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(-) Description

Title :  CRYSTAL STRUCTURE OF MOORELLA THERMOACETICA SELB(377-511)
 
Authors :  O. Ganichkin, M. C. Wahl
Date :  27 Aug 07  (Deposition) - 11 Sep 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Transcription, Protein Conformational Change, Transcription Elongation Factor Selb, Selenoprotein Biosynthesis, Protein Dynamics, Nucleotide-Binding, Cytoplasm, Gtp-Binding, Selenocysteine, Winged-Helix Domain, Protein Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Ganichkin, M. C. Wahl
Conformational Switches In Winged-Helix Domains 1 And 2 Of Bacterial Translation Elongation Factor Selb.
Acta Crystallogr. , Sect. D V. 63 1075 2007
PubMed-ID: 17881825  |  Reference-DOI: 10.1107/S0907444907042229

(-) Compounds

Molecule 1 - SELENOCYSTEINE-SPECIFIC ELONGATION FACTOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM-11
    Expression System Strain: ROSETTA 2 (DE3)
    Expression System Taxid: 562
    Fragment: WINGED-HELIX DOMAINS 1 AND 2, RESIDUES 377-511
    Organism Scientific: MOORELLA THERMOACETICA
    Organism Taxid: 1525
    Synonym: SELB, SELB TRANSLATION FACTOR

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2NA2Ligand/IonSODIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:407 , ARG A:427BINDING SITE FOR RESIDUE CL A1512
2AC2SOFTWARELEU A:394 , ASP A:395 , HOH A:2079 , HOH A:2179BINDING SITE FOR RESIDUE CL A1513
3AC3SOFTWAREARG A:494 , HOH A:2193BINDING SITE FOR RESIDUE CL A1514
4AC4SOFTWAREPHE A:474 , SER A:475 , ARG A:476 , HOH A:2048 , HOH A:2294BINDING SITE FOR RESIDUE CL A1515
5AC5SOFTWAREASP A:395 , ASN A:430 , ASP A:431 , HOH A:2005 , HOH A:2037BINDING SITE FOR RESIDUE NA A1516
6AC6SOFTWARELEU A:425 , LEU A:460 , HOH A:2038 , HOH A:2052 , HOH A:2058BINDING SITE FOR RESIDUE NA A1517

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V9V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V9V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V9V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V9V)

(-) Exons   (0, 0)

(no "Exon" information available for 2V9V)

(-) 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:135
 aligned with SELB_MOOTH | Q46455 from UniProtKB/Swiss-Prot  Length:634

    Alignment length:135
                                   386       396       406       416       426       436       446       456       466       476       486       496       506     
           SELB_MOOTH   377 GSPEKILAQIIQEHREGLDWQEAATRASLSLEETRKLLQSMAAAGQVTLLRVENDLYAISTERYQAWWQAVTRALEEFHSRYPLRPGLAREELRSRYFSRLPARVYQALLEEWSREGRLQLAANTVALAGFTPSF 511
               SCOP domains d2v9va1 A:377-437 automated matches                          d2v9va2 A:438-511 automated matches                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains SelB-wing_1-2v9vA01 A:377-437                                ---------SelB-wing_2-2v9vA02 A:447-504                             ------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eehhhhhhhhh.hhhhhhhhhhhhhhh..eeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhh...hhhhhhhhhhhhhhh..eee...eeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v9v A 377 GSPEKILAQIIQEHREGLDWQEAATRASLSLEETRKLLQSMAAAGQVTLLRVENDLYAISTERYQAWWQAVTRALEEFHSRYPLRPGLAREELRSRYFSRLPARVYQALLEEWSREGRLQLAANTVALAGFTPSF 511
                                   386       396       406       416       426       436       446       456       466       476       486       496       506
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V9V)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: SelB-wing_1] (3)
(-)
Clan: no clan defined [family: SelB-wing_2] (3)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SELB_MOOTH | Q46455)
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:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0001514    selenocysteine incorporation    The incorporation of selenocysteine into a peptide; uses a special tRNA that recognizes the UGA codon as selenocysteine, rather than as a termination codon. Selenocysteine is synthesized from serine before its incorporation; it is not a posttranslational modification of peptidyl-cysteine.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  2v9v
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 Related Entries

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

UniProtKB/Swiss-Prot
        SELB_MOOTH | Q46455: 1lva 1wsu 2ply 2uwm

(-) Related Entries Specified in the PDB File

1lva CRYSTAL STRUCTURE OF A C-TERMINAL FRAGMENT OF MOORELLATHERMOACETICA ELONGATION FACTOR SELB
1wsu C-TERMINAL DOMAIN OF ELONGATION FACTOR SELB COMPLEXED WITHSECIS RNA