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(-) Description

Title :  CRYSTAL STRUCTURE OF A WIDELY CONSERVED GTPASE ERA
 
Authors :  X. Chen, X. Ji
Date :  01 Dec 98  (Deposition) - 12 Jul 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Era, Gtpase, Rna-Binding, Ras-Like, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Chen, D. L. Court, X. Ji
Crystal Structure Of Era: A Gtpase-Dependent Cell Cycle Regulator Containing An Rna Binding Motif.
Proc. Natl. Acad. Sci. Usa V. 96 8396 1999
PubMed-ID: 10411886  |  Reference-DOI: 10.1073/PNAS.96.15.8396
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (GTP-BINDING PROTEIN ERA)
    Cellular Location: CYTOPLASM/MEMBRANE
    Chains: A, B
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: TAP106

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:18 , VAL A:19 , GLY A:20 , LYS A:21 , SER A:22BINDING SITE FOR RESIDUE SO4 A 302
2AC2SOFTWARETHR A:23 , ASN A:26 , LYS A:27 , THR A:36 , THR A:215 , LYS A:282BINDING SITE FOR RESIDUE SO4 A 303
3AC3SOFTWAREASN B:18 , VAL B:19 , GLY B:20 , LYS B:21 , SER B:22BINDING SITE FOR RESIDUE SO4 B 303
4AC4SOFTWARETHR B:23 , ASN B:26 , LYS B:27 , THR B:36 , THR B:215 , LYS B:282BINDING SITE FOR RESIDUE SO4 B 304
5AC5SOFTWARELYS A:32 , TYR A:212 , HOH A:374 , HOH A:405BINDING SITE FOR RESIDUE SO4 A 305
6HGAUTHORCYS A:8 , HIS A:51 , CYS B:8 , HIS B:51MERCURY ATOM-BINDING SITES IN EMP DERIVATIVE USED IN MAD PHASING

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_ERAPS51713 Era-type guanine nucleotide-binding (G) domain profile.ERA_ECOLI7-175
 		  2A:7-175
B:7-175
2KH_TYPE_2PS50823 Type-2 KH domain profile.ERA_ECOLI206-283
 		  2A:206-283
B:206-283

(-) Exons   (0, 0)

(no "Exon" information available for 1EGA)

(-) 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:292
 aligned with ERA_ECOLI | P06616 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:292
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293  
            ERA_ECOLI     4 DKSYCGFIAIVGRPNVGKSTLLNKLLGQKISITSRKAQTTRHRIVGIHTEGAYQAIYVDTPGLHMEEKRAINRLMNKAASSSIGDVELVIFVVEGTRWTPDDEMVLNKLREGKAPVILAVNKVDNVQEKADLLPHLQFLASQMNFLDIVPISAETGLNVDTIAAIVRKHLPEATHHFPEDYITDRSQRFMASEIIREKLMRFLGAELPYSVTVEIERFVSNERGGYDINGLILVEREGQKKMVIGNKGAKIKTIGIEARKDMQEMFEAPVHLELWVKVKSGWADDERALRSL 295
               SCOP domains d1egaa1 A:4-182 GTPase Era, N-terminal domain                                                                                                                                      d1egaa2 A:183-295 GTPase Era C-terminal domain                                                                    SCOP domains
               CATH domains 1egaA01 A:4-184 P-loop containing nucleotide triphosphate hydrolases                                                                                                                 ----1egaA02 A:189-294  [code=3.30.300.20, no name defined]                                                    - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee......hhhhhhhhh...eee...........eeeeeee..eeeeee......hhhhhhhhhhh............eeeeeee.....hhhhhhhhhhh....eeeeeee.......hhhhhhhhhhhhhh....eeee........hhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhh....eeeeeeeee......eeeeeeeee..hhhhhhhh.hhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....hhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---G_ERA  PDB: A:7-175 UniProt: 7-175                                                                                                                                       ------------------------------KH_TYPE_2  PDB: A:206-283 UniProt: 206-283                                    ------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ega A   4 DKSYCGFIAIVGRPNVGKSTLLNKLLGQKISITSRKAQTTRHRIVGIHTEGAYQAIYVDTPGLHMEEKRAINRLMNKAASSSIGDVELVIFVVEGTRWTPDDEMVLNKLREGKAPVILAVNKVDNVQEKADLLPHLQFLASQMNFLDIVPISAETGLNVDTIAAIVRKHLPEATHHFPEDYITDRSQRFMASEIIREKLMRFLGAELPYSVTVEIERFVSNERGGYDINGLILVEREGQKKMVIGNKGAKIKTIGIEARKDMQEMFEAPVHLELWVKVKSGWADDERALRSL 295
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293  


