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(-) Description

Title :  E. COLI ELONGATION FACTOR EF-TU COMPLEXED WITH THE ANTIBIOTIC KIRROMYCIN, A GTP ANALOG, AND PHE-TRNA
 
Authors :  O. Kristensen, P. Nissen, J. Nyborg
Date :  24 Jan 03  (Deposition) - 27 May 04  (Release) - 19 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase/Nuclear Protein, Hydrolase, Gtpase, Translation Elongation Factor, Transfer Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. C. Nielsen, O. Kristensen, M. Kjeldgaard, S. Thirup, P. Nissen
Kirromycin Defines A Specific Domain Arrangement Of Elongation Factor Ef-Tu
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ELONGATION FACTOR TU
    ChainsA
    EC Number3.6.1.48
    Organism ScientificESCHERICHIA COLI
    Organism Taxid511693
    StrainBL21
    SynonymEF-TU, P-43
 
Molecule 2 - TRANSFER-RNA, PHE
    ChainsB
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    Other DetailsAMINO-ACYLATED (PHE) AT THE 3' END
    Other Details - SourceSIGMA-ALDRICH COMPOUND

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (15, 18)

Asymmetric/Biological Unit (15, 18)
No.NameCountTypeFull Name
11MA1Mod. Nucleotide6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE
22MG1Mod. Nucleotide2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
35MC2Mod. Nucleotide5-METHYLCYTIDINE-5'-MONOPHOSPHATE
47MG1Mod. Nucleotide7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE
5GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
6H2U2Mod. Nucleotide5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
7KIR1Ligand/IonKIRROMYCIN
8M2G1Mod. NucleotideN2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE
9MG1Ligand/IonMAGNESIUM ION
10OMC1Mod. NucleotideO2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
11OMG1Mod. NucleotideO2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
12PHA1Mod. Amino AcidPHENYLALANINAL
13PSU2Mod. NucleotidePSEUDOURIDINE-5'-MONOPHOSPHATE
14SUC1Ligand/IonSUCROSE
15YG1Mod. ResidueWYBUTOSINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:120 , ARG A:123 , GLN A:124 , VAL A:125 , TYR A:160 , ASP A:161 , LYS A:313 , ASP A:314 , GLU A:315 , ARG A:333 , ARG A:373 , PHE A:374 , ALA A:375 , ALA A:385BINDING SITE FOR RESIDUE KIR A1394
2AC2SOFTWAREGLU A:3 , PHE A:5 , GLU A:6 , THR A:8 , LYS A:9 , TYR A:39 , GLY A:40 , GLU A:68 , ASP A:70 , HIS A:75 , LYS A:263BINDING SITE FOR RESIDUE SUC A1396
3AC3SOFTWAREVAL A:20 , ASP A:21 , HIS A:22 , GLY A:23 , LYS A:24 , THR A:25 , THR A:26 , PHE A:46 , ILE A:60 , THR A:61 , GLY A:83 , HIS A:84 , ASN A:135 , LYS A:136 , ASP A:138 , MET A:139 , SER A:173 , ALA A:174 , LEU A:175 , MG A:1398BINDING SITE FOR RESIDUE GNP A1397
4AC4SOFTWARETHR A:25 , THR A:61 , GNP A:1397BINDING SITE FOR RESIDUE MG A1398

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OB2)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ile A:199 -Pro A:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OB2)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_TR_1PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature.EFTU2_ECOLI51-66  1A:50-65

(-) Exons   (0, 0)

(no "Exon" information available for 1OB2)

