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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RIBOSOMAL INTERACTING GTPASE YJEQ FROM THE ENTEROBACTERIAL SPECIES SALMONELLA TYPHIMURIUM.
 
Authors :  C. E. Nichols, D. K. Stammers
Date :  20 Sep 07  (Deposition) - 29 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Yjeq, Gtpase, Circularly Permuted, Gtp-Binding, Hydrolase, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. E. Nichols, C. Johnson, H. K. Lamb, M. Lockyer, I. G. Charles, A. R. Hawkins, D. K. Stammers
Structure Of The Ribosomal Interacting Gtpase Yjeq From The Enterobacterial Species Salmonella Typhimurium.
Acta Crystallogr. , Sect. F V. 63 922 2007
PubMed-ID: 18007041  |  Reference-DOI: 10.1107/S1744309107048609

(-) Compounds

Molecule 1 - PROBABLE GTPASE ENGC
    Chains: A
    EC Number: 3.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMUT99
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PET3A
    Gene: ENGC
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 99287
    Strain: LT2

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:305 , CYS A:310 , HIS A:312 , CYS A:318BINDING SITE FOR RESIDUE ZN A 359
2AC2SOFTWAREHIS A:268 , HOH A:738BINDING SITE FOR RESIDUE MG A 360
3AC3SOFTWAREASN A:168 , LYS A:169 , ASP A:171 , LEU A:172 , GLU A:176 , SER A:199 , SER A:200 , HIS A:201 , SER A:224 , GLY A:225 , VAL A:226 , GLY A:227 , LYS A:228 , SER A:229 , SER A:230 , HOH A:712 , HOH A:772BINDING SITE FOR RESIDUE GDP A 600

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:141 -Pro A:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_CPPS51721 Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile.RSGA_SALTY104-273  1A:112-281
2ENGC_GTPASEPS50936 EngC GTPase domain profile.RSGA_SALTY121-271  1A:129-279
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_CPPS51721 Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile.RSGA_SALTY104-273  1A:112-281
2ENGC_GTPASEPS50936 EngC GTPase domain profile.RSGA_SALTY121-271  1A:129-279
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_CPPS51721 Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile.RSGA_SALTY104-273  2A:112-281
2ENGC_GTPASEPS50936 EngC GTPase domain profile.RSGA_SALTY121-271  2A:129-279

(-) Exons   (0, 0)

(no "Exon" information available for 2RCN)

(-) Sequences/Alignments

Asymmetric 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:278
 aligned with RSGA_SALTY | Q8ZKB0 from UniProtKB/Swiss-Prot  Length:350

    Alignment length:303
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334   
           RSGA_SALTY    35 LFGEPAEGIVISRFGMHADVESADGEVHRCNIRRTIRSLVTGDRVVWRPGKAAAEGVNVKGIVEAVHERTSVLTRPDFYDGVKPIAANIDQIVIVSAILPELSLNIIDRYLVGCETLQVEPLIVLNKIDLLDDEGMDFVNEQMDIYRNIGYRVLMVSSHTQDGLKPLEEALTGRISIFAGQSGVGKSSLLNALLGLQNEILTNDVSNVSGLGQHTTTAARLYHFPHGGDVIDSPGVREFGLWHLEPEQITQGFVEFHDYLGHCKYRDCKHDADPGCAIREAVENGAIAETRFENYHRILESMA 337
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------       ----------2rcnA02      A:111-283 P-loop containing nucleotide triphosphate hydrolases                                                                                                  2rcnA03 A:284-345 Probable gtpase engc; domain 3               CATH domains
               Pfam domains ---------------------------------------------------       ------------------     ---------------------------------------------------------DUF258-2rcnA01 A:181-342                                                                                                                                          --- Pfam domains
         Sec.struct. author .....eeeeeeeee..eeeeee....eeeeee...........eeeee...-------..eeeeee.....eeee.-----.eeeee...eeeeeee.....hhhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhhhhhhh....eee.......hhhhhhhhhh..eeeee.....hhhhhhhhhhh........-------------...eeee.....eeeehhhhhh......hhhhhhhhhhhhhhhh...............hhhhhhhhh...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------------G_CP  PDB: A:112-281 UniProt: 104-273                                                                                                                                     ---------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------ENGC_GTPASE  PDB: A:129-279 UniProt: 121-271                                                                                                           ------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rcn A  43 LFGEPAEGIVISRFGMHADVESADGEVHRCNIRRTIRSLVTGDRVVWRPGK-------VKGIVEAVHERTSVLTRP-----VKPIAANIDQIVIVSAILPELSLNIIDRYLVGCETLQVEPLIVLNKIDLLDDEGMDFVNEQMDIYRNIGYRVLMVSSHTQDGLKPLEEALTGRISIFAGQSGVGKSSLLNALLGLQNEILTN-------------TAARLYHFPHGGDVIDSPGVREFGLWHLEPEQITQGFVEFHDYLGHCKYRDCKHDADPGCAIREAVENGAIAETRFENYHRILESMA 345
                                    52        62        72        82        92|      102       112     |   - |     132       142       152       162       172       182       192       202       212       222       232       242  |      -      |262       272       282       292       302       312       322       332       342   
                                                                             93     101              118   124                                                                                                                      245           259
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (RSGA_SALTY | Q8ZKB0)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.

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        RSGA_SALTY | Q8ZKB0: 4a2i

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