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Protein

Arabinose 5-phosphate isomerase KdsD

Gene

kdsD

Organism
Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the biosynthesis of 3-deoxy-D-manno-octulosonate (KDO), a unique 8-carbon sugar component of lipopolysaccharides (LPSs). Catalyzes the reversible aldol-ketol isomerization between D-ribulose 5-phosphate (Ru5P) and D-arabinose 5-phosphate (A5P).1 Publication

Catalytic activityi

D-arabinose 5-phosphate = D-ribulose 5-phosphate.1 Publication

Temperature dependencei

Specific activity decreases significantly at 5 degrees Celsius compared to specific activity at 37 degrees Celsius.1 Publication

Pathwayi: 3-deoxy-D-manno-octulosonate biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes 3-deoxy-D-manno-octulosonate from D-ribulose 5-phosphate.
Proteins known to be involved in the 3 steps of the subpathway in this organism are:
  1. Arabinose 5-phosphate isomerase KdsD (kdsD)
  2. 2-dehydro-3-deoxyphosphooctonate aldolase (kdsA)
  3. no protein annotated in this organism
This subpathway is part of the pathway 3-deoxy-D-manno-octulosonate biosynthesis, which is itself part of Carbohydrate biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes 3-deoxy-D-manno-octulosonate from D-ribulose 5-phosphate, the pathway 3-deoxy-D-manno-octulosonate biosynthesis and in Carbohydrate biosynthesis.

Pathwayi: lipopolysaccharide biosynthesis

This protein is involved in the pathway lipopolysaccharide biosynthesis, which is part of Bacterial outer membrane biogenesis.
View all proteins of this organism that are known to be involved in the pathway lipopolysaccharide biosynthesis and in Bacterial outer membrane biogenesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei56 – 561Catalytically relevant
Metal bindingi79 – 791ZincBy similarity
Binding sitei79 – 791SubstrateBy similarity
Binding sitei85 – 851SubstrateCurated
Sitei108 – 1081Catalytically relevantBy similarity
Sitei149 – 1491Catalytically relevantBy similarity
Sitei190 – 1901Catalytically relevant

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Carbohydrate metabolism, Lipopolysaccharide biosynthesis

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

UniPathwayiUPA00030.
UPA00357; UER00473.

Names & Taxonomyi

Protein namesi
Recommended name:
Arabinose 5-phosphate isomerase KdsD (EC:5.3.1.13)
Short name:
API
Alternative name(s):
Pa-KdsD
Gene namesi
Name:kdsD
Ordered Locus Names:PA4457
OrganismiPseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
Taxonomic identifieri208964 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
Proteomesi
  • UP000002438 Componenti: Chromosome

Organism-specific databases

PseudoCAPiPA4457.

Pathology & Biotechi

Disruption phenotypei

Cells are not viable.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi56 – 561K → A: 100-fold reduction in catalytic activity compared to the wild-type. 1 Publication
Mutagenesisi85 – 851H → A: 200-fold reduction in catalytic activity compared to the wild-type. 1 Publication
Mutagenesisi190 – 1901H → A: 400-fold reduction in catalytic activity compared to the wild-type. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 326326Arabinose 5-phosphate isomerase KdsDPRO_0000417165Add
BLAST

Proteomic databases

PaxDbiQ9HVW0.

Interactioni

Subunit structurei

Homotetramer.By similarity

Protein-protein interaction databases

STRINGi208964.PA4457.

Structurei

3D structure databases

ProteinModelPortaliQ9HVW0.
SMRiQ9HVW0. Positions 7-180, 196-326.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini38 – 181144SISPROSITE-ProRule annotationAdd
BLAST
Domaini207 – 26559CBS 1PROSITE-ProRule annotationAdd
BLAST
Domaini274 – 32653CBS 2PROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni72 – 732Substrate bindingBy similarity
Regioni111 – 12010Substrate bindingBy similarity
Regioni145 – 1473Substrate bindingBy similarity

Sequence similaritiesi

Belongs to the SIS family. GutQ/KpsF subfamily.Curated
Contains 2 CBS domains.PROSITE-ProRule annotation
Contains 1 SIS domain.PROSITE-ProRule annotation

Keywords - Domaini

CBS domain, Repeat

Phylogenomic databases

eggNOGiENOG4105C2X. Bacteria.
COG0517. LUCA.
COG0794. LUCA.
HOGENOMiHOG000264729.
InParanoidiQ9HVW0.
KOiK06041.
OMAiLMACLMR.
OrthoDBiEOG6RFZWS.
PhylomeDBiQ9HVW0.

