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Protein

LPS-assembly protein LptD

Gene

lptD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Together with LptE, is involved in the assembly of lipopolysaccharide (LPS) at the surface of the outer membrane. Contributes to n-hexane resistance.UniRule annotation8 Publications

GO - Biological processi

  • Gram-negative-bacterium-type cell outer membrane assembly Source: EcoCyc
  • lipopolysaccharide transport Source: EcoliWiki
  • response to organic substance Source: InterPro
Complete GO annotation...

Enzyme and pathway databases

BioCyciEcoCyc:EG11569-MONOMER.
ECOL316407:JW0053-MONOMER.
MetaCyc:EG11569-MONOMER.

Protein family/group databases

TCDBi1.B.42.1.2. the outer membrane lipopolysaccharide export porin (lps-ep) family.

Names & Taxonomyi

Protein namesi
Recommended name:
LPS-assembly protein LptDUniRule annotation
Alternative name(s):
Organic solvent tolerance protein
Gene namesi
Name:lptDUniRule annotation
Synonyms:imp, ostA, yabG
Ordered Locus Names:b0054, JW0053
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11569. lptD.

Subcellular locationi

GO - Cellular componenti

  • cell outer membrane Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cell outer membrane, Membrane

Pathology & Biotechi

Disruption phenotypei

Mutations alter the permeability of the outer membrane resulting in increased sensitivity to detergents, antibiotics and dyes. Depletion leads to filamentation followed by membrane rupture and cell lysis.2 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi529 – 538Missing : Impairs assembly of the LptD/LptE complex. Does not form native disulfide bonds. Severely compromises outer membrane integrity. 1 Publication10

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 24UniRule annotation2 PublicationsAdd BLAST24
ChainiPRO_000002027625 – 784LPS-assembly protein LptDAdd BLAST760

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi31 ↔ 724
Disulfide bondi173 ↔ 725

Post-translational modificationi

Contains two intramolecular disulfide bonds. At least one disulfide bond is required for activity, and protein is probably fully oxidized in vivo.

Keywords - PTMi

Disulfide bond

Proteomic databases

EPDiP31554.
PaxDbiP31554.
PRIDEiP31554.

2D gel databases

SWISS-2DPAGEP31554.

Expressioni

Inductioni

Constitutively expressed.1 Publication

Interactioni

Subunit structurei

Component of the lipopolysaccharide transport and assembly complex. Interacts with LptE and LptA. May interact with LptE during assembly of LptD by the beta-barrel assembly machine.UniRule annotation6 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
lptAP0ADV13EBI-549369,EBI-1132001
lptEP0ADC13EBI-549369,EBI-1119442

Protein-protein interaction databases

BioGridi4259723. 246 interactors.
DIPiDIP-10029N.
IntActiP31554. 8 interactors.
MINTiMINT-1293333.
STRINGi511145.b0054.

