6RXR: CobB Ac2

Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16Cr-2'OH-ADPr peptide intermediate after co-crystallisation. Determined by X-ray diffraction at 1.7 Å resolution. Released 15 Apr 2020.

Method: X-ray diffraction
Resolution: 1.7 Å
Organisms: Escherichia coli (strain K12), Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 8
Atoms: 8,315
Mol. weight: 119.75 kDa
Ligands: KMQ
Released: 15 Apr 2020

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

Secondary structure: helices and β-sheets

6RXR contains 62 α-helices and 53 β-strands across 8 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, 12 β-strands

Element	Residues	Length	Sheet
β-strand	43-47	5	1
α-helix	49-51	3
α-helix	53-55	3
α-helix	58-61	4
β-strand	66-67	2	2
β-strand	70-71	2	2
α-helix	72-75	4
α-helix	78-83	6
α-helix	85-99	15
α-helix	108-120	13
α-helix	121-123	3
β-strand	124-128	5	1
α-helix	134-138	5
β-strand	144-145	2	1
β-strand	148-155	8	3
β-strand	161-163	3	3
β-strand	183-187	5	3
α-helix	188-189	2
α-helix	193-194	2
α-helix	197-206	10
β-strand	209-213	5	1
β-strand	219-220	2	4
α-helix	222-224	3
α-helix	225-231	7
β-strand	235-240	6	1
α-helix	247-249	3
β-strand	252-255	4	1
α-helix	258-273	16

Chain B: 16 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	40-42	3
β-strand	43-47	5	5
α-helix	49-51	3
α-helix	53-55	3
β-strand	66-67	2	6
β-strand	70-71	2	6
α-helix	72-75	4
α-helix	78-83	6
α-helix	85-99	15
α-helix	108-120	13
α-helix	121-123	3
β-strand	124-128	5	5
α-helix	134-138	5
β-strand	144-145	2	5
β-strand	148-155	8	7
β-strand	161-163	3	7
β-strand	183-187	5	7
α-helix	188-189	2
α-helix	193-194	2
α-helix	197-206	10
β-strand	209-213	5	5
β-strand	219-220	2	8
α-helix	222-224	3
α-helix	225-231	7
β-strand	235-240	6	5
α-helix	247-249	3
β-strand	252-255	4	5
α-helix	258-273	16

Chain C: 15 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	43-47	5	9
α-helix	49-51	3
α-helix	53-55	3
β-strand	66-67	2	10
β-strand	70-71	2	10
α-helix	72-75	4
α-helix	78-83	6
α-helix	85-99	15
α-helix	108-120	13
α-helix	121-123	3
β-strand	124-128	5	9
α-helix	134-138	5
β-strand	144-145	2	9
β-strand	148-155	8	11
β-strand	161-163	3	11
β-strand	183-187	5	11
α-helix	188-189	2
α-helix	193-194	2
α-helix	197-206	10
β-strand	209-213	5	9
β-strand	219-220	2	12
α-helix	222-224	3
α-helix	225-231	7
β-strand	235-240	6	9
α-helix	247-249	3
β-strand	252-255	4	9
α-helix	258-273	16

Chain D: 15 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	43-47	5	13
α-helix	49-51	3
α-helix	53-55	3
β-strand	61	1	14
β-strand	66-67	2	14
β-strand	70-71	2	14
α-helix	72-75	4
α-helix	78-83	6
α-helix	85-99	15
α-helix	108-120	13
α-helix	121-123	3
β-strand	124-128	5	13
α-helix	134-138	5
β-strand	144-145	2	13
β-strand	148-155	8	15
β-strand	161-163	3	15
β-strand	183-187	5	15
α-helix	188-189	2
α-helix	193-194	2
α-helix	197-206	10
β-strand	209-213	5	13
β-strand	219-220	2	16
α-helix	222-224	3
α-helix	225-231	7
β-strand	235-240	6	13
α-helix	247-249	3
β-strand	252-255	4	13
α-helix	258-273	16

Chains E, F, G and H: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	17-18	2	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NAD-dependent protein deacylase	A, B, C, D	protein	254	Escherichia coli (strain K12)	P75960 (AlphaFold model)
Histone H4	E, F, G, H	protein	11	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P02309 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>6RXR_1 NAD-dependent protein deacylase (chains A, B, C, D)
MGSSHHHHHHSQDPKPRVLVLTGAGISAESGIRTFRAADGLWEEHRVEDVGTPEGFDRDP
ELVQAFYNARRRQLQQPEIQPNAAHLALAKLQDALGDRFLLVTQNCDNLHERAGNTNVIH
MHGELLKVRCSQSGQALDWTGDVTPEDKCHCCQFPAPLRPHVVWFGEMPLGMDEIYMALS
MADIFIAIGTSGHVYPAAGFVHEAKLHGAHTVELNLEPSQVGNEFAEKYYGPASQVVPEF
VEKLLKGLKAGSIA

Sequence of entity 2 (E, F, G, H), FASTA

>6RXR_2 Histone H4 (chains E, F, G, H)
KGGAKRHRKIL

Ligands and cofactors

ID	Name	Formula	Copies
KMQ	[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]…	C19 H29 N5 O14 P2	4

Primary citation

Evolved, Selective Erasers of Distinct Lysine Acylations. Spinck, M., Neumann-Staubitz, P., Ecke, M. et al. Angew Chem Int Ed Engl (2020) 59:11142-11149. DOI 10.1002/anie.202002899 · PubMed

Other PDB entries of the same protein (UniProt P75960 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6RXK 1.35 Å, Crystal structure of CobB wt in complex with H4K16-Butyryl peptide
6RXS 1.6 Å, Crystal structure of CobB Ac3(A76G,Y92A, I131L, V187Y) in complex with H4K16-Acetyl…
6RXJ 1.6 Å, Crystal structure of CobB wt in complex with H4K16-Acetyl peptide
6RXQ 1.7 Å, Crystal structure of CobB Ac2 (A76G,I131C,V162A) in complex with H4K16Cr-2'OH-ADPr…
6RXP 1.8 Å, Crystal structure of CobB Ac2 (A76G,I131C,V162A) in complex with H4K16-Crotonyl peptide
6RXM 1.92 Å, Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16-Acetyl peptide
6RXO 1.95 Å, Crystal structure of CobB Ac2 (A76G, I131C, V162A) in complex with H4K16-Buturyl peptide
1S5P 1.96 Å, Structure and substrate binding properties of cobB, a Sir2 homolog protein deacetylase…
6RXL 2.3 Å, Crystal structure of CobB wt in complex with H4K16-Crotonyl peptide
8ZSF 3.24 Å, CryoEM Helical Structure of KomC

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