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(-) Description

Title :  EF-TU COMPLEXED WITH A GTP ANALOG AND THE ANTIBIOTIC GE2270 A
 
Authors :  A. Parmeggiani, I. M. Krab, S. Okamura, R. C. Nielsen, J. Nyborg, P. Nis
Date :  18 Nov 05  (Deposition) - 16 Mar 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase-Antibiotic Complex, Thiopeptide, Antibiotic, Antibacterial, Thiazole, Oxazole, Hydrolase, Gtpase, Translation Elongation Factor, Protein Synthesis, Nucleotide-Binding, Phosphorylation (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-B
    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-B
 
Molecule 2 - THIOCILLIN GE2270
    Chains: B
    Organism Scientific: PLANOBISPORA ROSEA
    Organism Taxid: 35762
    Synonym: GE22700A

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (10, 13)

Asymmetric/Biological Unit (10, 13)
No.NameCountTypeFull Name
1BB61Mod. Amino Acid(2Z)-2-AMINO-3-SULFANYLBUT-2-ENOIC ACID
2BB71Mod. Amino Acid(2Z)-2-AMINO-4-METHOXY-3-SULFANYLBUT-2-ENOICACID
3BB81Mod. Amino Acid(2S,3S)-BETA-HYDROXY-PHENYLALANINE
4BB94Mod. Amino Acid(2Z)-2-AMINO-3-SULFANYLPROP-2-ENOIC ACID
5GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
6MEN1Mod. Amino AcidN-METHYL ASPARAGINE
7MG1Ligand/IonMAGNESIUM ION
8MH61Mod. Amino Acid3-HYDROXY-2-IMINOPROPANOIC ACID
9NH21Mod. Amino AcidAMINO GROUP
10PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL 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:2015 , HOH A:2042 , HOH A:2057 , HOH A:2082 , HOH A:2359 , HOH A:2360 , HOH A:2361 , HOH A:2362BINDING SITE FOR RESIDUE GNP A1406
2AC2SOFTWARETHR A:25 , THR A:62 , GNP A:1406 , HOH A:2042 , HOH A:2082BINDING SITE FOR RESIDUE MG A1407
3AC3SOFTWAREASP A:143 , GLU A:145 , LEU A:146 , LEU A:149 , THR A:230 , THR A:236 , VAL A:293 , SER A:294 , ARG A:295 , HOH A:2256 , HOH A:2257 , HOH A:2363BINDING SITE FOR RESIDUE PEG A1409
4AC4SOFTWARESER B:13 , PRO B:14BINDING SITE FOR RESIDUE NH2 B 15
5AC5SOFTWAREGLU A:4 , PHE A:5 , HIS A:67 , VAL A:68 , SER A:78 , GLN A:98 , GLU A:226 , ASP A:227 , PHE A:229 , ARG A:234 , THR A:239 , THR A:268 , GLY A:269 , GLU A:271 , HIS A:273 , ARG A:274 , ASN A:285 , VAL A:286 , GLY A:287 , LEU A:289 , HOH A:2236 , HOH A:2248 , NH2 B:15 , HOH B:2003 , HOH B:2004 , HOH B:2005 , HOH B:2006BINDING SITE FOR CHAIN B OF THIOCILLIN GE2270

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C77)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2C77)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C77)

(-) 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_THET852-67  1A:51-66

(-) Exons   (0, 0)

(no "Exon" information available for 2C77)

