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(-) Description

Title :  CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS ELONGATION FACTOR TU (EF-TU) IN COMPLEX WITH THE GTP ANALOGUE GPPNHP.
 
Authors :  T. Hogg, J. R. Mesters, R. Hilgenfeld
Date :  03 May 00  (Deposition) - 07 Jun 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Gtpase, Molecular Switch, Trna, Ribosome, Q-Beta Replicase, Chaperone, Disulfide Isomerase, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Hilgenfeld, J. R. Mesters, T. Hogg
Insights Into The Gtpase Mechanism Of Ef-Tu From Structural Studies
The Ribosome: Structure, V. 28 347 2000 Function, Antibiotics, And Cellular Interactions
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ELONGATION FACTOR TU (EF-TU)
    Chains: A
    Fragment: INTACT WILD-TYPE EF-TU
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Other Details: BINARY COMPLEX WITH GUANOSINE-5'-(BETA, GAMMA-IMIDO) TRIPHOSPHATE (GPPNHP)
    Synonym: EF-TU

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:25 , THR A:62 , GNP A:406 , HOH A:414 , HOH A:417BINDING SITE FOR RESIDUE MG A 407
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 , GLN A:354 , MG A:407 , HOH A:411 , HOH A:414 , HOH A:417 , HOH A:442 , HOH A:473 , HOH A:540 , HOH A:594 , HOH A:612BINDING SITE FOR RESIDUE GNP A 406

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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_THETH52-67  1A:51-66

(-) Exons   (0, 0)

(no "Exon" information available for 1EXM)

(-) 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:403
 aligned with EFTU1_THETH | P60338 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:403
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403   
          EFTU1_THETH     4 GEFVRTKPHVNVGTIGHVDHGKTTLTAALTYVAAAENPNVEVKDYGDIDKAPEERARGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALLALEQMHRNPKTRRGENEWVDKIWELLDAIDEYIPTPVRDVDKPFLMPVEDVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRRTVVTGVEMHRKTLQEGIAGDNVGVLLRGVSREEVERGQVLAKPGSITPHTKFEASVYVLKKEEGGRHTGFFSGYRPQFYFRTTDVTGVVQLPPGVEMVMPGDNVTFTVELIKPVALEEGLRFAIREGGRTVGAGVVTKILE 406
               SCOP domains d1exma3 A:3-212 Elongation factor Tu (EF-Tu), N-terminal (G) domain                                                                                                                                               d1exma1 A:213-312 Elongation factor Tu (EF-Tu), domain 2                                            d1exma2 A:313-405 Elongation factor Tu (EF-Tu)                                                SCOP domains
               CATH domains 1exmA01 A:3-213 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                               --1exmA02 A:216-307 Translation factors                                                       ---1exmA03 A:311-404 Translation factors                                                         - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeee.....hhhhhhhhhhhhhhhhh......hhhhhh.hhhhhhhh.....eeeeee....eeeeee...hhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhh....eeeeeehhhhh.hhhhhhhhhhhhhhhhhhh........eee.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh...........eee..eeeee...eeeeeee....eee...eeeee......eeeeeeeeee..ee..eee...eeeeee............eee.......eeeeeeeeee.hhhhh............eeee..eeeeeeee............eeeeeeeeeeee......eeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------G_TR_1          --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1exm A   3 GEFIRTKPHVNVGTIGHVDHGKTTLTAALTFVTAAENPNVEVKDYGDIDKAPEERARGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALLALEQMHRNPKTRRGENEWVDKIWELLDAIDEYIPTPVRDVDKPFLMPVEDVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRKTVVTGVEMHRKTLQEGIAGDNVGVLLRGVSREEVERGQVLAKPGSITPHTKFEASVYVLKKEEGGRHTGFFSGYRPQFYFRTTDVTGVVQLPPGVEMVMPGDNVTFTVELIKPVALEEGLRFAIREGGRTVGAGVVTKILE 405
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402
   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 1EXM)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (EFTU1_THETH | P60338)
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
        EFTU1_THETH | P60338: 1aip 1ha3 4h9g 4lbv 4lbw 4lby 4lbz 4lc0

(-) Related Entries Specified in the PDB File

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