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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)DescriptionActionsGraphical viewLength
Binding sitei134Allosteric effector; via amide nitrogen1 Publication1
Binding sitei168Substrate1 Publication1
Binding sitei184Allosteric effector1 Publication1
Binding sitei224NAD/NADP; via amide nitrogen2 Publications1
Binding sitei228NAD/NADP2 Publications1
Binding sitei244NAD/NADP2 Publications1
Active sitei2631 Publication1
Active sitei2971 Publication1
Binding sitei395NAD/NADP2 Publications1
Binding sitei424Substrate1 Publication1
Binding sitei456Substrate; via amide nitrogen1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi165 – 167NAD/NADP2 Publications3
Nucleotide bindingi191 – 194NAD/NADP2 Publications4
Nucleotide bindingi265 – 266NAD/NADP2 Publications2

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)DescriptionActionsGraphical viewLength
ChainiPRO_00004226541 – 501NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenaseAdd BLAST501

Interactioni

Subunit structurei

Homotetramer. Dimer of dimers.3 Publications

Protein-protein interaction databases

STRINGi768679.TTX_1169.

Structurei

Secondary structure

1501
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi4 – 6Combined sources3
Turni7 – 9Combined sources3
Beta strandi10 – 13Combined sources4
Beta strandi16 – 19Combined sources4
Beta strandi24 – 28Combined sources5
Beta strandi33 – 37Combined sources5
Turni39 – 41Combined sources3
Beta strandi44 – 49Combined sources6
Helixi53 – 65Combined sources13
Helixi67 – 72Combined sources6
Helixi76 – 92Combined sources17
Helixi94 – 105Combined sources12
Helixi109 – 124Combined sources16
Helixi126 – 132Combined sources7
Beta strandi136 – 140Combined sources5
Turni145 – 148Combined sources4
Beta strandi149 – 157Combined sources9
Beta strandi159 – 164Combined sources6
Beta strandi167 – 169Combined sources3
Helixi172 – 183Combined sources12
Beta strandi187 – 191Combined sources5
Beta strandi194 – 196Combined sources3
Helixi198 – 210Combined sources13
Beta strandi216 – 219Combined sources4
Helixi224 – 231Combined sources8
Beta strandi238 – 243Combined sources6
Helixi245 – 255Combined sources11
Beta strandi257 – 263Combined sources7
Beta strandi268 – 272Combined sources5
Helixi278 – 290Combined sources13
Helixi291 – 294Combined sources4
Beta strandi300 – 306Combined sources7
Helixi307 – 322Combined sources16
Helixi342 – 357Combined sources16
Beta strandi361 – 364Combined sources4
Beta strandi370 – 372Combined sources3
Beta strandi377 – 380Combined sources4
Helixi383 – 386Combined sources4
Helixi390 – 393Combined sources4
Beta strandi398 – 408Combined sources11
Helixi409 – 417Combined sources9
Beta strandi419 – 428Combined sources10
Helixi432 – 441Combined sources10
Beta strandi444 – 449Combined sources6
Beta strandi458 – 460Combined sources3
Helixi466 – 468Combined sources3
Beta strandi469 – 471Combined sources3
Turni475 – 478Combined sources4
Helixi479 – 482Combined sources4
Beta strandi483 – 491Combined sources9
Beta strandi495 – 499Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO57693.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni72 – 79Allosteric effector binding1 Publication8
Regioni154 – 155Allosteric effector binding1 Publication2
Regioni296 – 298Substrate binding1 Publication3

Sequence similaritiesi

Belongs to the aldehyde dehydrogenase family.Curated

Phylogenomic databases

eggNOGiarCOG01252. Archaea.
COG1012. LUCA.
KOiK18978.

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
PDB 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.
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.
KOiK18978.

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...

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: November 2, 2016
This is version 79 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.