6P81: Ubiquitin-like protein SMT3,Beta sliding clamp

Structure of DNA polymerase III, beta subunit/ beta sliding clamp from Klebsiella pneumoniae, expressed with an N-terminal His-Smt3 fusion tag, in complex with Griselimycin. Determined by X-ray diffraction at 1.75 Å resolution. Released 10 Jul 2019.

Method: X-ray diffraction
Resolution: 1.75 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Klebsiella pneumoniae IS22, Streptomyces caelicus
Chains: 2
Atoms: 3,949
Mol. weight: 53.16 kDa
Ligands: PG5, CA
Released: 10 Jul 2019

Explore 6P81 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6P81 contains 19 α-helices and 34 β-strands across 1 chain. 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: 19 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	-75--69	7	1
β-strand	-64--58	7	1
α-helix	-52--43	10
α-helix	-38--36	3
β-strand	-35--31	5	1
β-strand	-28--27	2	1
α-helix	-26--25	2
β-strand	-11--5	7	1
β-strand	2-6	5	2
α-helix	7-17	11
β-strand	24	1	3
β-strand	27	1	3
α-helix	28-31	4
β-strand	32-38	7	4
β-strand	41-47	7	4
β-strand	51-58	8	4
β-strand	64	1	2
β-strand	66-71	6	4
α-helix	72-81	10
α-helix	83	1
β-strand	87-93	7	2
β-strand	96-101	6	2
β-strand	104-109	6	2
β-strand	111	1	4
α-helix	113-115	3
α-helix	119-121	3
β-strand	126-130	5	4
α-helix	132-142	11
α-helix	143-145	3
α-helix	153-156	4
β-strand	158-172	15	5
β-strand	176-195	20	5
α-helix	197-205	9
β-strand	214-218	5	4
β-strand	222-227	6	4
β-strand	230-235	6	4
α-helix	236	1
β-strand	237	1	5
α-helix	244-246	3
β-strand	254-259	6	5
α-helix	260-271	12
β-strand	280-286	7	6
β-strand	289-295	7	6
β-strand	301-307	7	6
β-strand	309	1	5
β-strand	315-320	6	6
α-helix	321-330	10
β-strand	335-340	6	5
β-strand	347-351	5	5
β-strand	354-361	8	5
α-helix	362-363	2
β-strand	364	1	6
α-helix	365	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-like protein SMT3,Beta sliding clamp	A	protein	462	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Klebsiella pneumoniae IS22	P0A988 (AlphaFold model)
Griselimycin	B	protein	11	Streptomyces caelicus

Sequence of entity 1 (A), FASTA

>6P81_1 Ubiquitin-like protein SMT3,Beta sliding clamp (chains A)
MGHHHHHHSGEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDS
LRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGMKFTVEREHLLKPLQQVSGPLGGR
PTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPE
GAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQF
SMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELM
RMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLK
QAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYV
LDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL

Sequence of entity 2 (B), FASTA

>6P81_2 Griselimycin (chains B)
XVPTLPLVPXG

Ligands and cofactors

ID	Name	Formula	Copies
PG5	1-methoxy-2-[2-(2-methoxy-ethoxy]-ethane	C8 H18 O4	1
CA	Calcium ion	Ca	1

Water and common crystallization additives (CL, ACT) are not listed.

Primary citation

Structure of DNA polymerase III, beta subunit/ beta sliding clamp from Klebsiella pneumoniae, expressed with an N-terminal His-Smt3 fusion tag, in complex with Griselimycin. Abendroth, J., Lorimer, D.D., Horanyi, P.S. et al. To be published.

Other PDB entries of the same protein (UniProt P0A988 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8PAY 1.21 Å, Structure of the E.coli DNA polymerase sliding clamp with a covalently bound peptide 2.
8PAT 1.45 Å, Structure of the E.coli DNA polymerase sliding clamp with a covalently bound peptide 3.
4K3L 1.5 Å, E. coli sliding clamp in complex with AcLF dipeptide
8CIY 1.54 Å, DNA-polymerase sliding clamp (DnaN) from Escherichia coli in complex with…
7AZ8 1.61 Å, DNA polymerase sliding clamp from Escherichia coli with peptide 43 bound
4MJR 1.62 Å, E. coli sliding clamp in complex with (S)-Carprofen
6FVM 1.63 Å, Mutant DNA polymerase sliding clamp from Escherichia coli with bound P7 peptide
3D1G 1.64 Å, Structure of a small molecule inhibitor bound to a DNA sliding clamp
1OK7 1.65 Å, A Conserved protein binding-site on Bacterial Sliding Clamps
7AZ7 1.65 Å, DNA polymerase sliding clamp from Escherichia coli with peptide 37 bound
4N96 1.7 Å, E. coli sliding clamp in complex with 6-nitroindazole
4N98 1.7 Å, E. coli sliding clamp in complex with 4'-fluorobiphenyl-4-carboxylic acid

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