PDBsum entry 3i55

Ribosome/antibiotic

PDB id: 3i55

Contents

Protein chains

237 a.a. *

337 a.a. *

246 a.a. *

140 a.a. *

172 a.a. *

119 a.a. *

29 a.a. *

160 a.a. *

70 a.a. *

142 a.a. *

132 a.a. *

145 a.a. *

194 a.a. *

186 a.a. *

115 a.a. *

143 a.a. *

95 a.a. *

150 a.a. *

81 a.a. *

119 a.a. *

53 a.a. *

65 a.a. *

154 a.a. *

82 a.a. *

142 a.a. *

73 a.a. *

56 a.a. *

46 a.a. *

92 a.a. *

DNA/RNA

Ligands

MYL

Metals

_SR ×108

_NA ×75

_CL ×22

_MG ×93

_CD ×5

__K ×2

Waters ×7823

* Residue conservation analysis

PDB id:

3i55

Name:

Ribosome/antibiotic

Title:

Co-crystal structure of mycalamide a bound to the large ribosomal subunit

Structure:

23s ribosomal RNA. Chain: 0. 50s ribosomal protein l2p. Chain: a. Synonym: hmal2, hl4. 50s ribosomal protein l3p. Chain: b. Synonym: hmal3, hl1. 50s ribosomal protein l4p.

Source:

Haloarcula marismortui atcc 43049. Organism_taxid: 272569. Haloarcula marismortui. Halobacterium marismortui. Organism_taxid: 2238. Synthetic: yes

Resolution:

3.11Å R-factor: 0.210 R-free: 0.260

Authors:

G.Gurel,G.Blaha,T.A.Steitz,P.B.Moore

Key ref:

G.Gürel et al. (2009). Structures of triacetyloleandomycin and mycalamide A bind to the large ribosomal subunit of Haloarcula marismortui. Antimicrob Agents Chemother, 53, 5010-5014. PubMed id: 19738021

Date:

03-Jul-09 Release date: 09-Mar-10

Protein chain

P20276  (RL2_HALMA) -  Large ribosomal subunit protein uL2 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 240 a.a.

Struc: 237 a.a.

Protein chain

P20279  (RL3_HALMA) -  Large ribosomal subunit protein uL3 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 338 a.a.

Struc: 337 a.a.

Protein chain

P12735  (RL4_HALMA) -  Large ribosomal subunit protein uL4 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 246 a.a.

Struc: 246 a.a.

Protein chain

P14124  (RL5_HALMA) -  Large ribosomal subunit protein uL5 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 177 a.a.

Struc: 140 a.a.

Protein chain

P14135  (RL6_HALMA) -  Large ribosomal subunit protein uL6 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 178 a.a.

Struc: 172 a.a.

Protein chain

P12743  (RL7A_HALMA) -  Large ribosomal subunit protein eL8 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 120 a.a.

Struc: 119 a.a.

Protein chain

P15825  (RL10_HALMA) -  Large ribosomal subunit protein uL10 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 348 a.a.

Struc: 29 a.a.*

Protein chain

P60617  (RL10E_HALMA) -  Large ribosomal subunit protein uL16 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 177 a.a.

Struc: 160 a.a.

Protein chain

P14122  (RL11_HALMA) -  Large ribosomal subunit protein uL11 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 162 a.a.

Struc: 70 a.a.

Protein chain

P29198  (RL13_HALMA) -  Large ribosomal subunit protein uL13 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 145 a.a.

Struc: 142 a.a.

Protein chain

P22450  (RL14_HALMA) -  Large ribosomal subunit protein uL14 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 132 a.a.

Struc: 132 a.a.

Protein chain

P12737  (RL15_HALMA) -  Large ribosomal subunit protein uL15 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 165 a.a.

Struc: 145 a.a.

Protein chain

P60618  (RL15E_HALMA) -  Large ribosomal subunit protein eL15 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 196 a.a.

Struc: 194 a.a.

Protein chain

P14123  (RL18_HALMA) -  Large ribosomal subunit protein uL18 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 187 a.a.

Struc: 186 a.a.

Protein chain

P12733  (RL18E_HALMA) -  Large ribosomal subunit protein eL18 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 116 a.a.

Struc: 115 a.a.

Protein chain

P14119  (RL19E_HALMA) -  Large ribosomal subunit protein eL19 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 149 a.a.

Struc: 143 a.a.

Protein chain

P12734  (RL21_HALMA) -  Large ribosomal subunit protein eL21 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 96 a.a.

Struc: 95 a.a.

Protein chain

P10970  (RL22_HALMA) -  Large ribosomal subunit protein uL22 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 155 a.a.

Struc: 150 a.a.

Protein chain

P12732  (RL23_HALMA) -  Large ribosomal subunit protein uL23 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 85 a.a.

Struc: 81 a.a.

Protein chain

P10972  (RL24_HALMA) -  Large ribosomal subunit protein uL24 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 120 a.a.

Struc: 119 a.a.

Protein chain

P14116  (RL24E_HALMA) -  Large ribosomal subunit protein eL24 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 67 a.a.

Struc: 53 a.a.

Protein chain

P10971  (RL29_HALMA) -  Large ribosomal subunit protein uL29 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 71 a.a.

Struc: 65 a.a.

Protein chain

P14121  (RL30_HALMA) -  Large ribosomal subunit protein uL30 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 154 a.a.

Struc: 154 a.a.

Protein chain

P18138  (RL31_HALMA) -  Large ribosomal subunit protein eL31 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 92 a.a.

Struc: 82 a.a.

Protein chain

P12736  (RL32_HALMA) -  Large ribosomal subunit protein eL32 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 241 a.a.

Struc: 142 a.a.

Protein chain

P60619  (RL37A_HALMA) -  Large ribosomal subunit protein eL43 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 92 a.a.

Struc: 73 a.a.

Protein chain

P32410  (RL37_HALMA) -  Large ribosomal subunit protein eL37 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 57 a.a.

Struc: 56 a.a.

Protein chain

P22452  (RL39_HALMA) -  Large ribosomal subunit protein eL39 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 50 a.a.

Struc: 46 a.a.

Protein chain

P32411  (RL44E_HALMA) -  Large ribosomal subunit protein eL42 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)

Seq: 92 a.a.

Struc: 92 a.a.

* PDB and UniProt seqs differ at 11 residue positions (black crosses)

DNA/RNA chains

U-A-U-G-C-C-A-G-C-U-G-G-U-G-G-A-U-U-G-C-U-C-G-G-C-U-C-A-G-G-C-G-C-U-G-A-U-G-A- ... 2754 bases

U-U-A-G-G-C-G-G-C-C-A-C-A-G-C-G-G-U-G-G-G-G-U-U-G-C-C-U-C-C-C-G-U-A-C-C-C-A-U- 122 bases

C-C-5AA-X-PO2-A-C-C 8 bases

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, 1, 2, 3: E.C.?

Antimicrob Agents Chemother 53:5010-5014 (2009)

PubMed id: 19738021

Structures of triacetyloleandomycin and mycalamide A bind to the large ribosomal subunit of Haloarcula marismortui.

G.Gürel, G.Blaha, T.A.Steitz, P.B.Moore.

ABSTRACT

Structures have been obtained for the complexes that triacetyloleandomycin and mycalamide A form with the large ribosomal subunit of Haloarcula marismortui. Triacetyloleandomycin binds in the nascent peptide tunnel and inhibits the activity of ribosomes by blocking the growth of the nascent peptide chain. Mycalamide A binds to the E site and inhibits protein synthesis by occupying the space normally occupied by the CCA end of E-site-bound tRNAs.