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(-) Description

Title :  INTACT ELONGATION FACTOR TU IN COMPLEX WITH GDP
 
Authors :  G. Polekhina, S. Thirup, M. Kjeldgaard, P. Nissen, C. Lippmann, J. Nyborg
Date :  23 May 96  (Deposition) - 05 Jun 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Elongation Factor, Protein Biosynthesis, Gtp-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Polekhina, S. Thirup, M. Kjeldgaard, P. Nissen, C. Lippmann, J. Nyborg
Helix Unwinding In The Effector Region Of Elongation Factor Ef-Tu-Gdp.
Structure V. 4 1141 1996
PubMed-ID: 8939739  |  Reference-DOI: 10.1016/S0969-2126(96)00122-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ELONGATION FACTOR TU
    Chains: A, B, C
    Organism Scientific: THERMUS AQUATICUS
    Organism Taxid: 271
    Strain: YT-1

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1GDP3Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG3Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:25 , ASP A:81 , CYS A:82 , GDP A:407 , HOH A:419BINDING SITE FOR RESIDUE MG A 408
2AC2SOFTWARETHR B:25 , CYS B:82 , GDP B:407 , HOH B:419BINDING SITE FOR RESIDUE MG B 408
3AC3SOFTWARETHR C:25 , CYS C:82 , GDP C:407 , HOH C:419BINDING SITE FOR RESIDUE MG C 408
4AC4SOFTWAREASP A:21 , GLY A:23 , LYS A:24 , THR A:25 , THR A:26 , TYR A:47 , ASN A:136 , LYS A:137 , ASP A:139 , SER A:174 , ALA A:175 , LEU A:176 , MG A:408 , HOH A:419 , MET B:140 , LEU B:176 , GDP B:407BINDING SITE FOR RESIDUE GDP A 407
5AC5SOFTWAREMET A:140 , LEU A:176 , GDP A:407 , ASP B:21 , HIS B:22 , GLY B:23 , LYS B:24 , THR B:25 , THR B:26 , TYR B:47 , ASN B:136 , LYS B:137 , ASP B:139 , SER B:174 , ALA B:175 , LEU B:176 , MG B:408 , HOH B:419BINDING SITE FOR RESIDUE GDP B 407
6AC6SOFTWAREASP C:21 , HIS C:22 , GLY C:23 , LYS C:24 , THR C:25 , THR C:26 , TYR C:47 , ASN C:136 , LYS C:137 , ASP C:139 , MET C:140 , SER C:174 , ALA C:175 , LEU C:176 , MG C:408 , HOH C:419BINDING SITE FOR RESIDUE GDP C 407

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_TR_1PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature.EFTU_THEAQ52-67
 
 		  3A:51-66
B:51-66
C:51-66

(-) Exons   (0, 0)

(no "Exon" information available for 1TUI)

