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(-) Description

Title :  CRYSTAL STRUCTURE OF A C-TERMINAL FRAGMENT OF MOORELLA THERMOACETICA ELONGATION FACTOR SELB
 
Authors :  M. Selmer, X. -D. Su
Date :  28 May 02  (Deposition) - 21 Aug 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.12
Chains :  Asym./Biol. Unit :  A
Keywords :  Winged-Helix, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Selmer, X. D. Su
Crystal Structure Of An Mrna-Binding Fragment Of Moorella Thermoacetica Elongation Factor Selb.
Embo J. V. 21 4145 2002
PubMed-ID: 12145214  |  Reference-DOI: 10.1093/EMBOJ/CDF408
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SELENOCYSTEINE-SPECIFIC ELONGATION FACTOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL FRAGMENT
    Gene: SELB(AMINO ACIDS 370-634)
    Organism Scientific: MOORELLA THERMOACETICA
    Organism Taxid: 1525
    Synonym: SELB TRANSLATION FACTOR, SELB

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION
3Y12Ligand/IonYTTRIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:487 , GLU A:579 , GLU A:582 , HOH A:656 , HOH A:685BINDING SITE FOR RESIDUE Y1 A 743
2AC2SOFTWAREASP A:600 , ASP A:627 , HOH A:729 , HOH A:732 , HOH A:738BINDING SITE FOR RESIDUE Y1 A 744
3AC3SOFTWAREARG A:599 , SER A:605 , ARG A:606 , LYS A:628BINDING SITE FOR RESIDUE SO4 A 745

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LVA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LVA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LVA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1LVA)

(-) Exons   (0, 0)

(no "Exon" information available for 1LVA)

(-) 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:258
 aligned with SELB_MOOTH | Q46455 from UniProtKB/Swiss-Prot  Length:634

    Alignment length:258
                                   386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626        
           SELB_MOOTH   377 GSPEKILAQIIQEHREGLDWQEAATRASLSLEETRKLLQSMAAAGQVTLLRVENDLYAISTERYQAWWQAVTRALEEFHSRYPLRPGLAREELRSRYFSRLPARVYQALLEEWSREGRLQLAANTVALAGFTPSFSETQKKLLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKINDEFYWHRQALGEAREVIKNLASTGPFGLAEARDALGSSRKYVLPLLEYLDQVKFTRRVGDKRVVVGN 634
               SCOP domains d1lvaa1 A:377-437                                            d1lvaa2 A:438-510 C-terminal fragment of elongation factor SelB          d1lvaa3 A:511-574 C-terminal fragment of elongation factor SelB d1lvaa4 A:575-634                                            SCOP domains
               CATH domains 1lvaA01 A:377-436                                           1lvaA02 A:437-505 'winged helix' repressor DNA binding domain        ------1lvaA03 A:512-573 'winged helix' repressor DNA binding domain 1lvaA04 A:574-633                                           - CATH domains
               Pfam domains SelB-wing_1-1lvaA01 A:377-437                                ---------SelB-wing_2-1lvaA02 A:447-504                             ----------------------------------------------------------------------------SelB-wing_3-1lvaA03 A:581-632                       -- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh....eehhhhhhhhh.hhhhhhhhhhhhhhh..eeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhh...hhhhhhhhhhhhhhh..eeee..eeee.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1lva A 377 GSPEKILAQIIQEHREGLDWQEAATRASLSLEETRKLLQSmAAAGQVTLLRVENDLYAISTERYQAWWQAVTRALEEFHSRYPLRPGLAREELRSRYFSRLPARVYQALLEEWSREGRLQLAANTVALAGFTPSFSETQKKLLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKINDEFYWHRQALGEAREVIKNLASTGPFGLAEARDALGSSRKYVLPLLEYLDQVKFTRRVGDKRVVVGN 634
                                   386       396       406       416|      426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626        
                                                                  417-MSE
   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, 4)

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

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: SelB-wing_1] (3)
(-)
Clan: no clan defined [family: SelB-wing_2] (3)
(-)
Clan: no clan defined [family: SelB-wing_3] (4)

(-) 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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  1lva
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 Related Entries

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

UniProtKB/Swiss-Prot
        SELB_MOOTH | Q46455: 1wsu 2ply 2uwm 2v9v

(-) Related Entries Specified in the PDB File

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