Structurei

Secondary structure

1784
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi233 – 236Combined sources4
Turni237 – 239Combined sources3
Beta strandi240 – 244Combined sources5
Beta strandi247 – 249Combined sources3
Beta strandi252 – 254Combined sources3
Beta strandi256 – 264Combined sources9
Helixi265 – 267Combined sources3
Beta strandi269 – 279Combined sources11
Beta strandi284 – 292Combined sources9
Helixi296 – 299Combined sources4
Beta strandi300 – 302Combined sources3
Beta strandi310 – 321Combined sources12
Turni322 – 324Combined sources3
Beta strandi325 – 336Combined sources12
Helixi339 – 342Combined sources4
Beta strandi346 – 348Combined sources3
Beta strandi353 – 365Combined sources13
Beta strandi368 – 379Combined sources12
Beta strandi388 – 403Combined sources16
Beta strandi406 – 421Combined sources16
Beta strandi426 – 441Combined sources16
Beta strandi443 – 453Combined sources11
Beta strandi455 – 461Combined sources7
Helixi463 – 469Combined sources7
Beta strandi470 – 472Combined sources3
Beta strandi476 – 480Combined sources5
Beta strandi483 – 491Combined sources9
Beta strandi493 – 495Combined sources3
Turni498 – 500Combined sources3
Beta strandi505 – 516Combined sources12
Helixi522 – 524Combined sources3
Helixi538 – 540Combined sources3
Beta strandi545 – 550Combined sources6
Beta strandi556 – 567Combined sources12
Beta strandi575 – 586Combined sources12
Beta strandi603 – 614Combined sources12
Beta strandi617 – 629Combined sources13
Turni630 – 633Combined sources4
Beta strandi634 – 659Combined sources26
Helixi661 – 667Combined sources7
Helixi670 – 673Combined sources4
Helixi676 – 679Combined sources4
Beta strandi682 – 691Combined sources10
Turni694 – 696Combined sources3
Beta strandi699 – 706Combined sources8
Turni707 – 710Combined sources4
Beta strandi711 – 720Combined sources10
Beta strandi729 – 740Combined sources12
Turni741 – 744Combined sources4
Beta strandi745 – 755Combined sources11
Beta strandi760 – 762Combined sources3
Helixi769 – 773Combined sources5
Beta strandi776 – 778Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4RHBX-ray3.35A/C203-784[»]
ProteinModelPortaliP31554.
SMRiP31554.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domaini

Contains an N-terminal soluble domain that is likely periplasmic and interacts with LptA, and a C-terminal transmembrane domain, which is predicted to be a beta-barrel and interacts with LptE. Residues 529-538 play a key role in interaction with LptE.3 Publications

Sequence similaritiesi

Belongs to the LptD family.UniRule annotation

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4105E7H. Bacteria.
COG1452. LUCA.
HOGENOMiHOG000218450.
InParanoidiP31554.
KOiK04744.
OMAiDYSHLDW.
PhylomeDBiP31554.

Family and domain databases

HAMAPiMF_01411. LPS_assembly_LptD. 1 hit.
InterProiIPR020889. LipoPS_assembly_LptD.
IPR005653. OstA-like_N.
IPR007543. OstA_C.
[Graphical view]
PfamiPF03968. OstA. 1 hit.
PF04453. OstA_C. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P31554-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKRIPTLLA TMIATALYSQ QGLAADLASQ CMLGVPSYDR PLVQGDTNDL
60 70 80 90 100
PVTINADHAK GDYPDDAVFT GSVDIMQGNS RLQADEVQLH QKEAPGQPEP
110 120 130 140 150
VRTVDALGNV HYDDNQVILK GPKGWANLNT KDTNVWEGDY QMVGRQGRGK
160 170 180 190 200
ADLMKQRGEN RYTILDNGSF TSCLPGSDTW SVVGSEIIHD REEQVAEIWN
210 220 230 240 250
ARFKVGPVPI FYSPYLQLPV GDKRRSGFLI PNAKYTTTNY FEFYLPYYWN
260 270 280 290 300
IAPNMDATIT PHYMHRRGNI MWENEFRYLS QAGAGLMELD YLPSDKVYED
310 320 330 340 350
EHPNDDSSRR WLFYWNHSGV MDQVWRFNVD YTKVSDPSYF NDFDNKYGSS
360 370 380 390 400
TDGYATQKFS VGYAVQNFNA TVSTKQFQVF SEQNTSSYSA EPQLDVNYYQ
410 420 430 440 450
NDVGPFDTRI YGQAVHFVNT RDDMPEATRV HLEPTINLPL SNNWGSINTE
460 470 480 490 500
AKLLATHYQQ TNLDWYNSRN TTKLDESVNR VMPQFKVDGK MVFERDMEML
510 520 530 540 550
APGYTQTLEP RAQYLYVPYR DQSDIYNYDS SLLQSDYSGL FRDRTYGGLD
560 570 580 590 600
RIASANQVTT GVTSRIYDDA AVERFNISVG QIYYFTESRT GDDNITWEND
610 620 630 640 650
DKTGSLVWAG DTYWRISERW GLRGGIQYDT RLDNVATSNS SIEYRRDEDR
660 670 680 690 700
LVQLNYRYAS PEYIQATLPK YYSTAEQYKN GISQVGAVAS WPIADRWSIV
710 720 730 740 750
GAYYYDTNAN KQADSMLGVQ YSSCCYAIRV GYERKLNGWD NDKQHAVYDN
760 770 780
AIGFNIELRG LSSNYGLGTQ EMLRSNILPY QNTL
Length:784
Mass (Da):89,671
Last modified:November 1, 1997 - v2
Checksum:i906EA3FE8F8D3E1E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB013134 Genomic DNA. Translation: BAA34130.1.
U00096 Genomic DNA. Translation: AAC73165.1.
AP009048 Genomic DNA. Translation: BAB96622.1.
PIRiF64726.
RefSeqiNP_414596.1. NC_000913.3.
WP_000746151.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73165; AAC73165; b0054.
BAB96622; BAB96622; BAB96622.
GeneIDi945011.
KEGGiecj:JW0053.
eco:b0054.
PATRICi32115207. VBIEscCol129921_0055.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB013134 Genomic DNA. Translation: BAA34130.1.
U00096 Genomic DNA. Translation: AAC73165.1.
AP009048 Genomic DNA. Translation: BAB96622.1.
PIRiF64726.
RefSeqiNP_414596.1. NC_000913.3.
WP_000746151.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4RHBX-ray3.35A/C203-784[»]
ProteinModelPortaliP31554.
SMRiP31554.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259723. 246 interactors.
DIPiDIP-10029N.
IntActiP31554. 8 interactors.
MINTiMINT-1293333.
STRINGi511145.b0054.

