

Entry informationi

Entry nameiDACB_HAEIN
AccessioniPrimary (citable) accession number: P45161
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: May 27, 2015
This is version 111 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, Complete proteome, Reference proteome

Documents

  1. Haemophilus influenzae
    Haemophilus influenzae (strain Rd): entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. Peptidase families
    Classification of peptidase families and list of entries
  5. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.