8UX2: NAD--protein-threonine ADP-ribosyltransferase

Name: PDB 8UX2: Chromobacterium violaceum mono-ADP-ribosyltransferase CteC in complex with NAD+
Published: 2024-01-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Chromobacterium violaceum mono-ADP-ribosyltransferase CteC in complex with NAD+. Determined by X-ray diffraction at 1.87 Å resolution. Released 17 Jan 2024.

Method: X-ray diffraction
Resolution: 1.87 Å
Organism: Chromobacterium violaceum
Chains: 3
Atoms: 6,061
Mol. weight: 84.91 kDa
Ligands: CA, NAD
Released: 17 Jan 2024

Explore 8UX2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8UX2 contains 45 α-helices and 42 β-strands across 3 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: 15 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	39-42	4
α-helix	46-57	12
β-strand	62-67	6	1
α-helix	70-72	3
α-helix	73-78	6
α-helix	79-86	8
β-strand	96-98	3	2
β-strand	99-101	3	1
β-strand	107	1	3
β-strand	117-121	5	1
β-strand	126-131	6	2
β-strand	157	1	4
α-helix	159-166	8
α-helix	169-173	5
α-helix	181-187	7
α-helix	191-193	3
β-strand	194	1	4
β-strand	196	1	2
α-helix	199-201	3
α-helix	202-205	4
α-helix	207-212	6
β-strand	216	1	3
α-helix	217-219	3
β-strand	220-224	5	2
α-helix	227-229	3
β-strand	230-234	5	1
α-helix	240-255	16
β-strand	262-266	5	1
β-strand	269-273	5	1

Chain B: 17 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	39-42	4
α-helix	46-57	12
β-strand	62-67	6	5
α-helix	70-72	3
α-helix	73-78	6
α-helix	79-85	7
β-strand	96-98	3	6
β-strand	99-101	3	5
β-strand	107	1	7
β-strand	117-121	5	5
β-strand	126-131	6	6
α-helix	140-141	2
α-helix	149-152	4
β-strand	157	1	8
α-helix	159-166	8
α-helix	169-173	5
α-helix	181-186	6
α-helix	191-193	3
β-strand	194	1	8
β-strand	196	1	6
α-helix	199-201	3
α-helix	202-205	4
α-helix	207-212	6
β-strand	216	1	7
α-helix	217-219	3
β-strand	220-224	5	6
α-helix	227-229	3
β-strand	230-235	6	5
α-helix	240-255	16
β-strand	262-266	5	5
β-strand	269-273	5	5

Chain C: 13 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	46-58	13
β-strand	62-67	6	9
α-helix	70-72	3
α-helix	73-78	6
α-helix	79-85	7
β-strand	96-98	3	10
β-strand	99-101	3	9
β-strand	107	1	11
β-strand	117-121	5	9
β-strand	126-131	6	10
β-strand	157	1	12
α-helix	159-166	8
α-helix	169-173	5
α-helix	181-187	7
α-helix	191-193	3
β-strand	194	1	12
β-strand	196	1	10
α-helix	199-205	7
α-helix	207-212	6
β-strand	216	1	11
α-helix	217-219	3
β-strand	220-224	5	10
α-helix	227-229	3
β-strand	230-235	6	9
α-helix	240-255	16
β-strand	262-266	5	9
β-strand	269-273	5	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NAD(+)--protein-threonine ADP-ribosyltransferase	A, B, C	protein	246	Chromobacterium violaceum	Q7NY09 (AlphaFold model)

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

>8UX2_1 NAD(+)--protein-threonine ADP-ribosyltransferase (chains A, B, C)
GPLGSGVPHEITGGNRQEKLAQLMRQFESGGLYLRTVSDHRDEFENTFMPKLDACLGHGC
DERYWSSATFIQQGLNGKVHDPHADRTGLIISADARLGGFSTFDAATANVPSGLEPSQYF
PGQFPKFDMMGAYQATWNEDIFSVDATAVSEQQMDELGIPDEYRSVFDFDRIQEKMAQPR
LAGREVEPTEAKICYQPKDVLGIYVDVDSPASQSKARELQQAMREQGFDLPFIAYRGGAA
QELASV

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	3
NAD	Nicotinamide-adenine-dinucleotide	C21 H27 N7 O14 P2	3

Water and common crystallization additives (EDO) are not listed.

Primary citation

Crystal structure of bacterial ubiquitin ADP-ribosyltransferase CteC reveals a substrate-recruiting insertion. Zhang, Z., Rondon-Cordero, H.M., Das, C. J Biol Chem (2023) 300:105604-105604. DOI 10.1016/j.jbc.2023.105604 · PubMed

Other PDB entries of the same protein (UniProt Q7NY09 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8HTD 1.85 Å, Crystal structure of an effector from Chromobacterium violaceum in complex with ubiquitin
8HTF 2.15 Å, Crystal structure of an effector in complex with ubiquitin
8HTC 2.2 Å, Crystal structure of a SeMet-labeled effector from Chromobacterium violaceum in complex…
8HTE 2.31 Å, Crystal structure of an effector mutant in complex with ubiquitin

Browse structure collections

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