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(-) Description

Title :  YEAST GUANINE NUCLEOTIDE EXCHANGE FACTOR EEF1BALPHA K205A MUTANT IN COMPLEX WITH EEF1A AND GDP
 
Authors :  Y. R. Pittman, L. Valente, M. G. Jeppesen, G. R. Andersen, S. Patel, T. G. Kinzy
Date :  04 Oct 05  (Deposition) - 02 May 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  G-Protein/Gef Complex, Eef1A, Eef1Balpha, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. R. Pittman, L. Valente, M. G. Jeppesen, G. R. Andersen, S. Patel, T. G. Kinzy
Mg2+ And A Key Lysine Modulate Exchange Activity Of Eukaryotic Translation Elongation Factor 1B Alpha
J. Biol. Chem. V. 281 19457 2006
PubMed-ID: 16675455  |  Reference-DOI: 10.1074/JBC.M601076200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ELONGATION FACTOR 1-ALPHA
    Chains: A
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: EF-1-ALPHA, TRANSLATION ELONGATION FACTOR 1A, EUKARYOTIC ELONGATION FACTOR 1A, EEF1A, ELONGATION FACTOR 1A
 
Molecule 2 - ELONGATION FACTOR-1 BETA
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET11D
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN
    Gene: TEF5
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: EF-1-BETA, TRANSLATION ELONGATION FACTOR 1B ALPHA, EUKARYOTIC ELONGATION FACTOR 1BALPHA, EEF1BALPHA, ELONGATION FACTOR 1BALPHA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:15 , VAL A:16 , ASP A:17 , SER A:18 , GLY A:19 , LYS A:20 , SER A:21 , THR A:22 , ASN A:153 , LYS A:154 , ASP A:156 , SER A:192 , GLY A:193 , TRP A:194 , HOH A:473 , HOH A:531 , HOH A:554 , HOH A:593BINDING SITE FOR RESIDUE GDP A 0

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B7B)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:279 -Pro A:280

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B7B)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_TR_1PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature.EF1A_YEAST61-76  1A:61-76
2EF1BD_2PS00825 Elongation factor 1 beta/beta'/delta chain signature 2.EF1B_YEAST195-206  1B:1195-1206

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YAL003W1YAL003W.1I:142176-14225580EF1B_YEAST1-27270--
1.2YAL003W2YAL003W.2I:142622-143162541EF1B_YEAST27-2061801B:1117-120690
2.2YPR080W2YPR080W.1XVI:700592-7019681377EF1A_YEAST1-4584581A:2-441440

(-) 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:440
 aligned with EF1A_YEAST | P02994 from UniProtKB/Swiss-Prot  Length:458

    Alignment length:440
                                    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       411       421       431       441
          EF1A_YEAST      2 GKEKSHINVVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYQVTVIDAPGHRDFIKNMITGTSQADCAILIIAGGVGEFEAGISKDGQTREHALLAFTLGVRQLIVAVNKMDSVKWDESRFQEIVKETSNFIKKVGYNPKTVPFVPISGWNGDNMIEATTNAPWYKGWEKETKAGVVKGKTLLEAIDAIEQPSRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMVVTFAPAGVTTEVKSVEMHHEQLEQGVPGDNVGFNVKNVSVKEIRRGNVCGDAKNDPPKGCASFNATVIVLNHPGQISAGYSPVLDCHTAHIACRFDELLEKNDRRSGKKLEDHPKFLKSGDAALVKFVPSKPMCVEAFSEYPPLGRFAVRDMRQTVAVGVIKSVDK  441
               SCOP domains d2b7ba3 A:2-240 Elongation factor eEF-1alpha, N-terminal (G) domain                                                                                                                                                                            d2b7ba1 A:241-334 Elongation factor eEF-1alpha, domain 2                                      d2b7ba2 A:335-441 Elongation factor eEF-1alpha, C-terminal domain                                           SCOP domains
               CATH domains 2b7bA01 A:2-236 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                       --2b7bA02 A:239-327 Translation factors                                                    -----2b7bA03 A:333-440 Translation factors                                                                       - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.......eeee...eeeeeee.....hhhhhhhhh.....eeeeeee.hhhhhhhhh...hhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhhhhh.hhhhh.eee.....................eeeee..eeeee.hhhhhhhh.............eeeeeeeee...eeeeeee..........eeeee...eeee..eeee..ee........eeeee.............eeee..........eeeeeeee.............eeee..eeeeeeeeeeeeee......eeee.........eeeeeeee...........hhhh.eeeeee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------G_TR_1          ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.2  PDB: A:2-441 UniProt: 1-458 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                       Transcript 2
                2b7b A    2 GKEKSHINVVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYQVTVIDAPGHRDFIKNMITGTSQADCAILIIAGGVGEFEAGISKDGQTREHALLAFTLGVRQLIVAVNKMDSVKWDESRFQEIVKETSNFIKKVGYNPKTVPFVPISGWNGDNMIEATTNAPWYKGWEKETKAGVVKGKTLLEAIDAIEQPSRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMVVTFAPAGVTTEVKSVEMHHEQLEQGVPGDNVGFNVKNVSVKEIRRGNVCGDAKNDPPKGCASFNATVIVLNHPGQISAGYSPVLDCHTAHIACRFDELLEKNDRRSGKKLEDHPKFLKSGDAALVKFVPSKPMCVEAFSEYPPLGRFAVRDMRQTVAVGVIKSVDK  441
                                    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       411       421       431       441