(-) 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 A from PDB  Type:PROTEIN  Length:397
 aligned with EFTU_THEAQ | Q01698 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:397
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       
           EFTU_THEAQ    10 KPHVNVGTIGHVDHGKTTLTAALTYVAAAENPNVEVKDYGDIDKAPEERARGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALLALEEMHKNPKTKRGENEWVDKIWELLDAIDEYIPTPVRDVDKPFLMPVEDVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRKTVVTGVEMHRKTLQEGIAGDNVGLLLRGVSREEVERGQVLAKPGSITPHTKFEASVYILKKEEGGRHTGFFTGYRPQFYFRTTDVTGVVRLPQGVEMVMPGDNVTFTVELIKPVALEEGLRFAIREGGRTVGAGVVTKILE 406
               SCOP domains d1tuia3 A:9-212 Elongation factor Tu (EF-Tu), N-terminal (G) domain                                                                                                                                         d1tuia1 A:213-313 Elongation factor Tu (EF-Tu), domain 2                                             d1tuia2 A:314-405 Elongation factor Tu (EF-Tu)                                               SCOP domains
               CATH domains 1tuiA01 A:9-213 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                         --1tuiA02 A:216-307 Translation factors                                                       ---1tuiA03 A:311-404 Translation factors                                                         - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee........hhhhhhhhhhhhhhh........hhhhh..............eeeeee....eeeeee...hhhhhhhhhh.......eeeeee......hhhhhhhhhhhhh....eeeeee.hhh...hhhhhhhhhhhhhhhhh.........eee..hhhhhhhhhh.........hhhhhhhhhhhhhhhh......hhh...eee..eeeee...eeeeeee....eee...eeeee......eeee............eee...eeeeee............eeee....eee.eeeeeeee..................eeee..eeeeeeeee...........eeeeeeee...eee....eeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------G_TR_1          --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tui A   9 KPHVNVGTIGHVDHGKTTLTAALTYVAAAENPNVEVKDYGDIDKAPEERARGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALLALEEMHKNPKTKRGENEWVDKIWELLDAIDEYIPTPVRDVDKPFLMPVEDVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRKTVVTGVEMHRKTLQEGIAGDNVGLLLRGVSREEVERGQVLAKPGSITPHTKFEASVYILKKEEGGRHTGFFTGYRPQFYFRTTDVTGVVRLPQGVEMVMPGDNVTFTVELIKPVALEEGLRFAIREGGRTVGAGVVTKILE 405
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       


Chain B from PDB  Type:PROTEIN  Length:397
 aligned with EFTU_THEAQ | Q01698 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:397
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       
           EFTU_THEAQ    10 KPHVNVGTIGHVDHGKTTLTAALTYVAAAENPNVEVKDYGDIDKAPEERARGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALLALEEMHKNPKTKRGENEWVDKIWELLDAIDEYIPTPVRDVDKPFLMPVEDVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRKTVVTGVEMHRKTLQEGIAGDNVGLLLRGVSREEVERGQVLAKPGSITPHTKFEASVYILKKEEGGRHTGFFTGYRPQFYFRTTDVTGVVRLPQGVEMVMPGDNVTFTVELIKPVALEEGLRFAIREGGRTVGAGVVTKILE 406
               SCOP domains d1tuib3 B:9-212 Elongation factor Tu (EF-Tu), N-terminal (G) domain                                                                                                                                         d1tuib1 B:213-312 Elongation factor Tu (EF-Tu), domain 2                                            d1tuib2 B:313-405 Elongation factor Tu (EF-Tu)                                                SCOP domains
               CATH domains 1tuiB01 B:9-213 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                         --1tuiB02 B:216-307 Translation factors                                                       ---1tuiB03 B:311-404 Translation factors                                                         - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee........hhhhhhhhhhhhhhhh.......hhhhh..............eeeeee....eeeeee...hhhhhhhhhh.......eeeeee......hhhhhhhhhhhhh....eeeeee.hhh...hhhhhhhhhhhhhhhhh.........eee..hhhhhhhhhh.........hhhhhhhhhhhhhhhh......hhh...eee..eeeee...eeeeeee....eee...eeeee......eeee............eee...eeeeee............eeee....eee.eeeeeeee..hhh.............eeee..eeeeeeeee...........eeeeeeee...eee....eeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------G_TR_1          --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tui B   9 KPHVNVGTIGHVDHGKTTLTAALTYVAAAENPNVEVKDYGDIDKAPEERARGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALLALEEMHKNPKTKRGENEWVDKIWELLDAIDEYIPTPVRDVDKPFLMPVEDVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRKTVVTGVEMHRKTLQEGIAGDNVGLLLRGVSREEVERGQVLAKPGSITPHTKFEASVYILKKEEGGRHTGFFTGYRPQFYFRTTDVTGVVRLPQGVEMVMPGDNVTFTVELIKPVALEEGLRFAIREGGRTVGAGVVTKILE 405
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       


