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Protein

Arabinose 5-phosphate isomerase KdsD

Gene

kdsD

Organism
Yersinia pestis
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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) (By similarity).By similarity

Catalytic activityi

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

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. 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC (kdsC)
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
Sitei59 – 591Catalytically relevantBy similarity
Metal bindingi82 – 821ZincBy similarity
Binding sitei82 – 821SubstrateBy similarity
Binding sitei88 – 881SubstrateBy similarity
Sitei111 – 1111Catalytically relevantBy similarity
Sitei152 – 1521Catalytically relevantBy similarity
Sitei193 – 1931Catalytically relevantBy similarity
Binding sitei275 – 2751SubstrateBy similarity

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

BioCyciYPES214092:GKDD-3534-MONOMER.
UniPathwayiUPA00030.
UPA00357; UER00473.

Names & Taxonomyi

Protein namesi
Recommended name:
Arabinose 5-phosphate isomerase KdsD (EC:5.3.1.13)
Short name:
API
Short name:
L-API
Gene namesi
Name:kdsD
Ordered Locus Names:YPO3577, y0149, YP_3832
OrganismiYersinia pestis
Taxonomic identifieri632 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeYersinia
Proteomesi
  • UP000000815 Componenti: Chromosome
  • UP000001019 Componenti: Chromosome
  • UP000002490 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 328328Arabinose 5-phosphate isomerase KdsDPRO_0000136581Add
BLAST

Proteomic databases

PRIDEiQ8D1Q8.

Interactioni

Subunit structurei

Homotetramer.By similarity

Protein-protein interaction databases

STRINGi187410.y0149.

Structurei

3D structure databases

ProteinModelPortaliQ8D1Q8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini41 – 184144SISPROSITE-ProRule annotationAdd
BLAST
Domaini210 – 26859CBS 1PROSITE-ProRule annotationAdd
BLAST
Domaini277 – 32852CBS 2PROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni75 – 762Substrate bindingBy similarity
Regioni114 – 12310Substrate bindingBy similarity
Regioni148 – 1503Substrate 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.
KOiK06041.
OMAiLMACLMR.
OrthoDBiEOG6RFZWS.

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.

Q8D1Q8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSTFDLQPGV DFQQAGKQVL QIEREGLAQL DQYINEDFSR ACEAIFRCHG
60 70 80 90 100
KVVVMGMGKS GHIGCKIAAT FASTGTPAFF VHPGEASHGD LGMITPQDIV
110 120 130 140 150
LAISNSGESN EILTLIPVLK RQKILLICMS SNPESTMGKA ADIHLCINVP
160 170 180 190 200
QEACPLGLAP TTSTTATLVM GDALAVALLK ARGFTQEDFA LSHPGGALGR
210 220 230 240 250
KLLLRISDIM HTGTEIPTVS PDASLRDALL EITRKSLGLT VICDDSMRIK
260 270 280 290 300
GIFTDGDLRR VFDMGIDLNN AKIADVMTRG GIRVPPNILA VDALNLMESR
310 320
HITALLVADG DQLLGVVHMH DMLRAGVV
Length:328
Mass (Da):35,062
Last modified:September 26, 2003 - v2
Checksum:iAE9A2411E9CC2020
GO

Sequence cautioni

The sequence AAM83742.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
The sequence AAS63979.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL590842 Genomic DNA. Translation: CAL22165.1.
AE009952 Genomic DNA. Translation: AAM83742.1. Different initiation.
AE017042 Genomic DNA. Translation: AAS63979.1. Different initiation.
PIRiAB0435.
RefSeqiWP_002210119.1. NZ_LIXY01000015.1.
YP_002348464.1. NC_003143.1.

Genome annotation databases

EnsemblBacteriaiAAM83742; AAM83742; y0149.
AAS63979; AAS63979; YP_3832.
GeneIDi1176397.
KEGGiype:YPO3577.
ypj:CH55_2489.
ypk:y0149.
ypl:CH46_1513.
ypm:YP_3832.
ypv:BZ15_4158.
ypw:CH59_2470.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL590842 Genomic DNA. Translation: CAL22165.1.
AE009952 Genomic DNA. Translation: AAM83742.1. Different initiation.
AE017042 Genomic DNA. Translation: AAS63979.1. Different initiation.
PIRiAB0435.
RefSeqiWP_002210119.1. NZ_LIXY01000015.1.
YP_002348464.1. NC_003143.1.

3D structure databases

ProteinModelPortaliQ8D1Q8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi187410.y0149.

Proteomic databases

PRIDEiQ8D1Q8.

Protocols and materials databases

DNASUi1145095.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAM83742; AAM83742; y0149.
AAS63979; AAS63979; YP_3832.
GeneIDi1176397.
KEGGiype:YPO3577.
ypj:CH55_2489.
ypk:y0149.
ypl:CH46_1513.
ypm:YP_3832.
ypv:BZ15_4158.
ypw:CH59_2470.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayiUPA00030.
UPA00357; UER00473.
BioCyciYPES214092:GKDD-3534-MONOMER.

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

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: CO-92 / Biovar Orientalis.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: KIM10+ / Biovar Mediaevalis.
  3. "Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans."
    Song Y., Tong Z., Wang J., Wang L., Guo Z., Han Y., Zhang J., Pei D., Zhou D., Qin H., Pang X., Han Y., Zhai J., Li M., Cui B., Qi Z., Jin L., Dai R.
    , Chen F., Li S., Ye C., Du Z., Lin W., Wang J., Yu J., Yang H., Wang J., Huang P., Yang R.
    DNA Res. 11:179-197(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 91001 / Biovar Mediaevalis.

Entry informationi

Entry nameiKDSD_YERPE
AccessioniPrimary (citable) accession number: Q8D1Q8
Secondary accession number(s): Q0WB74, Q8ZB48
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 26, 2003
Last sequence update: September 26, 2003
Last modified: May 11, 2016
This is version 91 of the entry and version 2 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.