Chain B from PDB  Type:PROTEIN  Length:90
 aligned with EF1B_YEAST | P32471 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:90
                                   126       136       146       156       166       176       186       196       206
          EF1B_YEAST    117 PAAKSIVTLDVKPWDDETNLEEMVANVKAIEMEGLTWGAHQFIPIGFGIKKLQINCVVEDDKVSLDDLQQSIEEDEDHVQSTDIAAMQKL  206
               SCOP domains d2b7bb1 B:1117-1206                                                                        SCOP domains
               CATH domains 2b7bB00 B:1117-1206  [code=3.30.70.60, no name defined]                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeee......hhhhhhhhhhh.....eeeeeeeeeeee..eeeeeeeeeee....hhhhhhhhhh.......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------EF1BD_2      PROSITE
               Transcript 1 Exon 1.2  PDB: B:1117-1206 UniProt: 27-206 [INCOMPLETE]                                    Transcript 1
                2b7b B 1117 PAAKSIVTLDVKPWDDETNLEEMVANVKAIEMEGLTWGAHQFIPIGFGIKKLQINCVVEDDKVSLDDLQQSIEEDEDHVQSTDIAAMQAL 1206
                                  1126      1136      1146      1156      1166      1176      1186      1196      1206
   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, 4)

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  (3, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B7B)

(-) Gene Ontology  (26, 30)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (EF1A_YEAST | P02994)
molecular function
    GO:0019003    GDP binding    Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate.
    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:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0043022    ribosome binding    Interacting selectively and non-covalently with any part of a ribosome.
    GO:0003746    translation elongation factor activity    Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
    GO:0034198    cellular response to amino acid starvation    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of amino acids.
    GO:0006469    negative regulation of protein kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
    GO:0001933    negative regulation of protein phosphorylation    Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein.
    GO:0006409    tRNA export from nucleus    The directed movement of tRNA from the nucleus to the cytoplasm.
    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:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005853    eukaryotic translation elongation factor 1 complex    A multisubunit nucleotide exchange complex that binds GTP and aminoacyl-tRNAs, and catalyzes their codon-dependent placement at the A-site of the ribosome. In humans, the complex is composed of four subunits, alpha, beta, delta and gamma.
    GO:0000329    fungal-type vacuole membrane    The lipid bilayer surrounding a vacuole, the shape of which correlates with cell cycle phase. The membrane separates its contents from the cytoplasm of the cell. An example of this structure is found in Saccharomyces cerevisiae.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

Chain B   (EF1B_YEAST | P32471)
molecular function
    GO:0005085    guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0003746    translation elongation factor activity    Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
    GO:1990145    maintenance of translational fidelity    Suppression of the occurrence of translational errors, such as codon-anticodon mis-paring, during the process of translation of a protein using an mRNA template.
    GO:0032232    negative regulation of actin filament bundle assembly    Any process that stops, prevents, or reduces the frequency, rate or extent of the assembly of actin filament bundles.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0006449    regulation of translational termination    Any process that modulates the frequency, rate or extent of translational termination.
    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:0005853    eukaryotic translation elongation factor 1 complex    A multisubunit nucleotide exchange complex that binds GTP and aminoacyl-tRNAs, and catalyzes their codon-dependent placement at the A-site of the ribosome. In humans, the complex is composed of four subunits, alpha, beta, delta and gamma.

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 Related Entries

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

UniProtKB/Swiss-Prot
        EF1A_YEAST | P02994: 1f60 1g7c 1ije 1ijf 2b7c
        EF1B_YEAST | P32471: 1f60 1g7c 1ije 1ijf 2b7c

(-) Related Entries Specified in the PDB File

1f60 NATIVE EEF1A/EEF1BALPHA NUCLEOTIDE FREE COMPLEX
1g7c NATIVE EEF1A/EEF1BALPHA/GDPNP COMPLEX
1ije NATIVE EEF1A/EEF1BALPHA/GDP COMPLEX
1ijf NATIVE EEF1A/EEF1BALPHA/GDP/MG2+ COMPLEX
2b7c EEF1BALPHA K205A MUTANT IN COMPLEX WITH EEF1A