Family and domain databases

InterProiIPR000644. CBS_dom.
IPR004800. KdsD/KpsF-type.
IPR001347. SIS.
[Graphical view]
PfamiPF00571. CBS. 2 hits.
PF01380. SIS. 1 hit.
[Graphical view]
PIRSFiPIRSF004692. KdsD_KpsF. 1 hit.
SMARTiSM00116. CBS. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00393. kpsF. 1 hit.
PROSITEiPS51371. CBS. 2 hits.
PS51464. SIS. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9HVW0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNMSQNLDFI HSAQRTIGLE RDAVDSLLAR IGDDFVKACE LLLAGKGRVV
60 70 80 90 100
VVGMGKSGHV GKKIAATLAS TGTPSFFVHP AEASHGDMGM ITKDDVVLAL
110 120 130 140 150
SNSGSTAEIV TLLPLIKRLG ITLISMTGNP ESPLAKAAEV NLDASVGQEA
160 170 180 190 200
CPLNLAPTSS TTVTLVLGDA LAIALLEARG FTAEDFAFSH PGGALGRRLL
210 220 230 240 250
LKVEDVMHVG EGLPQVLLGT SLTGALMEMT RKGLGMTVVL DEHGKLAGIF
260 270 280 290 300
TDGDLRRALD RGIDVRQVTI DQVMTVHGKT VRAEILAAEA LKIMEDNKIG
310 320
ALVVVDADDR PVGALNMHDL LRAGVM
Length:326
Mass (Da):34,198
Last modified:March 1, 2001 - v1
Checksum:i510B3190C0F92C51
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE004091 Genomic DNA. Translation: AAG07845.1.
PIRiA83087.
RefSeqiNP_253147.1. NC_002516.2.
WP_003134758.1. NC_002516.2.

Genome annotation databases

EnsemblBacteriaiAAG07845; AAG07845; PA4457.
GeneIDi881001.
KEGGipae:PA4457.
PATRICi19843641. VBIPseAer58763_4667.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE004091 Genomic DNA. Translation: AAG07845.1.
PIRiA83087.
RefSeqiNP_253147.1. NC_002516.2.
WP_003134758.1. NC_002516.2.

3D structure databases

ProteinModelPortaliQ9HVW0.
SMRiQ9HVW0. Positions 7-180, 196-326.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi208964.PA4457.

Proteomic databases

PaxDbiQ9HVW0.

Protocols and materials databases

DNASUi881001.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAG07845; AAG07845; PA4457.
GeneIDi881001.
KEGGipae:PA4457.
PATRICi19843641. VBIPseAer58763_4667.

Organism-specific databases

PseudoCAPiPA4457.

Phylogenomic databases

eggNOGiENOG4105C2X. Bacteria.
COG0517. LUCA.
COG0794. LUCA.
HOGENOMiHOG000264729.
InParanoidiQ9HVW0.
KOiK06041.
OMAiLMACLMR.
OrthoDBiEOG6RFZWS.
PhylomeDBiQ9HVW0.

Enzyme and pathway databases

UniPathwayiUPA00030.
UPA00357; UER00473.

Family and domain databases

InterProiIPR000644. CBS_dom.
IPR004800. KdsD/KpsF-type.
IPR001347. SIS.
[Graphical view]
PfamiPF00571. CBS. 2 hits.
PF01380. SIS. 1 hit.
[Graphical view]
PIRSFiPIRSF004692. KdsD_KpsF. 1 hit.
SMARTiSM00116. CBS. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00393. kpsF. 1 hit.
PROSITEiPS51371. CBS. 2 hits.
PS51464. SIS. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228.
  2. "Targeting bacterial membranes: identification of Pseudomonas aeruginosa D-arabinose-5P isomerase and NMR characterisation of its substrate recognition and binding properties."
    Airoldi C., Sommaruga S., Merlo S., Sperandeo P., Cipolla L., Polissi A., Nicotra F.
    ChemBioChem 12:719-727(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, NMR SPECTROSCOPY, SUBSTRATE SPECIFICITY, DISRUPTION PHENOTYPE, MUTAGENESIS OF LYS-56; HIS-85 AND HIS-190.
    Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228.

Entry informationi

Entry nameiKDSD_PSEAE
AccessioniPrimary (citable) accession number: Q9HVW0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 16, 2012
Last sequence update: March 1, 2001
Last modified: November 11, 2015
This is version 78 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

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.