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(-) Description

Title :  CRYSTAL STRUCTURE OF GTP-BOUND LEPA FROM AQUIFEX AEOLICUS
 
Authors :  M. Kawazoe, C. Takemoto, T. Kaminishi, A. Nishino, R. Nakayama-Ushiko K. Hanawa-Suetsugu, T. Terada, M. Shirouzu, S. Yokoyama, Riken Stru Genomics/Proteomics Initiative (Rsgi)
Date :  20 Apr 07  (Deposition) - 29 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.94
Chains :  Asym./Biol. Unit :  A
Keywords :  G Domain, Beta-Barrel, Ferredoxin-Like Domain, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Kawazoe, C. Takemoto, T. Kaminishi, A. Nishino, R. Nakayama-Ushikoshi, K. Hanawa-Suetsugu, T. Terada, M. Shirouzu, S. Yokoyama
Crystal Structures Of Gtp-Binding Protein Lepa From Aquifex Aeolicus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GTP-BINDING PROTEIN LEPA
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-11A
    Expression System StrainB834(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneAQ_1725
    Organism ScientificAQUIFEX AEOLICUS
    Organism Taxid224324
    StrainVF5

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric/Biological Unit (2, 13)
No.NameCountTypeFull Name
1GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:16 , HIS A:17 , GLY A:18 , LYS A:19 , SER A:20 , THR A:21 , ASN A:133 , LYS A:134 , ASP A:136 , LEU A:137 , SER A:164 , ALA A:165 , LYS A:166 , HOH A:716 , HOH A:729BINDING SITE FOR RESIDUE GTP A 701

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:243 -Pro A:244

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_TR_1PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature.LEPA_AQUAE44-59  1A:56-59

(-) Exons   (0, 0)

(no "Exon" information available for 2YWG)

(-) 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:528
 aligned with LEPA_AQUAE | O67618 from UniProtKB/Swiss-Prot  Length:600

    Alignment length:551
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550 
           LEPA_AQUAE     1 MEQKNVRNFCIIAHVDHGKSTLADRLLEYTGAISEREKREQLLDTLDVERERGITVKMQAVRMFYKAKDGNTYKLHLIDTPGHVDFSYEVSRALAACEGALLLIDASQGIEAQTVANFWKAVEQDLVIIPVINKIDLPSADVDRVKKQIEEVLGLDPEEAILASAKEGIGIEEILEAIVNRIPPPKGDPQKPLKALIFDSYYDPYRGAVAFVRIFDGEVKPGDKIMLMSTGKEYEVTEVGAQTPKMTKFDKLSAGDVGYIAASIKDVRDIRIGDTITHAKNPTKEPVPGFQPAKPMVYAGIYPAEDTTYEELRDALEKYAINDAAIVYEPESSPALGMGFRVGFLGLLHMEIVQERLEREYGVKIITTAPNVIYRVKKKFTDEVIEVRNPMDFPDNAGLIEYVEEPFVLVTIITPKEYVGPIIQLCQEKRGIQKNMTYLDPNTVYLEYEMPLSEIIVDFHDKIKSISRGFASYDYEFIGYRPSDLIKLTVLINKKPVDALSFIVHADRAQKFARRVAEKLRETIPRQLFEVHIQVAKGGKVIASERIKPLR 551
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---GTP_EFTU-2ywgA02 A:4-184                                                                                                                                                             ----------------------GTP_EFTU_D2-2ywgA03 A:207-277                                          ----------------------------------------------------------------------------------------------------------------------------EFG_C-2ywgA01 A:402-491                                                                   LepA_C-2ywgA04 A:492-551                                     Pfam domains
         Sec.struct. author .....eeeeeeee....hhhhhhhhhhhhhhh-----------------------.....eeeeee.....eeeeeee....hhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhh......eee......hhhhhhhhhhhhh...........eeeeeeeeee...eeeeeeeeee.ee....eeee.....eee..eeeee...eeee..ee...eeeeeeee..........eeee..................eeeeeee....hhhhhhhhhhhhhhhh...eeeeeee...eeeeeeee.hhhhhhhhhhhhhh.....eee...ee.eeeee......eee.hhhhh..hhh.eeeeeeeeeeeeeeee..hhhhhhhhhhhh..eeeeeeeee..eeeeeeeeehhhhh.hhhhhhhhh.....eeeeeeeeeee..eeeeeeee....hhhhheeee..hhhhhhhhhhhhhhhhh......eeeeeee..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------G_TR_1          ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ywg A   1 mEQKNVRNFCIIAHVDHGKSTLADRLLEYTGA-----------------------VKmQAVRmFYKAKDGNTYKLHLIDTPGHVDFSYEVSRALAACEGALLLIDASQGIEAQTVANFWKAVEQDLVIIPVINKIDLPSADVDRVKKQIEEVLGLDPEEAILASAKEGIGIEEILEAIVNRIPPPKGDPQKPLKALIFDSYYDPYRGAVAFVRIFDGEVKPGDKImLmSTGKEYEVTEVGAQTPKmTKFDKLSAGDVGYIAASIKDVRDIRIGDTITHAKNPTKEPVPGFQPAKPmVYAGIYPAEDTTYEELRDALEKYAINDAAIVYEPESSPALGmGFRVGFLGLLHmEIVQERLEREYGVKIITTAPNVIYRVKKKFTDEVIEVRNPmDFPDNAGLIEYVEEPFVLVTIITPKEYVGPIIQLCQEKRGIQKNmTYLDPNTVYLEYEmPLSEIIVDFHDKIKSISRGFASYDYEFIGYRPSDLIKLTVLINKKPVDALSFIVHADRAQKFARRVAEKLRETIPRQLFEVHIQVAKGGKVIASERIKPLR 551
                            |       10        20        30 |       -         -     | |60  |     70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220     | 230       240     | 250       260       270       280       290     | 300       310       320       330       340       350       360       370       380       390|      400       410       420       430     | 440       450       460       470       480       490       500       510       520       530       540       550 
                            |                             32                      56 |    |                                                                                                                                                                226-MSE             246-MSE                                           296-MSE                                   338-MSE     350-MSE                                  391-MSE                                      436-MSE       450-MSE                                                                                                 
                            1-MSE                                                   58-MSE|                                                                                                                                                                  228-MSE                                                                                                                                                                                                                                                                                                                               
                                                                                         63-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  (0, 0)

(no "SCOP Domain" information available for 2YWG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (4, 4)

Asymmetric/Biological Unit
(-)
Clan: EF-G_C (20)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LEPA_AQUAE | O67618)
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:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    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: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:0045727    positive regulation of translation    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    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: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.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LEPA_AQUAE | O676182ywe 2ywf 2ywh

(-) Related Entries Specified in the PDB File

2ywe
2ywf
2ywh RELATED ID: AAE001001725.3 RELATED DB: TARGETDB