6PAU: Glycylpeptide N-tetradecanoyltransferase 2

Name: PDB 6PAU: Structure of Human NMT2 with myristoyl-lysine peptide and CoA products
Published: 2020-03-11
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Structure of Human NMT2 with myristoyl-lysine peptide and CoA products. Determined by X-ray diffraction at 1.93 Å resolution. Released 11 Mar 2020.

Method: X-ray diffraction
Resolution: 1.93 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,320
Mol. weight: 47.11 kDa
Ligands: MYR, 4PS, MG
Released: 11 Mar 2020

Explore 6PAU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6PAU contains 16 α-helices and 23 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 16 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	140-142	3
α-helix	149-153	5
β-strand	156-160	5	1
α-helix	166-179	14
β-strand	182	1	2
β-strand	188-190	3	2
α-helix	194-201	8
α-helix	208-210	3
β-strand	211-216	6	1
β-strand	222-235	14	1
β-strand	238-250	13	1
α-helix	252-254	3
α-helix	259-272	14
β-strand	279-283	5	1
β-strand	292-300	9	1
α-helix	303-308	6
α-helix	320-326	7
β-strand	338-340	3	1
α-helix	343-345	3
α-helix	346-356	11
α-helix	357-359	3
β-strand	362-364	3	1
α-helix	368-375	8
β-strand	378	1	1
β-strand	382-388	7	1
β-strand	394-402	9	1
β-strand	405-407	3	2
β-strand	415-416	2	2
β-strand	418-421	4	1
β-strand	425-426	2	1
α-helix	431-444	14
β-strand	449-453	5	1
α-helix	458-460	3
β-strand	468-469	2	1
β-strand	470	1	3
β-strand	471-479	9	1
α-helix	488-490	3
β-strand	491	1	1

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	8	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycylpeptide N-tetradecanoyltransferase 2	A	protein	383	Homo sapiens	O60551 (AlphaFold model)
Arf6 peptide	C	protein	7	Homo sapiens	P62330 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6PAU_1 Glycylpeptide N-tetradecanoyltransferase 2 (chains A)
KHRYQFWDTQPVPKLDEVITSHGAIEPDKDNVRQEPYSLPQGFMWDTLDLSDAEVLKELY
TLLNENYVEDDDNMFRFDYSPEFLLWALRPPGWLLQWHCGVRVSSNKKLVGFISAIPANI
RIYDSVKKMVEINFLCVHKKLRSKRVAPVLIREITRRVNLEGIFQAVYTAGVVLPKPIAT
CRYWHRSLNPRKLVEVKFSHLSRNMTLQRTMKLYRLPDVTKTSGLRPMEPKDIKSVRELI
NTYLKQFHLAPVMDEEEVAHWFLPREHIIDTFVVESPNGKLTDFLSFYTLPSTVMHHPAH
KSLKAAYSFYNIHTETPLLDLMSDALILAKSKGFDVFNALDLMENKTFLEKLKFGIGDGN
LQYYLYNWRCPGTDSEKVGLVLQ

Sequence of entity 2 (C), FASTA

>6PAU_2 Arf6 peptide (chains C)
KVLSKIF

Ligands and cofactors

ID	Name	Formula	Copies
MYR	Myristic acid	C14 H28 O2	1
4PS	4'-diphospho pantetheine	C11 H24 N2 O10 P2 S	1
MG	Magnesium ion	Mg	1

Water and common crystallization additives (SO4, GOL) are not listed.

Primary citation

NMT1 and NMT2 are lysine myristoyltransferases regulating the ARF6 GTPase cycle. Kosciuk, T., Price, I.R., Zhang, X. et al. Nat Commun (2020) 11:1067-1067. DOI 10.1038/s41467-020-14893-x · PubMed

Other PDB entries of the same protein (UniProt O60551 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4C2X 2.33 Å, Human N-myristoyltransferase isoform 2 (NMT2)
9NDP 2.82 Å, Structure of stalled ribosome and nascent chain in complex with NMT2 and NAC

Browse structure collections

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