Chain B from PDB  Type:PROTEIN  Length:293
 aligned with ERA_ECOLI | P06616 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:293
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293   
            ERA_ECOLI     4 DKSYCGFIAIVGRPNVGKSTLLNKLLGQKISITSRKAQTTRHRIVGIHTEGAYQAIYVDTPGLHMEEKRAINRLMNKAASSSIGDVELVIFVVEGTRWTPDDEMVLNKLREGKAPVILAVNKVDNVQEKADLLPHLQFLASQMNFLDIVPISAETGLNVDTIAAIVRKHLPEATHHFPEDYITDRSQRFMASEIIREKLMRFLGAELPYSVTVEIERFVSNERGGYDINGLILVEREGQKKMVIGNKGAKIKTIGIEARKDMQEMFEAPVHLELWVKVKSGWADDERALRSLG 296
               SCOP domains d1egab1 B:4-182 GTPase Era, N-terminal domain                                                                                                                                      d1egab2 B:183-296 GTPase Era C-terminal domain                                                                     SCOP domains
               CATH domains 1egaB01 B:4-184 P-loop containing nucleotide triphosphate hydrolases                                                                                                                 ----1egaB02 B:189-294  [code=3.30.300.20, no name defined]                                                    -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee......hhhhhhhhh...eee...........eeeeeee..eeeeee......hhhhhhhhhhh............eeeeeee.....hhhhhhhhhhh....eeeeeee.hhh...hhhhhhhhhhh.......eeeee.......hhhhhhhhhhh.................hhhhhhhhhhhhhhhh........eee.eeeee......eeeeeeeee..hhhhhhhh.hhhhhhhhhhhhhhhhhhh.....eeeeeeeee.....hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---G_ERA  PDB: B:7-175 UniProt: 7-175                                                                                                                                       ------------------------------KH_TYPE_2  PDB: B:206-283 UniProt: 206-283                                    ------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ega B   4 DKSYCGFIAIVGRPNVGKSTLLNKLLGQKISITSRKAQTTRHRIVGIHTEGAYQAIYVDTPGLHMEEKRAINRLMNKAASSSIGDVELVIFVVEGTRWTPDDEMVLNKLREGKAPVILAVNKVDNVQEKADLLPHLQFLASQMNFLDIVPISAETGLNVDTIAAIVRKHLPEATHHFPEDYITDRSQRFMASEIIREKLMRFLGAELPYSVTVEIERFVSNERGGYDINGLILVEREGQKKMVIGNKGAKIKTIGIEARKDMQEMFEAPVHLELWVKVKSGWADDERALRSLG 296
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EGA)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ERA_ECOLI | P06616)
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:0019843    rRNA binding    Interacting selectively and non-covalently with ribosomal RNA.
    GO:0043024    ribosomal small subunit binding    Interacting selectively and non-covalently with any part of the small ribosomal subunit.
    GO:0070181    small ribosomal subunit rRNA binding    Interacting selectively and non-covalently with the small ribosomal subunit RNA (SSU rRNA), a constituent of the small ribosomal subunit. In S. cerevisiae, this is the 18S rRNA.
biological process
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0042274    ribosomal small subunit biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a small ribosomal subunit; includes transport to the sites of protein synthesis.
    GO:0042254    ribosome biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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
        ERA_ECOLI | P06616: 1x1l 3ieu

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