PDBsum entry 4yhh

Ribosome

PDB id: 4yhh

Contents

Protein chains

226 a.a.

206 a.a.

208 a.a.

157 a.a.

101 a.a.

155 a.a.

138 a.a.

127 a.a.

99 a.a.

115 a.a.

124 a.a.

119 a.a.

60 a.a.

88 a.a.

85 a.a.

104 a.a.

73 a.a.

83 a.a.

99 a.a.

24 a.a.

DNA/RNA

Ligands

T1C

Metals

_MG ×103

_ZN ×2

PDB id:

4yhh

Name:

Ribosome

Title:

Crystal structure of the 30s ribosomal subunit from thermus thermophilus in complex with tigecycline

Structure:

16s ribosomal RNA. Chain: a. 30s ribosomal protein s2. Chain: b. 30s ribosomal protein s3. Chain: c. 30s ribosomal protein s4. Chain: d. 30s ribosomal protein s5.

Source:

Thermus thermophilus hb8. Organism_taxid: 300852. Organism_taxid: 300852

Resolution:

3.42Å R-factor: 0.231 R-free: 0.287

Authors:

A.Schedlbauer,T.Kaminishi,B.Ochoa-Lizarralde,N.Dhimole,S.Zhou, J.P.Lopez-Alonso,S.R.Connell,P.Fucini

Key ref:

A.Schedlbauer et al. (2015). Structural characterization of an alternative mode of tigecycline binding to the bacterial ribosome. Antimicrob Agents Chemother, 59, 2849-2854. PubMed id: 25753625 DOI: 10.1128/AAC.04895-14

Date:

27-Feb-15 Release date: 08-Apr-15

Protein chain

P80371  (RS2_THET8) -  Small ribosomal subunit protein uS2 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 256 a.a.

Struc: 226 a.a.

Protein chain

P80372  (RS3_THET8) -  Small ribosomal subunit protein uS3 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 239 a.a.

Struc: 206 a.a.

Protein chain

P80373  (RS4_THET8) -  Small ribosomal subunit protein uS4 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 209 a.a.

Struc: 208 a.a.

Protein chain

Q5SHQ5  (RS5_THET8) -  Small ribosomal subunit protein uS5 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 162 a.a.

Struc: 157 a.a.

Protein chain

Q5SLP8  (RS6_THET8) -  Small ribosomal subunit protein bS6 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 101 a.a.

Struc: 101 a.a.

Protein chain

P17291  (RS7_THET8) -  Small ribosomal subunit protein uS7 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 156 a.a.

Struc: 155 a.a.

Protein chain

P0DOY9  (RS8_THET8) -  Small ribosomal subunit protein uS8 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 138 a.a.

Struc: 138 a.a.

Protein chain

P80374  (RS9_THET8) -  Small ribosomal subunit protein uS9 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 128 a.a.

Struc: 127 a.a.

Protein chain

Q5SHN7  (RS10_THET8) -  Small ribosomal subunit protein uS10 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 105 a.a.

Struc: 99 a.a.

Protein chain

P80376  (RS11_THET8) -  Small ribosomal subunit protein uS11 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 129 a.a.

Struc: 115 a.a.

Protein chain

Q5SHN3  (RS12_THET8) -  Small ribosomal subunit protein uS12 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 132 a.a.

Struc: 124 a.a.

Protein chain

P80377  (RS13_THET8) -  Small ribosomal subunit protein uS13 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 126 a.a.

Struc: 119 a.a.

Protein chain

P0DOY6  (RS14Z_THET8) -  Small ribosomal subunit protein uS14 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 61 a.a.

Struc: 60 a.a.

Protein chain

Q5SJ76  (RS15_THET8) -  Small ribosomal subunit protein uS15 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 89 a.a.

Struc: 88 a.a.

Protein chain

Q5SJH3  (RS16_THET8) -  Small ribosomal subunit protein bS16 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 88 a.a.

Struc: 85 a.a.

Protein chain

P0DOY7  (RS17_THET8) -  Small ribosomal subunit protein uS17 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 105 a.a.

Struc: 104 a.a.

Protein chain

Q5SLQ0  (RS18_THET8) -  Small ribosomal subunit protein bS18 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 88 a.a.

Struc: 73 a.a.

Protein chain

Q5SHP2  (RS19_THET8) -  Small ribosomal subunit protein uS19 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 93 a.a.

Struc: 83 a.a.

Protein chain

P80380  (RS20_THET8) -  Small ribosomal subunit protein bS20 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 106 a.a.

Struc: 99 a.a.

Protein chain

Q5SIH3  (RSHX_THET8) -  Small ribosomal subunit protein bTHX from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 27 a.a.

Struc: 24 a.a.

DNA/RNA chain

G-U-U-G-G-A-G-A-G-U-U-U-G-A-U-C-C-U-G-G-C-U-C-A-G-G-G-U-G-A-A-C-G-C-U-G-G-C-G- ... 1507 bases

DOI no: 10.1128/AAC.04895-14

Antimicrob Agents Chemother 59:2849-2854 (2015)

PubMed id: 25753625

Structural characterization of an alternative mode of tigecycline binding to the bacterial ribosome.

A.Schedlbauer, T.Kaminishi, B.Ochoa-Lizarralde, N.Dhimole, S.Zhou, J.P.López-Alonso, S.R.Connell, P.Fucini.

ABSTRACT

Although both tetracycline and tigecycline inhibit protein synthesis by sterically hindering the binding of tRNA to the ribosomal A site, tigecycline shows increased efficacy in both in vitro and in vivo activity assays and escapes the most common resistance mechanisms associated with the tetracycline class of antibiotics. These differences in activities are attributed to the tert-butyl-glycylamido side chain found in tigecycline. Our structural analysis by X-ray crystallography shows that tigecycline binds the bacterial 30S ribosomal subunit with its tail in an extended conformation and makes extensive interactions with the 16S rRNA nucleotide C1054. These interactions restrict the mobility of C1054 and contribute to the antimicrobial activity of tigecycline, including its resistance to the ribosomal protection proteins.