PDBsum entry 5e1m

Transferase

PDB id: 5e1m

Contents

Protein chains

227 a.a.

Ligands

PRO-PRO-LYS-ARG-ILE-ALA ×2

SAH ×2

GOL ×3

UNX ×43

Waters ×417

PDB id:

5e1m

Name:

Transferase

Title:

Crystal structure of ntmt1 in complex with ppkria peptide

Structure:

N-terminal xaa-pro-lys n-methyltransferase 1. Chain: a, b. Synonym: alpha n-terminal protein methyltransferase 1a, methyltransferase-like protein 11a,n-terminal rcc1 methyltransferase, x-pro-lys n-terminal protein methyltransferase 1a,ntm1a. Engineered: yes. Rcc1. Chain: d, e. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ntmt1, c9orf32, mettl11a, nrmt, nrmt1, ad-003. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Other_details: synthetic peptide

Resolution:

1.75Å R-factor: 0.162 R-free: 0.188

Authors:

C.Dong,W.Tempel,C.Bountra,C.H.Arrowsmith,A.M.Edwards,J.Min,Structural Genomics Consortium (Sgc)

Key ref:

C.Dong et al. (2015). Structural basis for substrate recognition by the human N-terminal methyltransferase 1. Genes Dev, 29, 2343-2348. PubMed id: 26543161 DOI: 10.1101/gad.270611.115

Date:

29-Sep-15 Release date: 28-Oct-15

Protein chains

Q9BV86  (NTM1A_HUMAN) -  N-terminal Xaa-Pro-Lys N-methyltransferase 1 from Homo sapiens

Seq: 223 a.a.

Struc: 227 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.1.1.244 - protein N-terminal methyltransferase.
• Reaction:
  1. N-terminal L-alanyl-L-prolyl-L-lysyl-[protein] + 3 S-adenosyl-L- methionine = N-terminal N,N,N-trimethyl-L-alanyl-L-prolyl-L-lysyl- [protein] + 3 S-adenosyl-L-homocysteine + 3 H⁺
  2. N-terminal L-seryl-L-prolyl-L-lysyl-[protein] + 3 S-adenosyl-L- methionine = N-terminal N,N,N-trimethyl-L-seryl-L-prolyl-L-lysyl- [protein] + 3 S-adenosyl-L-homocysteine + 3 H⁺
  3. N-terminal L-prolyl-L-prolyl-L-lysyl-[protein] + 2 S-adenosyl-L- methionine = N-terminal N,N-dimethyl-L-prolyl-L-prolyl-L-lysyl-[protein] + 2 S-adenosyl-L-homocysteine + 2 H⁺

N-terminal L-alanyl-L-prolyl-L-lysyl-[protein] + 3 × S-adenosyl-L- methionine = N-terminal N,N,N-trimethyl-L-alanyl-L-prolyl-L-lysyl- [protein] + 3 × S-adenosyl-L-homocysteine + 3 × H(+) (Bound ligand (Het Group name = SAH) corresponds exactly)

N-terminal L-seryl-L-prolyl-L-lysyl-[protein] + 3 × S-adenosyl-L- methionine = N-terminal N,N,N-trimethyl-L-seryl-L-prolyl-L-lysyl- [protein] + 3 × S-adenosyl-L-homocysteine + 3 × H(+) (Bound ligand (Het Group name = SAH) corresponds exactly)

N-terminal L-prolyl-L-prolyl-L-lysyl-[protein] + 2 × S-adenosyl-L- methionine = N-terminal N,N-dimethyl-L-prolyl-L-prolyl-L-lysyl-[protein] + 2 × S-adenosyl-L-homocysteine + 2 × H(+) (Bound ligand (Het Group name = SAH) corresponds exactly)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1101/gad.270611.115

Genes Dev 29:2343-2348 (2015)

PubMed id: 26543161

Structural basis for substrate recognition by the human N-terminal methyltransferase 1.

C.Dong, Y.Mao, W.Tempel, S.Qin, L.Li, P.Loppnau, R.Huang, J.Min.

ABSTRACT

No abstract given.