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Literature summary for 3.6.5.3 extracted from

  • Simonson, T.; Satpati, P.
    Nucleotide recognition by the initiation factor aIF5B: free energy simulations of a neoclassical GTPase (2012), Proteins, 80, 2742-2757.
    View publication on PubMed
Search for more literature for 3.6.5.3

Crystallization (Commentary)

Crystallization (Comment) Organism
crystal structure analysis of enzyme complexed with the GTP analogue GDPNP and with GDP at 2.0 A resolution , PDB IDs 1G7T and 1G7S, enzyme in complex with GTP/Mg2+, modeling and molecular dynamics simulations Methanothermobacter thermautotrophicus

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
 additional information thermodynamics of nucleotide binding Methanothermobacter thermautotrophicus

Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+ required Methanothermobacter thermautotrophicus

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
GTP + H2O Methanothermobacter thermautotrophicus
-
 GDP + phosphate
-
 ?

Organism

Organism UniProt Comment Textmining
Methanothermobacter thermautotrophicus
-
-
-

Reaction

Reaction Comment Organism Reaction ID
GTP + H2O = GDP + phosphate catalytic mechanism, structure-function relationship, overview Methanothermobacter thermautotrophicus
a

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
GTP + H2O
-
 Methanothermobacter thermautotrophicus GDP + phosphate
-
 ?
GTP + H2O two models of the reaction mechanism using the crystal structure: I. Glu81 becomes protonated upon GTP binding, with preference to bind GDP apparently contradicting its assignment as ON, or II. Glu81 protonation/deprotonation defines the ON/OFF states. Protonated Glu81, is ON, whereas X-ray(GTP):GDP is OFF. The model postulates that distant conformational changes such as domain IV rotation are uncoupled from GTP/GDP exchange and do not affect the relative GTP/GDP binding affinities. Glu81-GTP interaction helps to hold switch 2 in place, if Glu81 is deprotonated, it and nearby residues move away from their crystal positions Methanothermobacter thermautotrophicus GDP + phosphate
-
 ?
additional information GTP/GDP binding analysis using molecular dynamics and a continuum electrostatic free energy method Methanothermobacter thermautotrophicus ?
-
 ?

Synonyms

Synonyms Comment Organism
aIF5B
-
 Methanothermobacter thermautotrophicus
GTPase aIF5B
-
 Methanothermobacter thermautotrophicus
initiation factor aIF5B
-
 Methanothermobacter thermautotrophicus

General Information

General Information Comment Organism
physiological function the GTPase aIF5B is a universally conserved initiation factor that assists ribosome assembly Methanothermobacter thermautotrophicus