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(-) Description

Title :  E. COLI CYSTEINYL-TRNA AND T. AQUATICUS ELONGATION FACTOR EF-TU:GTP TERNARY COMPLEX
 
Authors :  P. Nissen, M. Kjeldgaard, S. Thirup, J. Nyborg
Date :  04 Dec 98  (Deposition) - 07 Dec 98  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  P,R
Keywords :  Translation Elongation Factor, Transfer Rna, Protein Synthesis, Gene Regulation-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Nissen, S. Thirup, M. Kjeldgaard, J. Nyborg
The Crystal Structure Of Cys-Trnacys-Ef-Tu-Gdpnp Reveals General And Specific Features In The Ternary Complex And In Trna.
Structure Fold. Des. V. 7 143 1999
PubMed-ID: 10368282  |  Reference-DOI: 10.1016/S0969-2126(99)80021-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYSTEINYL TRNA
    Chains: R
    Engineered: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: AMINOACYL LINK BETWEEN A76 AND CYS77
    Synonym: CYS-TRNA
 
Molecule 2 - ELONGATION FACTOR TU
    Chains: P
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TUFA
    Organism Scientific: THERMUS AQUATICUS
    Organism Taxid: 271
    Strain: YT-1
    Synonym: EF-TU

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : PR

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 15)

Asymmetric/Biological Unit (9, 15)
No.NameCountTypeFull Name
14SU1Mod. Nucleotide4-THIOURIDINE-5'-MONOPHOSPHATE
25MU1Mod. Nucleotide5-METHYLURIDINE 5'-MONOPHOSPHATE
3CYS1Mod. Amino AcidCYSTEINE
4GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
5H2U2Mod. Nucleotide5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
6MG3Ligand/IonMAGNESIUM ION
7MIA1Mod. Nucleotide2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5'-MONOPHOSPHATE
8PSU3Mod. NucleotidePSEUDOURIDINE-5'-MONOPHOSPHATE
9SO42Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR P:25 , THR P:62 , GNP P:406 , HOH P:410 , HOH P:419BINDING SITE FOR RESIDUE MG P 407
2AC2SOFTWAREARG P:339 , VAL P:352 , ARG P:354 , HOH P:442 , HOH P:463 , HOH P:548BINDING SITE FOR RESIDUE SO4 P 408
3AC3SOFTWAREMET P:113 , PRO P:114 , ARG P:117 , HOH P:423BINDING SITE FOR RESIDUE SO4 P 409
4AC4SOFTWAREC R:75 , A R:76BINDING SITE FOR RESIDUE MG R 77
5AC5SOFTWAREG R:70BINDING SITE FOR RESIDUE MG R 179
6AC6SOFTWAREHIS P:67 , HIS P:273 , ARG P:274 , ASN P:285 , VAL P:286 , A R:76BINDING SITE FOR RESIDUE CYS R 976
7AC7SOFTWAREVAL P:20 , ASP P:21 , HIS P:22 , GLY P:23 , LYS P:24 , THR P:25 , THR P:26 , TYR P:47 , ILE P:61 , THR P:62 , GLY P:84 , ASN P:136 , LYS P:137 , ASP P:139 , MET P:140 , SER P:174 , ALA P:175 , LEU P:176 , MG P:407 , HOH P:410 , HOH P:419 , HOH P:524BINDING SITE FOR RESIDUE GNP P 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1B23)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1B23)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1B23)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_TR_1PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature.EFTU_THEAQ52-67  1P:51-66

(-) Exons   (0, 0)

(no "Exon" information available for 1B23)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain P from PDB  Type:PROTEIN  Length:405
 aligned with EFTU_THEAQ | Q01698 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:405
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401     
           EFTU_THEAQ     2 AKGEFIRTKPHVNVGTIGHVDHGKTTLTAALTYVAAAENPNVEVKDYGDIDKAPEERARGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALLALEEMHKNPKTKRGENEWVDKIWELLDAIDEYIPTPVRDVDKPFLMPVEDVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRKTVVTGVEMHRKTLQEGIAGDNVGLLLRGVSREEVERGQVLAKPGSITPHTKFEASVYILKKEEGGRHTGFFTGYRPQFYFRTTDVTGVVRLPQGVEMVMPGDNVTFTVELIKPVALEEGLRFAIREGGRTVGAGVVTKILE 406
               SCOP domains d1b23p3 P:1-212 Elongation factor Tu (EF-Tu), N-terminal (G) domain                                                                                                                                                 d1b23p1 P:213-312 Elongation factor Tu (EF-Tu), domain 2                                            d1b23p2 P:313-405 Elongation factor Tu (EF-Tu)                                                SCOP domains
               CATH domains 1b23P01 P:1-213 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                 --1b23P02 P:216-307 Translation factors                                                       ---1b23P03 P:311-404 Translation factors                                                         - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeee......hhhhhhhhhhhhhhh........hhhh...hhhhhh......eeeeee...eeeeeee....hhhhhhhhhhhhh..eeeeeee......hhhhhhhhhhhhh...eeeeeee.hhh...hhhhhhhhhhhhhhhhhh........eee..hhhhhhhhhh.........hhhhhhhhhhhhhhhh............eee..eeeee...eeeeeee....eee...eeeee.......eeeeeee........eee...eeeeee............eeee........eeeeeeee..hhh.............eeee..eeeeeeee............eeeeeeee..........eeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------G_TR_1          --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b23 P   1 AKGEFIRTKPHVNVGTIGHVDHGKTTLTAALTYVAAAENPNVEVKDYGDIDKAPEERARGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALLALEEMHKNPKTKRGENEWVDKIWELLDAIDEYIPTPVRDVDKPFLMPVEDVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRKTVVTGVEMHRKTLQEGIAGDNVGLLLRGVSREEVERGQVLAKPGSITPHTKFEASVYILKKEEGGRHTGFFTGYRPQFYFRTTDVTGVVRLPQGVEMVMPGDNVTFTVELIKPVALEEGLRFAIREGGRTVGAGVVTKILE 405
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400     


Chain R from PDB  Type:RNA  Length:74
                                                                                                          
                 1b23 R   1 GGCGCGUuAACAAAGCGGuuAUGUAGCGGAuUGCAaAuCCGUCUAGUCCGGuuCGACUCCGGAACGCGCCUCCA  76
                                   |10     || 21        31|    | |41    ||  52 ||     62        72    
                                   8-4SU  16| ||         32-PSU| |     46|     ||                     
                                           18 ||              37-MIA    48     ||                     
                                             20-H2U             39-PSU        54-5MU                  
                                              21-H2U                           55-PSU
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1B23)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain P   (EFTU_THEAQ | Q01698)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0003746    translation elongation factor activity    Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
    GO:0006414    translational elongation    The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        EFTU_THEAQ | Q01698: 1eft 1h1u 1ipm 1ipo 1ipq 1ipr 1ipu 1l1u 1mj1 1ob5 1ttt 1tui

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