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(-) Description

Title :  CRYSTAL STRUCTURE OF THE T84A MUTANT EF-G:GDPCP COMPLEX
 
Authors :  S. Hansson, D. T. Logan
Date :  12 Oct 06  (Deposition) - 23 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Elongation Factor, Nucleotide-Binding, P-Loop, Thr84Ala, Mutation, Gtp-Binding, Translation, Nucleotide- Binding, Protein Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Hansson, D. T. Logan
New Insights Into The Role Of The P-Loop Lysine: Implications From The Crystal Structure Of A Mutant Ef-G:Gdpcp Complex
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ELONGATION FACTOR G
    Chains: A
    EC Number: 3.6.1.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Mutation: YES
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: RIBOSOMAL TRANSLOCASE, EF-G

 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
1GCP1Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:21 , ASP A:22 , GLY A:24 , LYS A:25 , THR A:26 , THR A:27 , ASN A:137 , LYS A:138 , ASP A:140 , SER A:262 , ALA A:263 , LEU A:264 , TYR A:342 , ARG A:396 , MG A:950BINDING SITE FOR RESIDUE GCP A 900
2AC2SOFTWARETHR A:26 , GLU A:295 , GCP A:900BINDING SITE FOR RESIDUE MG A 950

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J7K)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:85 -Gly A:86

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J7K)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_TR_1PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature.EFG_THETH53-68  1A:65-68

(-) Exons   (0, 0)

(no "Exon" information available for 2J7K)

(-) 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:660
 aligned with EFG_THETH | P13551 from UniProtKB/Swiss-Prot  Length:691

    Alignment length:684
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684    
            EFG_THETH     5 VEYDLKRLRNIGIAAHIDAGKTTTTERILYYTGRIHKIGEVHEGAATMDFMEQERERGITITAAVTTCFWKDHRINIIDTPGHVDFTIEVERSMRVLDGAIVVFDSSQGVEPQSETVWRQAEKYKVPRIAFANKMDKTGADLWLVIRTMQERLGARPVVMQLPIGREDTFSGIIDVLRMKAYTYGNDLGTDIREIPIPEEYLDQAREYHEKLVEVAADFDENIMLKYLEGEEPTEEELVAAIRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDPNGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREEVEELKAGDLGAVVGLKETITGDTLVGEDAPRVILESIEVPEPVIDVAIEPKTKADQEKLSQALARLAEEDPTFRVSTHPETGQTIISGMGELHLEIIVDRLKREFKVDANVGKPQVAYRETITKPVDVEGKFIRQTGGRGQYGHVKIKVEPLPRGSGFEFVNAIVGGVIPKEYIPAVQKGIEEAMQSGPLIGFPVVDIKVTLYDGSYHEVDSSEMAFKIAGSMAIKEAVQKGDPVILEPIMRVEVTTPEEYMGDVIGDLNARRGQILGMEPRGNAQVIRAFVPLAEMFGYATDLRSKTQGRGSFVMFFDHYQEVPKQVQEKLI 688
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2j7kA01 A:5-286 P-loop containing nu                        cleotide triphosphate hydrolases                                                                                                                                                                                              ----------------2j7kA02 A:303-405 Translation factors                                                                  ---------------------------2j7kA03 A:433-483                                  2j7kA04 A:484-602  [code=3.30.230.10, no name defined]                                                                 2j7kA05 A:603-684  [code=3.30.70.240, no name defined]                            ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeeeee....hhhhhhhhhhhhhh...------------------------....eeeeee..eeeeee.........hhhhhhhhhh.eeeeeee.......hhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhh....eee.eeee.......eeee....eeeee.......eeee..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhh.........eee.....eee.........eeeeeeeeee...eeeeeeeeee..ee..eeeee....eeeeeeeeeee.........ee....eeeeee........eee..................eeeeeee..hhhhhhhhhhhhh........eee........eeee.hhhhhhhhhhhhhh.....eee...ee..eee....eeeeeeeeeee..eeeeeeeeeeeee......eeeee.........hhhhhhhhhhhhhh............eeeeeeeee......hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee...hhhhhhhhh....eeeeeeee..eeeeeeeee.hhh.hhhhhhhhh.....eeeeeeeeeee.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------G_TR_1          -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2j7k A   5 VEYDLKRLRNIGIAAHIDAGKTTTTERILYYTGRIH------------------------ITAAVTTCFWKDHRINIIDAPGHVDFTIEVERSMRVLDGAIVVFDSSQGVEPQSETVWRQAEKYKVPRIAFANKMDKTGADLWLVIRTMQERLGARPVVMQLPIGREDTFSGIIDVLRMKAYTYGNDLGTDIREIPIPEEYLDQAREYHEKLVEVAADFDENIMLKYLEGEEPTEEELVAAIRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDPNGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREEVEELKAGDLGAVVGLKETITGDTLVGEDAPRVILESIEVPEPVIDVAIEPKTKADQEKLSQALARLAEEDPTFRVSTHPETGQTIISGMGELHLEIIVDRLKREFKVDANVGKPQVAYRETITKPVDVEGKFIRQTGGRGQYGHVKIKVEPLPRGSGFEFVNAIVGGVIPKEYIPAVQKGIEEAMQSGPLIGFPVVDIKVTLYDGSYHEVDSSEMAFKIAGSMAIKEAVQKGDPVILEPIMRVEVTTPEEYMGDVIGDLNARRGQILGMEPRGNAQVIRAFVPLAEMFGYATDLRSKTQGRGSFVMFFDHYQEVPKQVQEKLI 688
                                    14        24        34     |   -         -         -|       74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684    
                                                              40                       65
   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  (0, 0)