Chain C from PDB  Type:PROTEIN  Length:397
 aligned with EFTU_THEAQ | Q01698 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:397
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       
           EFTU_THEAQ    10 KPHVNVGTIGHVDHGKTTLTAALTYVAAAENPNVEVKDYGDIDKAPEERARGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALLALEEMHKNPKTKRGENEWVDKIWELLDAIDEYIPTPVRDVDKPFLMPVEDVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRKTVVTGVEMHRKTLQEGIAGDNVGLLLRGVSREEVERGQVLAKPGSITPHTKFEASVYILKKEEGGRHTGFFTGYRPQFYFRTTDVTGVVRLPQGVEMVMPGDNVTFTVELIKPVALEEGLRFAIREGGRTVGAGVVTKILE 406
               SCOP domains d1tuic3 C:9-212 Elongation factor Tu (EF-Tu), N-terminal (G) domain                                                                                                                                         d1tuic1 C:213-312 Elongation factor Tu (EF-Tu), domain 2                                            d1tuic2 C:313-405 Elongation factor Tu (EF-Tu)                                                SCOP domains
               CATH domains 1tuiC01 C:9-213 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                         --1tuiC02 C:216-307 Translation factors                                                       ---1tuiC03 C:311-404 Translation factors                                                         - CATH domains
           Pfam domains (1) GTP_EFTU-1tuiC01 C:9-212                                                                                                                                                                                    ----------------------GTP_EFTU_D2-1tuiC04 C:235-305                                          ---GTP_EFTU_D3-1tuiC07 C:309-404                                                                   - Pfam domains (1)
           Pfam domains (2) GTP_EFTU-1tuiC02 C:9-212                                                                                                                                                                                    ----------------------GTP_EFTU_D2-1tuiC05 C:235-305                                          ---GTP_EFTU_D3-1tuiC08 C:309-404                                                                   - Pfam domains (2)
           Pfam domains (3) GTP_EFTU-1tuiC03 C:9-212                                                                                                                                                                                    ----------------------GTP_EFTU_D2-1tuiC06 C:235-305                                          ---GTP_EFTU_D3-1tuiC09 C:309-404                                                                   - Pfam domains (3)
         Sec.struct. author ..eeeee........hhhhhhhhhhhhhhhh.......hhhhh..............eeeeee....eeeeee...hhhhhhhhhh.......eeeeee......hhhhhhhhhhhhh....eeeeee.hhh...hhhhhhhhhhhhhhhhh.........eee..hhhhhhhhhh.........hhhhhhhhhhhhhhhh......hhh...eee..eeeee...eeeeeee....eee...eeeee......eeee............eee...eeeeee............eeee....eee.eeeeeeee..................eeee..eeeeeeeee...........eeeeeeee...eee....eeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------G_TR_1          --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tui C   9 KPHVNVGTIGHVDHGKTTLTAALTYVAAAENPNVEVKDYGDIDKAPEERARGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALLALEEMHKNPKTKRGENEWVDKIWELLDAIDEYIPTPVRDVDKPFLMPVEDVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRKTVVTGVEMHRKTLQEGIAGDNVGLLLRGVSREEVERGQVLAKPGSITPHTKFEASVYILKKEEGGRHTGFFTGYRPQFYFRTTDVTGVVRLPQGVEMVMPGDNVTFTVELIKPVALEEGLRFAIREGGRTVGAGVVTKILE 405
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398
   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, 9)

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

(-) CATH Domains  (2, 9)

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

(-) Pfam Domains  (3, 9)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Clan: no clan defined [family: GTP_EFTU_D2] (39)
(-)
Clan: no clan defined [family: GTP_EFTU_D3] (11)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (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: 1b23 1eft 1h1u 1ipm 1ipo 1ipq 1ipr 1ipu 1l1u 1mj1 1ob5 1ttt

(-) Related Entries Specified in the PDB File

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