ISDA: 1VQM

Deposition Date 2004-12-16

Release Date 2005-11-29

Last Version Date 2023-08-23

Entry Detail

PDB ID:

1VQM

Keywords:

RIBOSOME

Title:

The structure of the transition state analogue "DAN" bound to the large ribosomal subunit of haloarcula marismortui

Biological Source:

Source Organism:

Haloarcula marismortui (Taxon ID: 2238)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.30 Å

R-Value Free:

0.24

R-Value Work:

0.21

Space Group:

C 2 2 21

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:23S ribosomal rna
Chain IDs:A (auth: 0)
Chain Length:2922
Number of Molecules:1
Biological Source:Haloarcula marismortui

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L37e
Gene (Uniprot):rpl37e
Chain IDs:CA (auth: 1)
Chain Length:57
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P32410 Pfam ID:PF01907

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L39e
Gene (Uniprot):rpl39e
Chain IDs:DA (auth: 2)
Chain Length:50
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P22452 Pfam ID:PF00832

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L44E
Gene (Uniprot):rpl44e
Chain IDs:EA (auth: 3)
Chain Length:92
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P32411 Pfam ID:PF00935

Polymer Type:polyribonucleotide
Molecule:5'-R(*CP*CP*(PPU)P*(PO2)P*(DA)P*C*C)-3')
Chain IDs:C (auth: 4)
Chain Length:7
Number of Molecules:1
Biological Source:

Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:B (auth: 9)
Chain Length:122
Number of Molecules:1
Biological Source:Haloarcula marismortui

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2P
Gene (Uniprot):rpl2
Chain IDs:D (auth: A)
Chain Length:240
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P20276 Pfam ID:PF00181, PF03947

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3P
Chain IDs:E (auth: B)
Chain Length:338
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P20279 Pfam ID:PF00297

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4E
Gene (Uniprot):rpl4
Chain IDs:F (auth: C)
Chain Length:246
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P12735 Pfam ID:PF00573

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5P
Gene (Uniprot):rpl5
Chain IDs:G (auth: D)
Chain Length:177
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P14124 Pfam ID:PF00281, PF00673

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6P
Gene (Uniprot):rpl6
Chain IDs:H (auth: E)
Chain Length:178
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P14135 Pfam ID:PF00347

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L7AE
Gene (Uniprot):rpl7ae
Chain IDs:I (auth: F)
Chain Length:120
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P12743 Pfam ID:PF01248

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOG
Gene (Uniprot):rpl10
Chain IDs:J (auth: G)
Chain Length:348
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P15825 Pfam ID:PF00466, PF17777

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L10E
Chain IDs:K (auth: H)
Chain Length:171
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P60617 Pfam ID:PF00252

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L11P
Chain IDs:FA (auth: I)
Chain Length:162
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P14122 Pfam ID:PF03946, PF00298

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13P
Gene (Uniprot):rpl13
Chain IDs:L (auth: J)
Chain Length:145
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P29198 Pfam ID:PF00572

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14P
Gene (Uniprot):rpl14
Chain IDs:M (auth: K)
Chain Length:132
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P22450 Pfam ID:PF00238

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15P
Gene (Uniprot):rpl15
Chain IDs:N (auth: L)
Chain Length:165
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P12737 Pfam ID:PF00828

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L15E
Chain IDs:O (auth: M)
Chain Length:195
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P60618 Pfam ID:PF00827

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18P
Gene (Uniprot):rpl18
Chain IDs:P (auth: N)
Chain Length:187
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P14123 Pfam ID:PF17144

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18e
Gene (Uniprot):rpl18e
Chain IDs:Q (auth: O)
Chain Length:116
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P12733 Pfam ID:PF00828

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19E
Gene (Uniprot):rpl19e
Chain IDs:R (auth: P)
Chain Length:149
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P14119 Pfam ID:PF01280

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21e
Gene (Uniprot):rpl21e
Chain IDs:S (auth: Q)
Chain Length:96
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P12734 Pfam ID:PF01157

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22P
Gene (Uniprot):rpl22
Chain IDs:T (auth: R)
Chain Length:155
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P10970 Pfam ID:PF00237

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23P
Gene (Uniprot):rpl23
Chain IDs:U (auth: S)
Chain Length:85
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P12732 Pfam ID:PF00276

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24P
Gene (Uniprot):rpl24
Chain IDs:V (auth: T)
Chain Length:120
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P10972 Pfam ID:PF16906, PF00467

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24E
Gene (Uniprot):rpl24e
Chain IDs:W (auth: U)
Chain Length:66
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P14116 Pfam ID:PF01246

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29P
Gene (Uniprot):rpl29
Chain IDs:X (auth: V)
Chain Length:71
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P10971 Pfam ID:PF00831

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30P
Gene (Uniprot):rpl30
Chain IDs:Y (auth: W)
Chain Length:154
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P14121 Pfam ID:PF00327

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31e
Gene (Uniprot):rpl31e
Chain IDs:Z (auth: X)
Chain Length:92
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P18138 Pfam ID:PF01198

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32E
Gene (Uniprot):rpl32e
Chain IDs:AA (auth: Y)
Chain Length:241
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P12736 Pfam ID:PF14520, PF01655

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L37Ae
Chain IDs:BA (auth: Z)
Chain Length:83
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P60619 Pfam ID:PF01780

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
1MA	A	A	?
OMG	A	G	O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
OMU	A	U	O2'-METHYLURIDINE 5'-MONOPHOSPHATE
PPU	C	A	PUROMYCIN-5'-MONOPHOSPHATE
PSU	A	U	PSEUDOURIDINE-5'-MONOPHOSPHATE
UR3	A	U	3-METHYLURIDINE-5'-MONOPHOSHATE

Ligand Molecules

Primary Citation

Structural Insights into the Roles of Water and the 2' Hydroxyl of the P Site tRNA in the Peptidyl Transferase Reaction.

Schmeing, T.M, Huang, K.S, Kitchen, D.E, Strobel, S.A, Steitz, T.A.Show

Mol.Cell 20 437 448 (2005)

PMID: 16285925 DOI: 10.1016/j.molcel.2005.09.006

Abstact

Peptide bond formation is catalyzed at the peptidyl transferase center (PTC) of the large ribosomal subunit. Crystal structures of the large ribosomal subunit of Haloarcula marismortui (Hma) complexed with several analogs that represent either the substrates or the transition state intermediate of the peptidyl transferase reaction show that this reaction proceeds through a tetrahedral intermediate with S chirality. The oxyanion of the tetrahedral intermediate interacts with a water molecule that is positioned by nucleotides A2637 (E. coli numbering, 2602) and (methyl)U2619(2584). There are no Mg2+ ions or monovalent metal ions observed in the PTC that could directly promote catalysis. The A76 2' hydroxyl of the peptidyl-tRNA is hydrogen bonded to the alpha-amino group and could facilitate peptide bond formation by substrate positioning and by acting as a proton shuttle between the alpha-amino group and the A76 3' hydroxyl of the peptidyl-tRNA.

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Primary Citation of related structures