(no "SCOP Domain" information available for 2J7K)

(-) CATH Domains  (5, 5)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J7K)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (EFG_THETH | P13551)
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
        EFG_THETH | P13551: 1efg 1fnm 1ip8 1ipm 1ipo 1ipr 1jqm 1jqs 1ktv 1pn6 2bcw 2bm0 2bm1 2bv3 2efg 2om7 3izp 4m1k 4myt 4myu

(-) Related Entries Specified in the PDB File

1fnm STRUCTURE OF THERMUS THERMOPHILUS EF-G H573A
1ip8 RIBOSOMAL RNAS AND PROTEINS AS WELL AS FACTORS IN THE PRE-TRANSLOCATIONAL STATE
1ipm RIBOSOMAL RNAS AND PROTEINS AS WELL AS FACTORS
1ipo RIBOSOMAL RNAS AND PROTEINS AS WELL AS FACTORS
1ipr RIBOSOMAL RNAS AND PROTEINS AS WELL AS FACTORS
1jqm FITTING OF L11 PROTEIN AND ELONGATION FACTOR G (EF-G) INTHE CRYO-EM MAP OF E. COLI 70S RIBOSOME BOUND WITH EF-G,GDP AND FUSIDIC ACID
1jqs FITTING OF L11 PROTEIN AND ELONGATION FACTOR G (DOMAIN G'AND V) IN THE CRYO-EM MAP OF E. COLI 70S RIBOSOME BOUNDWITH EF- G AND GMPPCP, A NONHYDROLYSABLE GTP ANALOG
1ktv CRYSTAL STRUCTURE OF ELONGATION FACTOR G DIMER WITHOUTNUCLEOTIDE
1pn6 DOMAIN-WISE FITTING OF THE CRYSTAL STRUCTURE OFT.THERMOPHILUS EF-G INTO THE LOW RESOLUTION MAP OF THERELEASE COMPLEX.PUROMYCIN .EFG.GDPNP OF E.COLI 70S RIBOSOME.
2bcw COORDINATES OF THE N-TERMINAL DOMAIN OF RIBOSOMAL PROTEINL11,C-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L7/L12 AND APORTION OF THE G' DOMAIN OF ELONGATION FACTOR G, AS FITTEDINTO CRYO-EM MAP OF AN ESCHERICHIA COLI 70S*EF-G*GDP*FUSIDIC ACID COMPLEX
2bm0 RIBOSOMAL ELONGATION FACTOR G (EF-G) FUSIDIC ACID RESISTANT MUTANT T84A.
2bm1 RIBOSOMAL ELONGATION FACTOR G (EF-G) FUSIDIC ACID RESISTANT MUTANT G16V
2bv3 CRYSTAL STRUCTURE OF A MUTANT ELONGATION FACTOR G TRAPPED WITH A GTP ANALOGUE