› 4y49

X-ray diffraction
3.95Å resolution

Crystal structure of yeast N-terminal acetyltransferase (ppGpp) NatE in complex with a bisubstrate

Released:
DOI: 10.2210/pdb4y49/pdb
PDB entry 4y49 coloured by chain, front view.
PDB entry 4y49 coloured by chain, side view.
PDB entry 4y49 coloured by chain, top view.
Source organisms:
Entry authors: Dong J, Wang S, York JD

Function and Biology Details

Reactions catalysed: 
Acetyl-CoA + an N-terminal-L-alanyl-[protein] = an N-terminal-N(alpha)-acetyl-L-alanyl-[protein] + CoA
Acetyl-CoA + an N-terminal-L-methionyl-L-alanyl-[protein] = an N-terminal-N(alpha)-acetyl-L-methionyl-L-alanyl-[protein] + CoA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-134098 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
N-terminal acetyltransferase A complex subunit NAT1 Chains: A, G, M
Molecule details ›
Chains: A, G, M
Length: 854 amino acids
Theoretical weight: 99.08 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P12945 (Residues: 1-854; Coverage: 100%)
Gene names: AAA1, D2720, NAT1, YDL040C
Sequence domains: N-terminal acetyltransferase A, auxiliary subunit
N-terminal acetyltransferase A complex catalytic subunit ARD1 Chains: B, H, N
Molecule details ›
Chains: B, H, N
Length: 238 amino acids
Theoretical weight: 27.64 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P07347 (Residues: 1-238; Coverage: 100%)
Gene names: ARD1, YHR013C
Sequence domains: Acetyltransferase (GNAT) family
Structure domains: Aminopeptidase
N-alpha-acetyltransferase NAT5 Chains: C, I, O
Molecule details ›
Chains: C, I, O
Length: 176 amino acids
Theoretical weight: 19.75 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: Q08689 (Residues: 1-176; Coverage: 100%)
Gene names: NAT5, YOR253W
Sequence domains: Acetyltransferase (GNAT) family
Structure domains: Aminopeptidase
Melanocyte-stimulating hormone alpha Chains: E, K, Q
Molecule details ›
Chains: E, K, Q
Length: 8 amino acids
Theoretical weight: 1.06 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P01189 (Residues: 138-145; Coverage: 3%)
Gene name: POMC
Sequence domains: Corticotropin ACTH domain

Ligands and Environments


Cofactor: Ligand CMC 3 x CMC

Cofactor: Ligand ACO 3 x ACO
1 bound ligand:
Ligand G4P 3 x G4P
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P212121
Unit cell:
a: 111.723Å b: 146.486Å c: 254.107Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.358 0.355 0.421
Expression systems:
  • Escherichia coli
  • Not provided

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