Protein family/group databases

TCDBi1.B.42.1.2. the outer membrane lipopolysaccharide export porin (lps-ep) family.

2D gel databases

SWISS-2DPAGEP31554.

Proteomic databases

EPDiP31554.
PaxDbiP31554.
PRIDEiP31554.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73165; AAC73165; b0054.
BAB96622; BAB96622; BAB96622.
GeneIDi945011.
KEGGiecj:JW0053.
eco:b0054.
PATRICi32115207. VBIEscCol129921_0055.

Organism-specific databases

EchoBASEiEB1529.
EcoGeneiEG11569. lptD.

Phylogenomic databases

eggNOGiENOG4105E7H. Bacteria.
COG1452. LUCA.
HOGENOMiHOG000218450.
InParanoidiP31554.
KOiK04744.
OMAiDYSHLDW.
PhylomeDBiP31554.

Enzyme and pathway databases

BioCyciEcoCyc:EG11569-MONOMER.
ECOL316407:JW0053-MONOMER.
MetaCyc:EG11569-MONOMER.

Miscellaneous databases

PROiP31554.

Family and domain databases

HAMAPiMF_01411. LPS_assembly_LptD. 1 hit.
InterProiIPR020889. LipoPS_assembly_LptD.
IPR005653. OstA-like_N.
IPR007543. OstA_C.
[Graphical view]
PfamiPF03968. OstA. 1 hit.
PF04453. OstA_C. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiLPTD_ECOLI
AccessioniPrimary (citable) accession number: P31554
Secondary accession number(s): P75631
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: November 1, 1997
Last modified: November 2, 2016
This is version 142 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The correct assembly of LptD depends on the thiol:disulfide interchange proteins DsbA and DsbC, the chaperone proteins SurA and Skp, LptE and the chaperone/protease BepA (PubMed:20615876, PubMed:20566849, PubMed:21257904, PubMed:21257909, PubMed:23772069, PubMed:24003122). BepA can also promote degradation of incorrectly folded LptD (PubMed:24003122).6 Publications

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.