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Protein

NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase

Gene

gapN

Organism
Thermoproteus tenax
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the irreversible NAD(P)-dependent non-phosphorylating oxidation of glyceraldehyde-3-phosphate (GAP) to 3-phosphoglycerate (3PG). It is highly specific for D-GAP.2 Publications

Catalytic activityi

D-glyceraldehyde 3-phosphate + NAD(P)+ + H2O = 3-phospho-D-glycerate + NAD(P)H.2 Publications

Enzyme regulationi

Allosterically activated by AMP, ADP, glucose 1-phosphate (G1P), and fructose 6-phosphate (F6P).1 Publication

Kineticsi

Km applies to a data set exhibiting Michaelis-Menten kinetics. When an enzyme does not exhibit Michaelis-Menten kinetics the binding affinity is simply expressed as S0.5 which corresponds ot the observed substrate concentration for 0.5 x Vmax. S0.5 is 20 mM for NADP alone, 0.1 mM for NADP with G1P as effector, 0.2 mM for NADP with F6P as effector, 0.15 mM for NADP with AMP as effector and 0.2 mM for NADP with ADP as effector.

  1. KM=0.4 mM for NAD (with G1P as effector. PubMed:9497334)2 Publications
  2. KM=1.3 mM for NAD (with AMP as effector. PubMed:9497334)2 Publications
  3. KM=1.7 mM for NAD (with ADP as effector. PubMed:9497334)2 Publications
  4. KM=3.1 mM for NAD2 Publications
  1. Vmax=32.5 µmol/min/mg enzyme with NAD as substrate (with AMP as effector. PubMed:9497334)2 Publications
  2. Vmax=35 µmol/min/mg enzyme with NAD as substrate (with G1P as effector. PubMed:9497334)2 Publications
  3. Vmax=36 µmol/min/mg enzyme with NAD as substrate (with ADP as effector. PubMed:9497334)2 Publications
  4. Vmax=36 µmol/min/mg enzyme with NAD as substrate2 Publications
  5. Vmax=14 µmol/min/mg enzyme with NADP as substrate3 Publications
  6. Vmax=31 µmol/min/mg enzyme with NADP as substrate (with F6P as effector. PubMed:15288789)2 Publications
  7. Vmax=33 µmol/min/mg enzyme with NADP as substrate (with ADP as effector. PubMed:15288789)2 Publications
  8. Vmax=39 µmol/min/mg enzyme with NADP as substrate (with AMP as effector. PubMed:15288789)2 Publications
  9. Vmax=43 µmol/min/mg enzyme with NADP as substrate (with G1P as effector. PubMed:15288789)2 Publications

Temperature dependencei

Optimum temperature is 96 degrees Celsius. High thermostability.2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei134 – 1341Allosteric effector; via amide nitrogen1 Publication
Binding sitei168 – 1681Substrate1 Publication
Binding sitei184 – 1841Allosteric effector1 Publication
Binding sitei224 – 2241NAD/NADP; via amide nitrogen2 Publications
Binding sitei228 – 2281NAD/NADP2 Publications
Binding sitei244 – 2441NAD/NADP2 Publications
Active sitei263 – 26311 Publication
Active sitei297 – 29711 Publication
Binding sitei395 – 3951NAD/NADP2 Publications
Binding sitei424 – 4241Substrate1 Publication
Binding sitei456 – 4561Substrate; via amide nitrogen1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi165 – 1673NAD/NADP2 Publications
Nucleotide bindingi191 – 1944NAD/NADP2 Publications
Nucleotide bindingi265 – 2662NAD/NADP2 Publications

GO - Molecular functioni

  • glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity Source: UniProtKB
  • NAD binding Source: UniProtKB
  • NADP binding Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

NAD, NADP, Nucleotide-binding

Enzyme and pathway databases

BRENDAi1.2.1.B26. 6329.
SABIO-RKO57693.

Names & Taxonomyi

Protein namesi
Recommended name:
NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase (EC:1.2.1.902 Publications)
Alternative name(s):
Glyceraldehyde phosphate dehydrogenase (NAD(P))
Short name:
GAPN
Gene namesi
Name:gapN
OrganismiThermoproteus tenax
Taxonomic identifieri2271 [NCBI]
Taxonomic lineageiArchaeaCrenarchaeotaThermoproteiThermoprotealesThermoproteaceaeThermoproteus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 501501NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenasePRO_0000422654Add
BLAST

Interactioni

Subunit structurei

Homotetramer. Dimer of dimers.3 Publications

Protein-protein interaction databases

STRINGi768679.TTX_1169.