(-) 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:393
 aligned with EFTU2_ECOLI | P0CE48 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:393
                                    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   
          EFTU2_ECOLI     2 SKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLS 394
               SCOP domains d1ob2a3 A:1-204 Elongation factor Tu (EF-Tu), N-terminal (G) domain                                                                                                                                         d1ob2a1 A:205-296 Elongation factor Tu (EF-Tu), domain 2                                    d1ob2a2 A:297-393 Elongation factor Tu (EF-Tu)                                                    SCOP domains
               CATH domains --------1ob2A01 A:9-202 P-loop containing nucleotide triphosphate hydrolases                                                                                                                              --1ob2A02 A:205-299 Translation factors                                                          1ob2A03 A:300-392 Translation factors                                                        - CATH domains
               Pfam domains --------GTP_EFTU-1ob2A01 A:9-201                                                                                                                                                                         ----------------------GTP_EFTU_D2-1ob2A02 A:224-293                                         ---GTP_EFTU_D3-1ob2A03 A:297-392                                                                   - Pfam domains
         Sec.struct. author ..........eeeeeee.....hhhhhhhhhhhhhhhhh.....hhhhhh.hhhhhhhh.....eeeeee....eeeeee...hhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhh....eeeeeehhhhh.hhhhhhhhhhhhhhhhhhhh.......eee.hhhhhhhhhhhhhhhhhhhhhhhhhh............eee..eeee.....eeeeee..........eeeee.....eeee..................eeee.....hhhhh....eee......eeeeeeeeee..hhhhh............eeee..eeeeee..............eeeeeeeeeeeee.....eeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------G_TR_1          ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ob2 A   1 AKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLS 393
                                    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   

Chain B from PDB  Type:PROTEIN/RNA  Length:77
                                                                                                             
               SCOP domains ----------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............................................................................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 1ob2 B   1 GCGGAUUUAgCUCAGuuGGGAGAGCgCCAGAcUgAAgAucUGGAGgUCcUGUGUuCGaUCCACAGAAUUCGCACCAf  77
                                    10     || 20     |  30 | |  | 40     |  50    |  |60        70      |
                                    10-2MG ||       26-M2G | |  | ||     |  |     |  |                 77-PHA
                                          16-H2U          32-OMC| ||     |  |     |  |                   
                                           17-H2U           34-OMG||     |  |     |  |                   
                                                               37-YG     |  |     |  |                   
                                                                 39-PSU  |  |     |  |                   
                                                                  40-5MC |  |     |  |                   
                                                                        46-7MG    |  |                   
                                                                           49-5MC |  |                   
                                                                                 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

(-) CATH Domains  (2, 3)

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

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (EFTU2_ECOLI | P0CE48)
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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0003746    translation elongation factor activity    Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        EFTU2_ECOLI | P0CE481d8t 1dg1 1efc 1efm 1efu 1etu 1ls2 1qzd 2bvn 2hcj 2hdn 3agp 3agq 3avt 3avu 3avv 3avw 3avx 3avy 3ep2 3eq3 3eq4 3mmp 3vnu 3vnv 4fwt 4r71 4v69 4v6k 4v6l 5afi

(-) Related Entries Specified in the PDB File

1d8t CRYSTAL STRUCTURE OF ELONGATION FACTOR, TU ( EF-TU-MGGDP) COMPLEXED WITH GE2270A, A THIAZOLYL PEPTIDE ANTIBIOTIC
1dg1 WHOLE, UNMODIFIED, EF-TU(ELONGATION FACTOR TU).
1efc INTACT ELONGATION FACTOR FROM E.COLI
1efm TRYPSIN-MODIFIED ELONGATION FACTOR TU (EF-TU -GDP)
1efu ELONGATION FACTOR COMPLEX EF-TU/EF-TS FROM ESCHERICHIA COLI
1etu ELONGATION FACTOR TU (DOMAIN I) - GUANOSINE DIPHOSPHATE COMPLEX
1ls2 FITTING OF EF-TU AND TRNA IN THE LOW RESOLUTION CRYO-EM MAPOF AN EF-TU TERNARY COMPLEX (GDP AND KIRROMYCIN) BOUND TOE. COLI 70S RIBOSOME
1qzd EF-TU.KIRROMYCIN COORDINATES FITTED INTO THE CRYO-EM MAP OFEF-TU TERNARY COMPLEX (GDP .KIRROMYCIN) BOUND 70S RIBOSOME