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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.

Pathwayi: 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)DescriptionActionsGraphical viewLength
Active sitei69Acyl-ester intermediateBy similarity1
Active sitei72Proton acceptorBy similarity1
Active sitei310By similarity1
Binding sitei420SubstrateBy similarity1

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
Proteomesi
  • UP000000579 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 26Sequence analysisAdd BLAST26
ChainiPRO_000002724227 – 479D-alanyl-D-alanine carboxypeptidase DacBAdd BLAST453

Interactioni

Protein-protein interaction databases

STRINGi71421.HI1330.

Structurei

Secondary structure

1479
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi30 – 34Combined sources5
Beta strandi42 – 49Combined sources8
Turni50 – 53Combined sources4
Beta strandi54 – 60Combined sources7
Helixi68 – 71Combined sources4
Helixi72 – 82Combined sources11
Beta strandi90 – 97Combined sources8
Beta strandi108 – 111Combined sources4
Helixi120 – 132Combined sources13
Beta strandi142 – 145Combined sources4
Helixi160 – 162Combined sources3
Helixi166 – 168Combined sources3
Helixi177 – 179Combined sources3
Beta strandi180 – 186Combined sources7
Beta strandi196 – 198Combined sources3
Beta strandi206 – 208Combined sources3
Beta strandi212 – 214Combined sources3
Turni216 – 218Combined sources3
Helixi219 – 221Combined sources3
Beta strandi224 – 229Combined sources6
Turni230 – 232Combined sources3
Beta strandi233 – 241Combined sources9
Beta strandi247 – 252Combined sources6
Helixi256 – 270Combined sources15
Beta strandi289 – 295Combined sources7
Helixi299 – 309Combined sources11
Helixi312 – 327Combined sources16
Helixi333 – 346Combined sources14
Beta strandi359 – 361Combined sources3
Helixi370 – 382Combined sources13
Helixi384 – 387Combined sources4
Helixi390 – 392Combined sources3
Turni396 – 398Combined sources3
Helixi400 – 402Combined sources3
Helixi406 – 408Combined sources3
Turni411 – 416Combined sources6
Beta strandi418 – 424Combined sources7
Beta strandi427 – 435Combined sources9
Beta strandi441 – 450Combined sources10
Helixi463 – 478Combined sources16

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3A3DX-ray1.60A/B28-479[»]
3A3EX-ray2.40A/B28-479[»]
3A3FX-ray2.10A/B28-479[»]
3A3IX-ray2.00A/B28-479[»]
ProteinModelPortaliP45161.
SMRiP45161.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP45161.

Family & Domainsi

Sequence similaritiesi

Belongs to the peptidase S13 family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4106HRJ. Bacteria.
COG2027. LUCA.
KOiK07259.
OMAiAHSKPMK.
PhylomeDBiP45161.

Family and domain databases

Gene3Di3.40.710.10. 2 hits.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3A3DX-ray1.60A/B28-479[»]
3A3EX-ray2.40A/B28-479[»]
3A3FX-ray2.10A/B28-479[»]
3A3IX-ray2.00A/B28-479[»]
ProteinModelPortaliP45161.
SMRiP45161.
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

eggNOGiENOG4106HRJ. Bacteria.
COG2027. LUCA.
KOiK07259.
OMAiAHSKPMK.
PhylomeDBiP45161.

Enzyme and pathway databases

UniPathwayiUPA00219.

Miscellaneous databases

EvolutionaryTraceiP45161.

Family and domain databases

Gene3Di3.40.710.10. 2 hits.
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...

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: November 30, 2016
This is version 115 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

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.