6PAV: Glycylpeptide N-tetradecanoyltransferase 1

Name: PDB 6PAV: Structure of Human NMT1 with products CoA and myristoyl-lysine peptide with acetylated N-terminus
Published: 2020-03-11
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Structure of Human NMT1 with products CoA and myristoyl-lysine peptide with acetylated N-terminus. Determined by X-ray diffraction at 2.52 Å resolution. Released 11 Mar 2020.

Method: X-ray diffraction
Resolution: 2.52 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,519
Mol. weight: 94.44 kDa
Ligands: MYR, COA
Released: 11 Mar 2020

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

Secondary structure: helices and β-sheets

6PAV contains 37 α-helices and 50 β-strands across 4 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: 17 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	136	1	5
α-helix	140-142	3
α-helix	149-153	5
β-strand	156-160	5	6
α-helix	166-179	14
β-strand	182	1	7
β-strand	188-190	3	7
α-helix	194-201	8
α-helix	208-210	3
β-strand	211-216	6	6
β-strand	222-235	14	6
β-strand	238-250	13	6
α-helix	252-254	3
α-helix	259-273	15
β-strand	279-283	5	6
β-strand	290-300	11	6
α-helix	303-308	6
α-helix	320-326	7
β-strand	338-340	3	6
α-helix	343-345	3
α-helix	346-356	11
α-helix	357-359	3
β-strand	362-364	3	6
α-helix	368-375	8
β-strand	378	1	6
β-strand	382-388	7	6
β-strand	394-402	9	6
β-strand	405-407	3	7
α-helix	408	1
β-strand	415-416	2	7
β-strand	418-421	4	6
β-strand	425	1	6
α-helix	431-445	15
β-strand	449-452	4	6
α-helix	458-460	3
β-strand	468-469	2	6
β-strand	470	1	8
β-strand	471-479	9	6
β-strand	482	1	5
α-helix	488-490	3
β-strand	491	1	6

Chain B: 20 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	120-122	3
α-helix	126-127	2
β-strand	136	1	1
α-helix	140-142	3
α-helix	149-153	5
β-strand	156-160	5	2
α-helix	166-179	14
β-strand	182	1	3
β-strand	188-190	3	3
α-helix	194-201	8
α-helix	208-210	3
β-strand	211-216	6	2
β-strand	222-235	14	2
β-strand	238-250	13	2
α-helix	252-254	3
α-helix	259-273	15
β-strand	279-283	5	2
β-strand	292-300	9	2
α-helix	303-308	6
α-helix	320-326	7
β-strand	338-340	3	2
α-helix	343-345	3
α-helix	346-356	11
α-helix	357-359	3
β-strand	362-364	3	2
α-helix	368-375	8
β-strand	378	1	2
β-strand	382-388	7	2
β-strand	394-402	9	2
β-strand	405-407	3	3
α-helix	408	1
β-strand	415-416	2	3
β-strand	418-421	4	2
β-strand	425-426	2	2
α-helix	431-445	15
β-strand	449-453	5	2
α-helix	458-461	4
α-helix	463-465	3
β-strand	468-469	2	2
β-strand	470	1	4
β-strand	471-479	9	2
β-strand	482	1	1
α-helix	488-490	3
β-strand	491	1	2

Chains C and D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	8	1	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycylpeptide N-tetradecanoyltransferase 1	A, B	protein	388	Homo sapiens	P30419 (AlphaFold model)
acetyl-Arf6 peptide	D	protein	8	Homo sapiens	P62330 (AlphaFold model)
ARF6 peptide	C	protein	8	Homo sapiens	P62330 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6PAV_1 Glycylpeptide N-tetradecanoyltransferase 1 (chains A, B)
MEEASKRSYQFWDTQPVPKLGEVVNTHGPVEPDKDNIRQEPYTLPQGFTWDALDLGDRGV
LKELYTLLNENYVEDDDNMFRFDYSPEFLLWALRPPGWLPQWHCGVRVVSSRKLVGFISA
IPANIHIYDTEKKMVEINFLCVHKKLRSKRVAPVLIREITRRVHLEGIFQAVYTAGVVLP
KPVGTCRYWHRSLNPRKLIEVKFSHLSRNMTMQRTMKLYRLPETPKTAGLRPMETKDIPV
VHQLLTRYLKQFHLTPVMSQEEVEHWFYPQENIIDTFVVENANGEVTDFLSFYTLPSTIM
NHPTHKSLKAAYSFYNVHTQTPLLDLMSDALVLAKMKGFDVFNALDLMENKTFLEKLKFG
IGDGNLQYYLYNWKCPSMGAEKVGLVLQ

Sequence of entity 2 (D), FASTA

>6PAV_2 acetyl-Arf6 peptide (chains D)
XKVLSKIF

Sequence of entity 3 (C), FASTA

>6PAV_3 ARF6 peptide (chains C)
GKVLSKIF

Ligands and cofactors

ID	Name	Formula	Copies
MYR	Myristic acid	C14 H28 O2	2
COA	Coenzyme a	C21 H36 N7 O16 P3 S	2

Water and common crystallization additives (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 P30419 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5O6H 1.29 Å, Human NMT1 in complex with myristoyl-CoA and inhibitor IMP-917
3IU1 1.42 Å, Crystal Structure of human type-I N-myristoyltransferase with bound myristoyl-CoA
5O6J 1.45 Å, Human NMT1 in complex with myristoyl-CoA and inhibitor IMP-1031
7OWM 1.5 Å, HsNMT1 in complex with both MyrCoA and HCPA substrate peptide GKQNSKLR
3JTK 1.61 Å, Crystal Structure of human type-I N-myristoyltransferase with bound myristoyl-CoA and…
4C2Y 1.64 Å, Human N-myristoyltransferase (NMT1) with Myristoyl-CoA co-factor
7OWO 1.7 Å, HsNMT1 in complex with both MyrCoA and N-acetylated KSFSKPR peptide
3IU2 1.73 Å, Crystal Structure of human type-I N-myristoyltransferase with bound myristoyl-CoA and…
8Q3S 1.78 Å, HsNMT1 in complex with both MyrCoA and GNCFSKAR inhibitor peptide
3IWE 1.79 Å, Crystal Structure of human type-I N-myristoyltransferase with bound myristoyl-CoA and…
7OWP 1.81 Å, HsNMT1 in complex with both MyrCoA and ACE-G-(L-ORN)SFSKPR
5O9U 1.85 Å, HsNMT1 in complex with CoA and Myristoylated-GCSVSKKK octapeptide

Browse structure collections

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