6OKC: 3-oxoacyl-[acyl-carrier-protein] synthase 1

Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabB, and C12-crypto Acyl Carrier Protein, AcpP. Determined by X-ray diffraction at 1.55 Å resolution. Released 15 Apr 2020.

Method: X-ray diffraction
Resolution: 1.55 Å
Organism: Escherichia coli (strain K12)
Chains: 4
Atoms: 8,287
Mol. weight: 103.65 kDa
Ligands: MRJ
Released: 15 Apr 2020

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

Secondary structure: helices and β-sheets

6OKC contains 47 α-helices and 58 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: 20 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	1
β-strand	13	1	2
β-strand	16	1	2
α-helix	19-28	10
β-strand	33-35	3	3
α-helix	37-41	5
β-strand	48-50	3	3
α-helix	62-65	4
α-helix	70-85	16
α-helix	90-93	4
β-strand	99-104	6	1
α-helix	110-121	12
α-helix	126-129	4
α-helix	133-137	5
α-helix	141-147	7
β-strand	156-157	2	1
β-strand	158-160	3	4
β-strand	161	1	5
β-strand	163	1	5
α-helix	165-178	14
β-strand	184-191	8	1
α-helix	195-203	9
β-strand	207	1	6
α-helix	215-217	3
β-strand	223	1	7
β-strand	229	1	6
β-strand	231	1	8
β-strand	232	1	3
β-strand	234-242	9	1
α-helix	243-248	6
β-strand	255-264	10	1
α-helix	275-285	11
β-strand	294-296	3	1
α-helix	303-317	15
α-helix	321-322	2
β-strand	323-325	3	1
α-helix	328-331	4
β-strand	333	1	8
α-helix	335-337	3
α-helix	338-352	15
β-strand	354-355	2	9
β-strand	364	1	7
α-helix	366-368	3
β-strand	372-373	2	1
β-strand	378-379	2	9
β-strand	384-391	8	1
β-strand	395-402	8	1

Chain B: 19 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	10
β-strand	13	1	11
β-strand	16	1	11
α-helix	19-28	10
β-strand	33-35	3	12
α-helix	37-41	5
β-strand	48-50	3	12
α-helix	62-65	4
α-helix	70-86	17
α-helix	90-93	4
β-strand	99-104	6	10
α-helix	110-121	12
α-helix	126-129	4
α-helix	133-137	5
α-helix	141-147	7
β-strand	156-157	2	10
β-strand	158-160	3	4
β-strand	161	1	13
β-strand	163	1	13
α-helix	165-178	14
β-strand	184-191	8	10
α-helix	195-203	9
β-strand	207	1	14
α-helix	215-217	3
β-strand	223	1	15
β-strand	229	1	14
β-strand	231	1	16
β-strand	232	1	12
β-strand	234-242	9	10
α-helix	243-248	6
β-strand	255-264	10	10
α-helix	275-285	11
β-strand	294-296	3	10
α-helix	303-317	15
β-strand	323-325	3	10
α-helix	328-331	4
β-strand	333	1	16
α-helix	335-337	3
α-helix	338-352	15
β-strand	354-355	2	17
β-strand	364	1	15
α-helix	366-368	3
β-strand	373	1	10
β-strand	378-379	2	17
β-strand	384-391	8	10
β-strand	395-402	8	10

Chain C: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
β-strand	27	1	18
α-helix	36-50	15
α-helix	56-59	4
β-strand	64	1	18
α-helix	65-74	10

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
β-strand	27	1	19
α-helix	36-50	15
α-helix	56-59	4
β-strand	64	1	19
α-helix	65-73	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
3-oxoacyl-[acyl-carrier-protein] synthase 1	A, B	protein	406	Escherichia coli (strain K12)	P0A953 (AlphaFold model)
Acyl carrier protein	C, D	protein	78	Escherichia coli (strain K12)	P0A6A8 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6OKC_1 3-oxoacyl-[acyl-carrier-protein] synthase 1 (chains A, B)
MKRAVITGLGIVSSIGNNQQEVLASLREGRSGITFSQELKDSGMRSHVWGNVKLDTTGLI
DRKVVRFMSDASIYAFLSMEQAIADAGLSPEAYQNNPRVGLIAGSGGGSPRFQVFGADAM
RGPRGLKAVGPYVVTKAMASGVSACLATPFKIHGVNYSISSACATSAHCIGNAVEQIQLG
KQDIVFAGGGEELCWEMACEFDAMGALSTKYNDTPEKASRTYDAHRDGFVIAGGGGMVVV
EELEHALARGAHIYAEIVGYGATSDGADMVAPSGEGAVRCMKMAMHGVDTPIDYLNSHGT
STPVGDVKELAAIREVFGDKSPAISATKAMTGHSLGAAGVQEAIYSLLMLEHGFIAPSIN
IEELDEQAAGLNIVTETTDRELTTVMSNSFGFGGTNATLVMRKLKD

Sequence of entity 2 (C, D), FASTA

>6OKC_2 Acyl carrier protein (chains C, D)
MSTIEERVKKIIGEQLGVKQEEVTNNASFVEDLGADSLDTVELVMALEEEFDTEIPDEEA
EKITTVQAAIDYINGHQA

Ligands and cofactors

ID	Name	Formula	Copies
MRJ	N-[2-(dodecanoylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)…	C23 H46 N3 O8 P	2

Primary citation

Gating mechanism of elongating beta-ketoacyl-ACP synthases. Mindrebo, J.T., Patel, A., Kim, W.E. et al. Nat Commun (2020) 11:1727-1727. DOI 10.1038/s41467-020-15455-x · PubMed

Other PDB entries of the same protein (UniProt P0A953 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2VBA 1.36 Å, beta-ketoacyl-ACP synthase I (KAS) from E. coli with bound amino- thiazole inhibitor
2VB9 1.5 Å, beta-ketoacyl-ACP synthase I (KAS) from E. coli, apo structure
2VB8 1.52 Å, beta-ketoacyl-ACP synthase I (KAS) from E. coli with bound inhibitor thiolactomycin
2VB7 1.6 Å, beta-ketoacyl-ACP synthase I (KAS) from E. coli, apo structure after soak in PEG solution
2BYW 1.7 Å, Structure of Escherichia coli beta-ketoacyl (acyl carrier protein) synthase I LYS328ALA…
7SQI 1.7 Å, Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabB, and…
1EK4 1.85 Å, Beta-ketoacyl [acyl carrier protein] synthase I in complex with dodecanoic acid to 1.85…
2BZ4 1.86 Å, structure of E.coli KAS I H298Q mutant
2BUH 1.9 Å, E. Coli beta-ketoacyl (acyl carrier protein) synthase I, 120 K
8SMS 1.93 Å, Crosslinked Crystal Structure of Type II Fatty Acid Synthase, FabB, and cerulenin…
2BYZ 1.95 Å, Structure of E.coli KAS I H298Q mutant in complex with C12 fatty acid
1H4F 2.0 Å, E. Coli beta-ketoacyl [acyl carrier protein] synthase I K328R

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