1M90 image
Deposition Date 2002-07-26
Release Date 2002-09-06
Last Version Date 2023-11-15
Entry Detail
PDB ID:
1M90
Keywords:
Title:
Co-crystal structure of CCA-Phe-caproic acid-biotin and sparsomycin bound to the 50S ribosomal subunit
Biological Source:
Source Organism:
(Taxon ID: )Haloarcula marismortui (Taxon ID: 2238)
Method Details:
Experimental Method:
Resolution:
2.80 Å
R-Value Free:
0.22
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
C 2 2 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L37Ae
Chain IDs:BA (auth: 1)
Chain Length:73
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L37E
Gene (Uniprot):rpl37e
Chain IDs:CA (auth: 2)
Chain Length:56
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L39E
Gene (Uniprot):rpl39e
Chain IDs:DA (auth: 3)
Chain Length:48
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L44E
Gene (Uniprot):rpl44e
Chain IDs:EA (auth: 4)
Chain Length:92
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polyribonucleotide
Molecule:CCA
Chain IDs:C (auth: 5)
Chain Length:3
Number of Molecules:1
Biological Source:
Polymer Type:polyribonucleotide
Molecule:23S RRNA
Chain IDs:A
Chain Length:2922
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polyribonucleotide
Molecule:5S RRNA
Chain IDs:B
Chain Length:122
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L2
Gene (Uniprot):rpl2
Chain IDs:D (auth: C)
Chain Length:239
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L3
Gene (Uniprot):rpl3
Chain IDs:E (auth: D)
Chain Length:337
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L4
Gene (Uniprot):rpl4
Chain IDs:F (auth: E)
Chain Length:246
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L5
Gene (Uniprot):rpl5
Chain IDs:G (auth: F)
Chain Length:176
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L6
Gene (Uniprot):rpl6
Chain IDs:H (auth: G)
Chain Length:177
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L7AE
Gene (Uniprot):rpl7ae
Chain IDs:I (auth: H)
Chain Length:119
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L10
Gene (Uniprot):rpl10
Chain IDs:J (auth: I)
Chain Length:348
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L10E
Chain IDs:K (auth: J)
Chain Length:167
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L13
Gene (Uniprot):rpl13
Chain IDs:L (auth: K)
Chain Length:145
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L14
Gene (Uniprot):rpl14
Chain IDs:M (auth: L)
Chain Length:132
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L15
Gene (Uniprot):rpl15
Chain IDs:N (auth: M)
Chain Length:164
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L15E
Chain IDs:O (auth: N)
Chain Length:194
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L18
Gene (Uniprot):rpl18
Chain IDs:P (auth: O)
Chain Length:186
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L18E
Gene (Uniprot):rpl18e
Chain IDs:Q (auth: P)
Chain Length:115
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L19E
Gene (Uniprot):rpl19e
Chain IDs:R (auth: Q)
Chain Length:148
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L21E
Gene (Uniprot):rpl21e
Chain IDs:S (auth: R)
Chain Length:95
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L22
Gene (Uniprot):rpl22
Chain IDs:T (auth: S)
Chain Length:154
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L23
Gene (Uniprot):rpl23
Chain IDs:U (auth: T)
Chain Length:84
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L24
Gene (Uniprot):rpl24
Chain IDs:V (auth: U)
Chain Length:119
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L24E
Gene (Uniprot):rpl24e
Chain IDs:W (auth: V)
Chain Length:66
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L29
Gene (Uniprot):rpl29
Chain IDs:X (auth: W)
Chain Length:70
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L30
Gene (Uniprot):rpl30
Chain IDs:Y (auth: X)
Chain Length:154
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L31E
Gene (Uniprot):rpl31e
Chain IDs:Z (auth: Y)
Chain Length:91
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L32E
Gene (Uniprot):rpl32e
Chain IDs:AA (auth: Z)
Chain Length:240
Number of Molecules:1
Biological Source:Haloarcula marismortui
Primary Citation
Structural insights into peptide bond formation.
Proc.Natl.Acad.Sci.USA 99 11670 11675 (2002)
PMID: 12185246 DOI: 10.1073/pnas.172404099

Abstact

The large ribosomal subunit catalyzes peptide bond formation and will do so by using small aminoacyl- and peptidyl-RNA fragments of tRNA. We have refined at 3-A resolution the structures of both A and P site substrate and product analogues, as well as an intermediate analogue, bound to the Haloarcula marismortui 50S ribosomal subunit. A P site substrate, CCA-Phe-caproic acid-biotin, binds equally to both sites, but in the presence of sparsomycin binds only to the P site. The CCA portions of these analogues are bound identically by either the A or P loop of the 23S rRNA. Combining the separate P and A site substrate complexes into one model reveals interactions that may occur when both are present simultaneously. The alpha-NH(2) group of an aminoacylated fragment in the A site forms one hydrogen bond with the N3 of A2486 (2451) and may form a second hydrogen bond either with the 2' OH of the A-76 ribose in the P site or with the 2' OH of A2486 (2451). These interactions position the alpha amino group adjacent to the carbonyl carbon of esterified P site substrate in an orientation suitable for a nucleophilic attack.

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Primary Citation of related structures