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Protein

2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase

Gene
N/A
Organism
Sulfolobus solfataricus
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the degradation of glucose and galactose via the Entner-Doudoroff pathway. Catalyzes the reversible cleavage of 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-3-deoxygluconate (KDG) forming pyruvate and glyceraldehyde 3-phosphate or glyceraldehyde, respectively. It is also able to catalyze the reversible cleavage of 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) and 2-keto-3-deoxygalactonate (KDGal). It is equally active with both D- and L-glyceraldehyde.3 Publications

Catalytic activityi

2-dehydro-3-deoxy-6-phospho-D-gluconate = pyruvate + D-glyceraldehyde 3-phosphate.2 Publications
2-dehydro-3-deoxy-6-phospho-D-galactonate = pyruvate + D-glyceraldehyde 3-phosphate.2 Publications

Kineticsi

Kcat is 28.2 (sec-1) for KDG and 6.8 (sec-1) for KDGal.

  1. KM=0.1 mM for KDPG (at 60 degrees Celsius and at pH 6)3 Publications
  2. KM=0.17 mM for KDPGal (at 60 degrees Celsius and at pH 6)3 Publications
  3. KM=3.9 mM for pyruvate (at 70 degrees Celsius and at pH 6)3 Publications
  4. KM=3.9 mM for D-glyceraldehyde (at 70 degrees Celsius and at pH 6)3 Publications
  5. KM=5.2 mM for D,L-glyceraldehyde (at 70 degrees Celsius and at pH 6)3 Publications
  6. KM=7.1 mM for L-glyceraldehyde (at 70 degrees Celsius and at pH 6)3 Publications
  7. KM=9.9 mM for KDGal (at 60 degrees Celsius and at pH 6)3 Publications
  8. KM=25.7 mM for KDG (at 60 degrees Celsius and at pH 6)3 Publications
  1. Vmax=12.3 µmol/min/mg enzyme with KDGal as substrate (at 60 degrees Celsius and at pH 6)3 Publications
  2. Vmax=15.7 µmol/min/mg enzyme with pyruvate as substrate (at 70 degrees Celsius and at pH 6)3 Publications
  3. Vmax=17.1 µmol/min/mg enzyme with D,L-glyceraldehyde as substrate (at 70 degrees Celsius and at pH 6)3 Publications
  4. Vmax=18 µmol/min/mg enzyme with D-glyceraldehyde as substrate (at 70 degrees Celsius and at pH 6)3 Publications
  5. Vmax=18 µmol/min/mg enzyme with L-glyceraldehyde as substrate (at 70 degrees Celsius and at pH 6)3 Publications
  6. Vmax=51.4 µmol/min/mg enzyme with KDG as substrate (at 60 degrees Celsius and at pH 6)3 Publications

Temperature dependencei

Extremely thermostable.3 Publications

Pathwayi: 2-dehydro-3-deoxy-D-gluconate degradation

This protein is involved in step 2 of the subpathway that synthesizes D-glyceraldehyde 3-phosphate and pyruvate from 2-dehydro-3-deoxy-D-gluconate.
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. no protein annotated in this organism
  2. 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase
This subpathway is part of the pathway 2-dehydro-3-deoxy-D-gluconate degradation, which is itself part of Carbohydrate acid metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes D-glyceraldehyde 3-phosphate and pyruvate from 2-dehydro-3-deoxy-D-gluconate, the pathway 2-dehydro-3-deoxy-D-gluconate degradation and in Carbohydrate acid metabolism.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei130 – 1301Proton shuttleBy similarity
Active sitei155 – 1551Schiff-base intermediate with substrate1 Publication

GO - Molecular functioni

  • 2-dehydro-3-deoxy-6-phosphogalactonate aldolase activity Source: UniProtKB
  • 2-dehydro-3-deoxy-phosphogluconate aldolase activity Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Carbohydrate metabolism

Keywords - Ligandi

Schiff base

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-4861.
BRENDAi4.1.2.55. 6163.
SABIO-RKO54288.
UniPathwayiUPA00856; UER00829.

