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(-) Description

Title :  RIBOSOMAL ELONGATION FACTOR G (EF-G) FUSIDIC ACID RESISTANT MUTANT G16V
 
Authors :  S. Hansson, R. Singh, A. T. Gudkov, A. Liljas, D. T. Logan
Date :  09 Mar 05  (Deposition) - 04 May 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Switch Ii, Elongation Factor, Gtp-Binding, Mutation Gly16Val, Protein Biosynthesis, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Hansson, R. Singh, A. T. Gudkov, A. Liljas, D. T. Logan
Structural Insights Into Fusidic Acid Resistance And Sensitivity In Ef-G
J. Mol. Biol. V. 348 939 2005
PubMed-ID: 15843024  |  Reference-DOI: 10.1016/J.JMB.2005.02.066
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ELONGATION FACTOR G
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET13A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Mutation: YES
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Synonym: 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
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:26 , GLU A:295 , GDP A:1689 , HOH A:2034 , HOH A:2060BINDING SITE FOR RESIDUE MG A1690
2AC2SOFTWAREASP A:22 , ALA A:23 , GLY A:24 , LYS A:25 , THR A:26 , THR A:27 , ASN A:137 , LYS A:138 , ASP A:140 , LYS A:141 , SER A:262 , ALA A:263 , LEU A:264 , PRO A:294 , GLU A:295 , TYR A:342 , GLY A:347 , MG A:1690 , HOH A:2034 , HOH A:2060 , HOH A:2061 , HOH A:2062BINDING SITE FOR RESIDUE GDP A1689

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BM1)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:4 -Val A:5

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BM1)

(-) 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 2BM1)

(-) 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:685
                                    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       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683     
            EFG_THETH     4 KVEYDLKRLRNIGIAAHIDAGKTTTTERILYYTGRIHKIGEVHEGAATMDFMEQERERGITITAAVTTCFWKDHRINIIDTPGHVDFTIEVERSMRVLDGAIVVFDSSQGVEPQSETVWRQAEKYKVPRIAFANKMDKTGADLWLVIRTMQERLGARPVVMQLPIGREDTFSGIIDVLRMKAYTYGNDLGTDIREIPIPEEYLDQAREYHEKLVEVAADFDENIMLKYLEGEEPTEEELVAAIRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDPNGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREEVEELKAGDLGAVVGLKETITGDTLVGEDAPRVILESIEVPEPVIDVAIEPKTKADQEKLSQALARLAEEDPTFRVSTHPETGQTIISGMGELHLEIIVDRLKREFKVDANVGKPQVAYRETITKPVDVEGKFIRQTGGRGQYGHVKIKVEPLPRGSGFEFVNAIVGGVIPKEYIPAVQKGIEEAMQSGPLIGFPVVDIKVTLYDGSYHEVDSSEMAFKIAGSMAIKEAVQKGDPVILEPIMRVEVTTPEEYMGDVIGDLNARRGQILGMEPRGNAQVIRAFVPLAEMFGYATDLRSKTQGRGSFVMFFDHYQEVPKQVQEKLI 688
               SCOP domains d2bm1a2 A:4-282 Elongation factor G                          (EF-G), N-terminal (G) domain                                                                                                                                                                                             d2bm1a1 A:283-403 Elongation factor G (EF-G), domain II                                                                  d2bm1a4 A:404-478 Elongation factor G (EF-G)                               d2bm1a3 A:479-599 Elongation factor G (EF-G), domain IV                                                                  d2bm1a5 A:600-688 Elongation factor G (EF-G)                                              SCOP domains
               CATH domains 2bm1A01 A:4-286 P-loop containing nu                         cleotide triphosphate hydrolases                                                                                                                                                                                              ----------------2bm1A02 A:303-405 Translation factors                                                                  ---------------------------2bm1A03 A:433-483                                  2bm1A04 A:484-602  [code=3.30.230.10, no name defined]                                                                 2bm1A05 A:603-684  [code=3.30.70.240, no name defined]                            ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eeeeeeee....hhhhhhhhhhhhhhh.-------------------------....eeeeee..eeeeee.........hhhhhhhhhh.eeeeeee.......hhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhh..eee.eeee.hhhhh.eeee....eeeee.......eeee..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhh.hhhhh...eee.....eee.........eeeeeeee.......eeeeeeee.eee...eeee....eeeeeeeeeee.........eee...eeeeee........eee..................eeeee..........hhhhh.hhhhh....eee.......eeee..hhhhhhhhhhhh............eee..eee....eeeeeeeeee....eeeeeeeeeeee......eeeee..........hhhhhhhhhhhhhh...........eeeeeeeee......hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee..hhhhhhhhhhhhh..eeeeeee..eeeeeeeee.hhhh.hhhhhh...........eeeeeee.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------G_TR_1          -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bm1 A   4 KVEYDLKRLRNIVIAAHIDAGKTTTTERILYYTGRI-------------------------ITAAVTTCFWKDHRINIIDTPGHVDFTIEVERSMRVLDGAIVVFDSSQGVEPQSETVWRQAEKYKVPRIAFANKMDKTGADLWLVIRTMQERLGARPVVMQLPIGREDTFSGIIDVLRMKAYTYGNDLGTDIREIPIPEEYLDQAREYHEKLVEVAADFDENIMLKYLEGEEPTEEELVAAIRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDPNGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREEVEELKAGDLGAVVGLKETITGDTLVGEDAPRVILESIEVPEPVIDVAIEPKTKADQEKLSQALARLAEEDPTFRVSTHPETGQTIISGMGELHLEIIVDRLKREFKVDANVGKPQVAYRETITKPVDVEGKFIRQTGGRGQYGHVKIKVEPLPRGSGFEFVNAIVGGVIPKEYIPAVQKGIEEAMQSGPLIGFPVVDIKVTLYDGSYHEVDSSEMAFKIAGSMAIKEAVQKGDPVILEPIMRVEVTTPEEYMGDVIGDLNARRGQILGMEPRGNAQVIRAFVPLAEMFGYATDLRSKTQGRGSFVMFFDHYQEVPKQVQEKLI 688
                                    13        23        33     |   -         -         - |      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       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683     
                                                              39                        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  (4, 5)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) 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 2BM1)

(-) 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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  2bm1
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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 2bv3 2efg 2j7k 2om7 3izp 4m1k 4myt 4myu

(-) Related Entries Specified in the PDB File

1dar ELONGATION FACTOR G IN COMPLEX WITH GDP
1efg ELONGATION FACTOR G COMPLEXED WITH GUANOSINE 5'-DIPHOSPHATE
1elo ELONGATION FACTOR G WITHOUT NUCLEOTIDE
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.
2bm0 RIBOSOMAL ELONGATION FACTOR G (EF-G) FUSIDIC ACID RESISTANT MUTANT T84A
2efg TRANSLATIONAL ELONGATION FACTOR G COMPLEXED WITH GDP