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(-) Description

Title :  EF-TU COMPLEXED WITH A GTP ANALOG AND THE ANTIBIOTIC PULVOMYCIN
 
Authors :  A. Parmeggiani, I. M. Krab, S. Okamura, R. C. Nielsen, J. Nyborg, P. Nissen
Date :  18 Nov 05  (Deposition) - 16 Mar 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Gtpase, Translation Elongation Factor, Protein Synthesis, Antibiotic, Gtp-Binding, Nucleotide-Binding, Phosphorylation, Protein Biosynthesis, Elongation Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Parmeggiani, I. M. Krab, S. Okamura, R. C. Nielsen, J. Nyborg, P. Nissen
Structural Basis Of The Action Of Pulvomycin And Ge2270 A On Elongation Factor Tu.
Biochemistry V. 45 6846 2006
PubMed-ID: 16734421  |  Reference-DOI: 10.1021/BI0525122

(-) Compounds

Molecule 1 - ELONGATION FACTOR TU-A
    Chains: A
    EC Number: 3.1.5.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: DE3
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Other Details: TUFA GENE
    Strain: HB8
    Synonym: ELONGATION FACTOR TU, EF-TU-A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG1Ligand/IonMAGNESIUM ION
3PUL1Ligand/Ion(1S,2S,3E,5E,7E,10S,11S,12S)-12-[(2R,4E,6E,8Z,10R,12E,14E,16Z,18S,19Z)-10,18-DIHYDROXY-12,16,19-TRIMETHYL-11,22-DIOXOOXACYCLODOCOSA-4,6,8,12,14,16,19-HEPTAEN-2-YL]-2,11-DIHYDROXY-1,10-DIMETHYL-9-OXOTRIDECA-3,5,7-TRIEN-1-YL 6-DEOXY-2,4-DI-O-METHYL-BETA-L-GALACTOPYRANOSIDE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:25 , THR A:62 , GNP A:1406 , HOH A:2010 , HOH A:2035BINDING SITE FOR RESIDUE MG A1407
2AC2SOFTWAREVAL A:20 , ASP A:21 , HIS A:22 , GLY A:23 , LYS A:24 , THR A:25 , THR A:26 , TYR A:47 , ILE A:61 , THR A:62 , GLY A:84 , ASN A:136 , LYS A:137 , ASP A:139 , MET A:140 , SER A:174 , ALA A:175 , LEU A:176 , MG A:1407 , HOH A:2010 , HOH A:2035 , HOH A:2046 , HOH A:2113 , HOH A:2319 , HOH A:2320 , HOH A:2321 , HOH A:2322BINDING SITE FOR RESIDUE GNP A1406
3AC3SOFTWAREILE A:89 , THR A:94 , ALA A:97 , GLN A:98 , GLU A:226 , PHE A:229 , GLY A:240 , GLU A:271 , MET A:272 , HIS A:273 , VAL A:286 , ARG A:300 , TYR A:343 , PHE A:344 , ARG A:345 , THR A:346 , ARG A:385 , ALA A:387 , ARG A:389 , HOH A:2324 , HOH A:2325 , HOH A:2326 , HOH A:2327BINDING SITE FOR RESIDUE PUL A1408

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C78)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2C78)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C78)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_TR_1PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature.EFTU1_THET852-67  1A:51-66

(-) Exons   (0, 0)

(no "Exon" information available for 2C78)

(-) 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 EFTU1_THET8 | Q5SHN6 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       
          EFTU1_THET8    10 KPHVNVGTIGHVDHGKTTLTAALTYVAAAENPNVEVKDYGDIDKAPEERARGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALLALEQMHRNPKTRRGENEWVDKIWELLDAIDEYIPTPVRDVDKPFLMPVEDVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRRTVVTGVEMHRKTLQEGIAGDNVGVLLRGVSREEVERGQVLAKPGSITPHTKFEASVYVLKKEEGGRHTGFFSGYRPQFYFRTTDVTGVVQLPPGVEMVMPGDNVTFTVELIKPVALEEGLRFAIREGGRTVGAGVVTKILE 406
               SCOP domains d2c78a3 A:9-212 automated matches                                                                                                                                                                           d2c78a1 A:213-312 automated matches                                                                 d2c78a2 A:313-405 automated matches                                                           SCOP domains
               CATH domains 2c78A01 A:9-213 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                         --2c78A02 A:216-307 Translation factors                                                       ---2c78A03 A:311-404 Translation factors                                                         - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhhhhh.......hhhhhh.hhhhhhhh.....eeeeee....eeeeee...hhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhh....eeeeeehhhhh.hhhhhhhhhhhhhhhhhhh........eee.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh...........eee..eeeee...eeeeeee....eee...eeeee......eeeeeeeeee..eee.eee...eeeeee............eee.....eeeeeeeeeeee.hhhhh............eeee..eeeeeeee............eeeeeeeeeeeeee....eeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------G_TR_1          --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c78 A   9 KPHVNVGTIGHVDHGKTTLTAALTYVAAAENPNVEVKDYGDIDKAPEERARGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALLALEQMHRNPKTRRGENEWVDKIWELLDAIDEYIPTPVRDVDKPFLMPVEDVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRKTVVTGVEMHRKTLQEGIAGDNVGVLLRGVSREEVERGQVLAKPGSITPHTKFEASVYVLKKEEGGRHTGFFSGYRPQFYFRTTDVTGVVQLPPGVEMVMPGDNVTFTVELIKPVALEEGLRFAIREGGRTVGAGVVTKILE 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, 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 2C78)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (EFTU1_THET8 | Q5SHN6)
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:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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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  2c78
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  EFTU1_THET8 | Q5SHN6
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 Related Entries

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

UniProtKB/Swiss-Prot
        EFTU1_THET8 | Q5SHN6: 1ha3 1zc8 4v5g 4v5p 4v5q 4v5r 4v5s 4v8q

(-) Related Entries Specified in the PDB File

1ha3 ELONGATION FACTOR TU IN COMPLEX WITH AURODOX