Names & Taxonomyi

Protein namesi
Recommended name:
2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase (EC:4.1.2.552 Publications)
OrganismiSulfolobus solfataricus
Taxonomic identifieri2287 [NCBI]
Taxonomic lineageiArchaeaCrenarchaeotaThermoproteiSulfolobalesSulfolobaceaeSulfolobus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved1 Publication
Chaini2 – 2942932-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolasePRO_0000422658Add
BLAST

Interactioni

Subunit structurei

Homotetramer; dimer of dimers.3 Publications

Protein-protein interaction databases

STRINGi273057.SSO3197.

Structurei

Secondary structure

1
294
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 75Combined sources
Beta strandi16 – 183Combined sources
Helixi20 – 3213Combined sources
Beta strandi37 – 426Combined sources
Turni43 – 464Combined sources
Helixi47 – 493Combined sources
Helixi52 – 6312Combined sources
Beta strandi69 – 724Combined sources
Helixi78 – 8710Combined sources
Helixi88 – 903Combined sources
Beta strandi94 – 996Combined sources
Helixi109 – 12214Combined sources
Beta strandi127 – 1315Combined sources
Helixi133 – 1364Combined sources
Helixi142 – 1487Combined sources
Beta strandi151 – 1566Combined sources
Helixi161 – 17010Combined sources
Beta strandi174 – 1785Combined sources
Helixi181 – 1833Combined sources
Helixi184 – 1896Combined sources
Beta strandi194 – 1963Combined sources
Helixi198 – 2014Combined sources
Helixi204 – 21512Combined sources
Helixi219 – 23719Combined sources
Helixi241 – 25313Combined sources
Helixi269 – 28820Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1W37X-ray2.00A/B/C/D1-294[»]
1W3IX-ray1.70A/B/C/D2-294[»]
1W3NX-ray2.10A/B/C/D1-294[»]
1W3TX-ray2.10A/B/C/D1-294[»]
2YDAX-ray1.91A/B1-294[»]
ProteinModelPortaliO54288.
SMRiO54288. Positions 2-294.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO54288.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni43 – 442Substrate binding
Regioni130 – 1323Substrate binding
Regioni155 – 1573Substrate binding

Sequence similaritiesi

Belongs to the DapA family. KDPG aldolase subfamily.Curated

Phylogenomic databases

eggNOGiarCOG04172. Archaea.
COG0329. LUCA.
KOiK11395.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR002220. DapA-like.
[Graphical view]
PANTHERiPTHR12128. PTHR12128. 1 hit.
PfamiPF00701. DHDPS. 1 hit.
[Graphical view]
PIRSFiPIRSF001365. DHDPS. 1 hit.
PRINTSiPR00146. DHPICSNTHASE.
SMARTiSM01130. DHDPS. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

O54288-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPEIITPIIT PFTKDNRIDK EKLKIHAENL IRKGIDKLFV NGTTGLGPSL
60 70 80 90 100
SPEEKLENLK AVYDVTNKII FQVGGLNLDD AIRLAKLSKD FDIVGIASYA
110 120 130 140 150
PYYYPRMSEK HLVKYFKTLC EVSPHPVYLY NYPTATGKDI DAKVAKEIGC
160 170 180 190 200
FTGVKDTIEN IIHTLDYKRL NPNMLVYSGS DMLIATVAST GLDGNVAAGS
210 220 230 240 250
NYLPEVTVTI KKLAMERKID EALKLQFLHD EVIEASRIFG SLSSNYVLTK
260 270 280 290
YFQGYDLGYP RPPIFPLDDE EERQLIKKVE GIRAKLVELK ILKE
Length:294
Mass (Da):33,108
Last modified:June 1, 1998 - v1
Checksum:iD709A94ACF68B0EF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ224174 Genomic DNA. Translation: CAA11866.1.
RefSeqiWP_009991687.1. NZ_CP011057.1.