(-) 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:404
 aligned with EFTU2_THET8 | P60339 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:404
                                    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    
          EFTU2_THET8     3 KGEFIRTKPHVNVGTIGHVDHGKTTLTAALTFVTAAENPNVEVKDYGDIDKAPEERARGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALLALEQMHRNPKTRRGENEWVDKIWELLDAIDEYIPTPVRDVDKPFLMPVEDVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRKTVVTGVEMHRKTLQEGIAGDNVGVLLRGVSREEVERGQVLAKPGSITPHTKFEASVYVLKKEEGGRHTGFFSGYRPQFYFRTTDVTGVVQLPPGVEMVMPGDNVTFTVELIKPVALEEGLRFAIREGGRTVGAGVVTKILE 406
               SCOP domains d2c77a3 A:2-212 automated matches                                                                                                                                                                                  d2c77a1 A:213-312 automated matches                                                                 d2c77a2 A:313-405 automated matches                                                           SCOP domains
               CATH domains 2c77A01 A:2-213 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                --2c77A02 A:216-307 Translation factors                                                       ---2c77A03 A:311-404 Translation factors                                                         - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeee.....hhhhhhhhhhhhhhhhh......hhhhhh.hhhhhhhh.....eeeeee....eeeeee...hhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhh...eeeeeehhhhh.hhhhhhhhhhhhhhhhhhh........eee.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh...........eee..eeeee...eeeeeee....ee....eeeee......eeeeeeeeee..ee...ee...eeeeee...hhhhh....eee.....eeeeeeeeeeee.hhhhh.....ee.....eeee..eeeeeeee......ee....eeeeeeeeeeeeee....eeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------G_TR_1          --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c77 A   2 KGEFIRTKPHVNVGTIGHVDHGKTTLTAALTYVTAAENPNVEVKDYGDIDKAPEERARGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALLALEQMHRNPKTRRGENEWVDKIWELLDAIDEYIPTPVRDVDKPFLMPVEDVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRKTVVTGVEMHRKTLQEGIAGDNVGVLLRGVSREEVERGQVLAKPGSITPHTKFEASVYVLKKEEGGRHTGFFSGYRPQFYFRTTDVTGVVQLPPGVEMVMPGDNVTFTVELIKPVALEEGLRFAIREGGRTVGAGVVTKILE 405
                                    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       401    


Chain B from PDB  Type:PROTEIN  Length:15
 aligned with THCL_PLARO | Q7M0J8 from UniProtKB/Swiss-Prot  Length:14

    Alignment length:15
                                        14 
                                    10   | 
           THCL_PLARO     1 SCNCVCGFCCSCSP-   -
               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
                 2c77 B   1 ScncVcGfccscSPx  15
                             ||| | |10||  |
                             2-BB9 |||||  |
                              3-MEN|||||  |
                               4-BB6||||  |
                                 6-BB7||  |
                                   8-BB8  |
                                    9-BB9 |
                                    10-BB9|
                                     11-MH6
                                      12-BB9
   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 2C77)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (EFTU2_THET8 | P60339)
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.

Chain B   (THCL_PLARO | Q7M0J8)
biological process
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        EFTU2_THET8 | P60339: 1ha3 2p8w 2p8x 2p8z 3dwu 4v5l 4v68
        THCL_PLARO | Q7M0J8: 1d8t 3u2q 3u6b 3u6k

(-) Related Entries Specified in the PDB File

1d8t CRYSTAL STRUCTURE OF THE ELONGATION FACTOR EF-TU-MGGDP COMPLEXED WITH THE THIOPEPTIDE GE2270A.
1e9w CRYSTAL STRUCTURE OF THIOPEPTIDE THIOSTREPTON
1oln SOLUTION STRUCTURE OF THIOPEPTIDE THIOSTREPTON BINDING TO L11 SUBSTRATE FROM 50S RIBOSOMAL RNA
2c78 CRYSTAL STRUCTUE OF EF-TU COMPLEXED WITH A GTP ANALOG AND THE ANTIBIOTIC PULVOMYCIN
2jq7 SOLUTION STRUCTURE OF THE COMPLEX OF THIOPEPTIDE THIOSTREPTON AND RIBOSOMAL L11-RNA
2zjp CRYSTAL STRUCTURE OF NOSIHEPTIDE COMPLEXED WITH THE LARGE RIBOSOMAL SUBUNIT OF DEINOCOCCUS RADIODURANS
3cf5 CRYSTAL STRUCTURE OF RIBOSOMAL L11-RNA COMPLEXED WITH THE THIOPEPTIDE THIOSTREPTON