Structurei

Secondary structure

1
501
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 63Combined sources
Turni7 – 93Combined sources
Beta strandi10 – 134Combined sources
Beta strandi16 – 194Combined sources
Beta strandi24 – 285Combined sources
Beta strandi33 – 375Combined sources
Turni39 – 413Combined sources
Beta strandi44 – 496Combined sources
Helixi53 – 6513Combined sources
Helixi67 – 726Combined sources
Helixi76 – 9217Combined sources
Helixi94 – 10512Combined sources
Helixi109 – 12416Combined sources
Helixi126 – 1327Combined sources
Beta strandi136 – 1405Combined sources
Turni145 – 1484Combined sources
Beta strandi149 – 1579Combined sources
Beta strandi159 – 1646Combined sources
Beta strandi167 – 1693Combined sources
Helixi172 – 18312Combined sources
Beta strandi187 – 1915Combined sources
Beta strandi194 – 1963Combined sources
Helixi198 – 21013Combined sources
Beta strandi216 – 2194Combined sources
Helixi224 – 2318Combined sources
Beta strandi238 – 2436Combined sources
Helixi245 – 25511Combined sources
Beta strandi257 – 2637Combined sources
Beta strandi268 – 2725Combined sources
Helixi278 – 29013Combined sources
Helixi291 – 2944Combined sources
Beta strandi300 – 3067Combined sources
Helixi307 – 32216Combined sources
Helixi342 – 35716Combined sources
Beta strandi361 – 3644Combined sources
Beta strandi370 – 3723Combined sources
Beta strandi377 – 3804Combined sources
Helixi383 – 3864Combined sources
Helixi390 – 3934Combined sources
Beta strandi398 – 40811Combined sources
Helixi409 – 4179Combined sources
Beta strandi419 – 42810Combined sources
Helixi432 – 44110Combined sources
Beta strandi444 – 4496Combined sources
Beta strandi458 – 4603Combined sources
Helixi466 – 4683Combined sources
Beta strandi469 – 4713Combined sources
Turni475 – 4784Combined sources
Helixi479 – 4824Combined sources
Beta strandi483 – 4919Combined sources
Beta strandi495 – 4995Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1KY8X-ray2.40A1-501[»]
1UXNX-ray2.30A1-501[»]
1UXPX-ray2.55A1-501[»]
1UXQX-ray2.40A1-501[»]
1UXRX-ray2.30A1-501[»]
1UXTX-ray2.20A1-501[»]
1UXUX-ray2.25A1-501[»]
1UXVX-ray2.35A1-501[»]
ProteinModelPortaliO57693.
SMRiO57693. Positions 3-501.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO57693.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni72 – 798Allosteric effector binding1 Publication
Regioni154 – 1552Allosteric effector binding1 Publication
Regioni296 – 2983Substrate binding1 Publication

Sequence similaritiesi

Belongs to the aldehyde dehydrogenase family.Curated

Phylogenomic databases

eggNOGiarCOG01252. Archaea.
COG1012. LUCA.

Family and domain databases

Gene3Di3.40.309.10. 1 hit.
3.40.605.10. 1 hit.
InterProiIPR016161. Ald_DH/histidinol_DH.
IPR016163. Ald_DH_C.
IPR016162. Ald_DH_N.
IPR015590. Aldehyde_DH_dom.
[Graphical view]
PfamiPF00171. Aldedh. 1 hit.
[Graphical view]
SUPFAMiSSF53720. SSF53720. 1 hit.

Sequencei

Sequence statusi: Complete.

O57693-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRAGLLEGVI KEKGGVPVYP SYLAGEWGGS GQEIEVKSPI DLATIAKVIS
60 70 80 90 100
PSREEVERTL DVLFKRGRWS ARDMPGTERL AVLRKAADII ERNLDVFAEV
110 120 130 140 150
LVMNAGKPKS AAVGEVKAAV DRLRLAELDL KKIGGDYIPG DWTYDTLETE
160 170 180 190 200
GLVRREPLGV VAAITPFNYP LFDAVNKITY SFIYGNAVVV KPSISDPLPA
210 220 230 240 250
AMAVKALLDA GFPPDAIALL NLPGKEAEKI VADDRVAAVS FTGSTEVGER
260 270 280 290 300
VVKVGGVKQY VMELGGGDPA IVLEDADLDL AADKIARGIY SYAGQRCDAI
310 320 330 340 350
KLVLAERPVY GKLVEEVAKR LSSLRVGDPR DPTVDVGPLI SPSAVDEMMA
360 370 380 390 400
AIEDAVEKGG RVLAGGRRLG PTYVQPTLVE APADRVKDMV LYKREVFAPV
410 420 430 440 450
ASAVEVKDLD QAIELANGRP YGLDAAVFGR DVVKIRRAVR LLEVGAIYIN
460 470 480 490 500
DMPRHGIGYY PFGGRKKSGV FREGIGYAVE AVTAYKTIVF NYKGKGVWKY

E
Length:501
Mass (Da):54,090
Last modified:August 1, 1998 - v1
Checksum:i22F1C0084282EE1B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y10625 Genomic DNA. Translation: CAA71651.1.
PIRiT44939.