Genome annotation databases

GeneIDi25403419.
KEGGiag:CAA11866.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ224174 Genomic DNA. Translation: CAA11866.1.
RefSeqiWP_009991687.1. NZ_CP011057.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1W37X-ray2.00A/B/C/D1-294[»]
1W3IX-ray1.70A/B/C/D2-294[»]
1W3NX-ray2.10A/B/C/D1-294[»]
1W3TX-ray2.10A/B/C/D1-294[»]
2YDAX-ray1.91A/B1-294[»]
ProteinModelPortaliO54288.
SMRiO54288. Positions 2-294.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi273057.SSO3197.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi25403419.
KEGGiag:CAA11866.

Phylogenomic databases

eggNOGiarCOG04172. Archaea.
COG0329. LUCA.
KOiK11395.

Enzyme and pathway databases

UniPathwayiUPA00856; UER00829.
BioCyciMetaCyc:MONOMER-4861.
BRENDAi4.1.2.55. 6163.
SABIO-RKO54288.

Miscellaneous databases

EvolutionaryTraceiO54288.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR002220. DapA-like.
[Graphical view]
PANTHERiPTHR12128. PTHR12128. 1 hit.
PfamiPF00701. DHDPS. 1 hit.
[Graphical view]
PIRSFiPIRSF001365. DHDPS. 1 hit.
PRINTSiPR00146. DHPICSNTHASE.
SMARTiSM01130. DHDPS. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "An extremely thermostable aldolase from Sulfolobus solfataricus with specificity for non-phosphorylated substrates."
    Buchanan C.L., Connaris H., Danson M.J., Reeve C.D., Hough D.W.
    Biochem. J. 343:563-570(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-39, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, SUBUNIT.
    Strain: ATCC 35091 / DSM 1616 / JCM 8930 / NBRC 15331 / P1.
  2. "Metabolic pathway promiscuity in the archaeon Sulfolobus solfataricus revealed by studies on glucose dehydrogenase and 2-keto-3-deoxygluconate aldolase."
    Lamble H.J., Heyer N.I., Bull S.D., Hough D.W., Danson M.J.
    J. Biol. Chem. 278:34066-34072(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE STEREOSELECTIVITY, BIOPHYSICOCHEMICAL PROPERTIES.
    Strain: ATCC 35091 / DSM 1616 / JCM 8930 / NBRC 15331 / P1.
  3. "Promiscuity in the part-phosphorylative Entner-Doudoroff pathway of the archaeon Sulfolobus solfataricus."
    Lamble H.J., Theodossis A., Milburn C.C., Taylor G.L., Bull S.D., Hough D.W., Danson M.J.
    FEBS Lett. 579:6865-6869(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBSTRATE STEREOSELECTIVITY, BIOPHYSICOCHEMICAL PROPERTIES.
  4. "The structural basis for substrate promiscuity in 2-keto-3-deoxygluconate aldolase from the Entner-Doudoroff pathway in Sulfolobus solfataricus."
    Theodossis A., Walden H., Westwick E.J., Connaris H., Lamble H.J., Hough D.W., Danson M.J., Taylor G.L.
    J. Biol. Chem. 279:43886-43892(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF 2-294 IN COMPLEX WITH SUBSTRATE ANALOGS, ACTIVE SITE, SUBUNIT.
  5. "Sulfolobus sulfataricus 2-keto-3-deoxygluconate aldolase."
    Royer S.F., Crennell S.J., Angelopolou M., Hough D.W., Danson M.J., Bull S.D.
    Submitted (MAR-2011) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.91 ANGSTROMS), SUBUNIT.

Entry informationi

Entry nameiKDGA_SULSF
AccessioniPrimary (citable) accession number: O54288
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 26, 2013
Last sequence update: June 1, 1998
Last modified: May 11, 2016
This is version 65 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The metabolic pathway in Sulfolobus species contrasts with the situation observed in other microorganisms where separate enzymes exist for the catabolism of the two sugars, glucose and galactose.1 Publication

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  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.