6DUB | pdb_00006dub

Crystal structure of a methyltransferase

• PDB DOI: https://doi.org/10.2210/pdb6DUB/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-06-20 Released: 2018-07-25 
• Deposition Author(s): Dong, C., Tempel, W., Li, Y., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.178 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

An asparagine/glycine switch governs product specificity of human N-terminal methyltransferase NTMT2.

Dong, C., Dong, G., Li, L., Zhu, L., Tempel, W., Liu, Y., Huang, R., Min, J.

(2018) Commun Biol 1: 183-183

• PubMed: 30417120 
• DOI: https://doi.org/10.1038/s42003-018-0196-2
• Primary Citation Related Structures: 
  5UBB, 6DUB


• PubMed Abstract: 
  

  α-N-terminal methylation of proteins is an important post-translational modification that is catalyzed by two different N-terminal methyltransferases, namely NTMT1 and NTMT2. Previous studies have suggested that NTMT1 is a tri-methyltransferase, whereas NTMT2 is a mono-methyltransferase. Here, we report the first crystal structures, to our knowledge, of NTMT2 in binary complex with S-adenosyl-L-methionine as well as in ternary complex with S-adenosyl-L-homocysteine and a substrate peptide. Our structural observations combined with biochemical studies reveal that NTMT2 is also able to di-/tri-methylate the GPKRIA peptide and di-methylate the PPKRIA peptide, otherwise it is predominantly a mono-methyltransferase. The residue N89 of NTMT2 serves as a gatekeeper residue that regulates the binding of unmethylated versus monomethylated substrate peptide. Structural comparison of NTMT1 and NTMT2 prompts us to design a N89G mutant of NTMT2 that can profoundly alter its catalytic activities and product specificities.

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Organizational Affiliation: 
• Structural Genomics Consortium, University of Toronto, Toronto, M5G1L7, ON, Canada.
Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research, Institute for Drug Discovery, Purdue University, West Lafayette, IN, 47907, USA.
School of Life Sciences, Jinggangshan University, 343009, Ji'an, Jiangxi, China.
Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research, Institute for Drug Discovery, Purdue University, West Lafayette, IN, 47907, USA. [e-mail].
Structural Genomics Consortium, University of Toronto, Toronto, M5G1L7, ON, Canada. [e-mail].
Department of Physiology, University of Toronto, Toronto, M5S 1A8, ON, Canada. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 52.43 kDa 
• Atom Count: 4,160 
• Modeled Residue Count: 450 
• Deposited Residue Count: 456 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha N-terminal protein methyltransferase 1B	A, B	222	Homo sapiens	Mutation(s): 0  Gene Names: METTL11B, C1orf184, NRMT2 EC: 2.1.1.299
UniProt & NIH Common Fund Data Resources
Find proteins for Q5VVY1 (Homo sapiens) Explore Q5VVY1  Go to UniProtKB:  Q5VVY1
GTEx:  ENSG00000203740

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RCC1	C [auth E], D [auth F]	6	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P18754 (Homo sapiens) Explore P18754  Go to UniProtKB:  P18754
PHAROS:  P18754 GTEx:  ENSG00000180198

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	E [auth A], PA [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
GOL	F [auth A], G [auth A], QA [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
UNX	AA [auth A], AB [auth B], BA [auth A], BB [auth B], CA [auth A], CB [auth B], DA [auth A], DB [auth B], EA [auth A], EB [auth B], FA [auth A], FB [auth B], GA [auth A], GB [auth B], H [auth A], HA [auth A], HB [auth B], I [auth A], IA [auth A], IB [auth B], J [auth A], JA [auth A], JB [auth B], K [auth A], KA [auth A], KB [auth B], L [auth A], LA [auth A], LB [auth B], M [auth A], MA [auth A], MB [auth B], N [auth A], NA [auth A], NB [auth E], O [auth A], OA [auth A], OB [auth E], P [auth A], PB [auth E], Q [auth A], QB [auth F], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B], X [auth A], XA [auth B], Y [auth A], YA [auth B], Z [auth A], ZA [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.178 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36dub

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.359	α = 90
b = 44.359	β = 90
c = 262.058	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-07-25 
Deposition Author(s): Dong, C., Tempel, W., Li, Y., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2018-07-25
  Type: Initial release
  
• Version 1.1: 2018-11-28
  Changes: Data collection, Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description