Genome annotation databases

KEGGiag:CAA71651.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y10625 Genomic DNA. Translation: CAA71651.1.
PIRiT44939.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1KY8X-ray2.40A1-501[»]
1UXNX-ray2.30A1-501[»]
1UXPX-ray2.55A1-501[»]
1UXQX-ray2.40A1-501[»]
1UXRX-ray2.30A1-501[»]
1UXTX-ray2.20A1-501[»]
1UXUX-ray2.25A1-501[»]
1UXVX-ray2.35A1-501[»]
ProteinModelPortaliO57693.
SMRiO57693. Positions 3-501.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi768679.TTX_1169.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

KEGGiag:CAA71651.

Phylogenomic databases

eggNOGiarCOG01252. Archaea.
COG1012. LUCA.

Enzyme and pathway databases

BRENDAi1.2.1.B26. 6329.
SABIO-RKO57693.

Miscellaneous databases

EvolutionaryTraceiO57693.

Family and domain databases

Gene3Di3.40.309.10. 1 hit.
3.40.605.10. 1 hit.
InterProiIPR016161. Ald_DH/histidinol_DH.
IPR016163. Ald_DH_C.
IPR016162. Ald_DH_N.
IPR015590. Aldehyde_DH_dom.
[Graphical view]
PfamiPF00171. Aldedh. 1 hit.
[Graphical view]
SUPFAMiSSF53720. SSF53720. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "NAD+-dependent GAPDH from Thermoproteus tenax - the first identified archaeal member of the aldehyde dehydrogenase superfamily is a glycolytic enzyme with unusual regulatory properties."
    Brunner N.A., Brinkmann H., Siebers B., Hensel R.
    J. Biol. Chem. 273:6149-6156(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, ENZYME REGULATION.
    Strain: KRA 1.
  2. "Characterization of two D-glyceraldehyde-3-phosphate dehydrogenases from the extremely thermophilic archaebacterium Thermoproteus tenax."
    Hensel R., Laumann S., Lang J., Heumann H., Lottspeich F.
    Eur. J. Biochem. 170:325-333(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
    Strain: KRA 1.
  3. "The crystal structure of the allosteric non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeum Thermoproteus tenax."
    Pohl E., Brunner N., Wilmanns M., Hensel R.
    J. Biol. Chem. 277:19938-19945(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) IN COMPLEX WITH NADP, SUBUNIT.
  4. "Structural basis of allosteric regulation and substrate specificity of the non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase from Thermoproteus tenax."
    Lorentzen E., Hensel R., Knura T., Ahmed H., Pohl E.
    J. Mol. Biol. 341:815-828(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) IN COMPLEX WITH SUBSTRATE, EFFECTORS, NADP AND NAD, ACTIVE SITE, ALLOSTERIC REGULATION, SUBSTRATE SPECIFICITY, SUBUNIT.

Entry informationi

Entry nameiGAPN_THETE
AccessioniPrimary (citable) accession number: O57693
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 26, 2013
Last sequence update: August 1, 1998
Last modified: March 16, 2016
This is version 76 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

GapN is also able to utilize NADP as a cosubstrate but with remarkably different kinetic properties. In contrast to the NAD-dependent reaction, the NADP-dependent reaction does not follow classical Michaelis-Menten kinetics. The saturation kinetics of the NADP-dependent reaction shows an unexpectedly bumpy curve with several more or less pronounced intermediate plateaus, which can be explained by the assumption that the catalytic or binding constants first decrease, then increase with saturation. The first saturation phase is characterized by negative cooperativity. The later saturation phases display sigmoidal shapes indicating positive cooperativity. The negative cooperativity of the first saturation phase could also explain the strong inhibition of NADP on the NAD-dependent reaction if it is assumed that NADP excludes NAD more efficiently from the vacant cosubstrate-binding site than NADP itself (PubMed:15288789).1 Publication

Keywords - Technical termi

3D-structure, Allosteric enzyme

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.