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(-) Description

Title :  MEAB, A BACTERIAL HOMOLOG OF MMAA, BOUND TO GDP
 
Authors :  P. A. Hubbard, D. Padovani, T. Labunska, S. A. Mahlstedt, R. Banerjee, C. L. Drennan
Date :  14 Jul 07  (Deposition) - 28 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  G Protein, Gtpase, G3E, Metallochaperone, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. A. Hubbard, D. Padovani, T. Labunska, S. A. Mahlstedt, R. Banerjee, C. L. Drennan
Crystal Structure And Mutagenesis Of The Metallochaperone Meab: Insight Into The Causes Of Methylmalonic Aciduria.
J. Biol. Chem. V. 282 31308 2007
PubMed-ID: 17728257  |  Reference-DOI: 10.1074/JBC.M704850200

(-) Compounds

Molecule 1 - GTPASE/ATPASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MEAB
    Mutation: YES
    Organism Scientific: METHYLOBACTERIUM EXTORQUENS
    Organism Taxid: 272630
    Strain: AM1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:14 , ALA A:21 , ARG A:25 , HOH A:683 , HOH A:731 , HOH A:799BINDING SITE FOR RESIDUE PO4 A 500
2AC2SOFTWAREGLY A:247 , LEU A:248 , ASP A:249 , SER A:250 , HOH A:776 , HOH A:819BINDING SITE FOR RESIDUE PO4 A 501
3AC3SOFTWAREVAL A:63 , GLY A:65 , VAL A:66 , GLY A:67 , LYS A:68 , SER A:69 , THR A:70 , ASN A:201 , LYS A:202 , ASP A:204 , SER A:241 , GLY A:242 , LEU A:243 , HOH A:605 , HOH A:619 , HOH A:725 , HOH A:754 , HOH A:755 , HOH A:756 , HOH A:765 , HOH A:816 , HOH A:833BINDING SITE FOR RESIDUE GDP A 601
4AC4SOFTWAREGLY B:65 , VAL B:66 , GLY B:67 , LYS B:68 , SER B:69 , THR B:70 , ASN B:201 , LYS B:202 , ASP B:204 , SER B:241 , GLY B:242 , LEU B:243 , HOH B:658 , HOH B:668 , HOH B:697 , HOH B:709 , HOH B:712BINDING SITE FOR RESIDUE GDP B 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QM7)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:97 -Thr A:98
2Pro B:6 -Asp B:7

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QM7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QM7)

(-) Exons   (0, 0)

(no "Exon" information available for 2QM7)

(-) 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:314
 aligned with Q8RPA0_METEX | Q8RPA0 from UniProtKB/TrEMBL  Length:329

    Alignment length:323
                                    14        24        34        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   
         Q8RPA0_METEX     5 LPDMDTLRERLLAGDRAALARAITLAESRRADHRAAVRDLIDAVLPQTGRAIRVGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAVDPSSTRTGGSILGDKTRMARLAIDRNAFIRPSPSSGTLGGVAAKTRETMLLCEAAGFDVILVETVGVGQSETAVADLTDFFLVLMLPGAGDELQGIKKGILELADMIAVNKADDGDGERRASAAASEYRAALRILTPPSATWTPPVVTISGLHGKGLDSLWSRIEGHRSKLTATGEIAGKRREQDVKWMWALVHERLHQRLVGSAEVRQATAEAERAVAGGEHSPAAGADAIATLI 327
               SCOP domains d2qm7a1 A:5-327 Metallochaperone MeaB                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2qm7A01 A:5-52                                  2qm7A02 A:53-264 P-loop containing nucleotide          triphosphate hydrolases                                                                                                                                      --------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhh...eeeeeehhhhhh.---------.hhhhhh...eeee......hhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhh...eeeeee...hhhhh............eeee.....hhhhhhhhhhhhhhhhhhhhhh.........eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qm7 A   5 LPDMDTLRERLLAGDRAALARAITLAESRRADHRAAVRDLIDAVLPQTGRAIRVGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAVDPSSTRT---------RMARLAIDRNAFIRPSPSSGTLGGVAAKTRETMLLCEAAGFDVILVETVGVGQSETAVADLTDFFLVLMLPGAGDELQGIKKGIFELADMIAVNKADDGDGERRASAAASEYRAALHILTPPSATWTPPVVTISGLHGKGLDSLWSRIEDHRSKLTATGEIAGKRREQDVKWMWALVHERLHQRLVGSAEVRQATAEAERAVAGGEHSPAAGADAIATLI 327
                                    14        24        34        44        54        64        74        84        94   |     -   |   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324   
                                                                                                                        98       108                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:311
 aligned with Q8RPA0_METEX | Q8RPA0 from UniProtKB/TrEMBL  Length:329

    Alignment length:324
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325    
         Q8RPA0_METEX     6 PDMDTLRERLLAGDRAALARAITLAESRRADHRAAVRDLIDAVLPQTGRAIRVGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAVDPSSTRTGGSILGDKTRMARLAIDRNAFIRPSPSSGTLGGVAAKTRETMLLCEAAGFDVILVETVGVGQSETAVADLTDFFLVLMLPGAGDELQGIKKGILELADMIAVNKADDGDGERRASAAASEYRAALRILTPPSATWTPPVVTISGLHGKGLDSLWSRIEGHRSKLTATGEIAGKRREQDVKWMWALVHERLHQRLVGSAEVRQATAEAERAVAGGEHSPAAGADAIATLIGL 329
               SCOP domains d2qm7b_ B: Metallochapero   ne MeaB                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2qm7B01 B:6-52                                 2qm7B02 B:53-264 P-loop containing nucleotide           triphosphate hydrolases                                                                                                                                     ----------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------ArgK-2qm   7B01 B:23-297                                                                                                                                                                                                                                                           -------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------ArgK-2qm   7B02 B:23-297                                                                                                                                                                                                                                                           -------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh---hhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhh...eeeeeehhhhhh----------.hhhhhh...eee.......hhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhh...eeeeee...hhhhh.....hhhhhh.eeee.....hhhhhhhhhhhhhhhhhhh............eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qm7 B   6 PDMDTLRERLLAGDRAALARAITLA---RADHRAAVRDLIDAVLPQTGRAIRVGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAVDPSSTR----------RMARLAIDRNAFIRPSPSSGTLGGVAAKTRETMLLCEAAGFDVILVETVGVGQSETAVADLTDFFLVLMLPGAGDELQGIKKGIFELADMIAVNKADDGDGERRASAAASEYRAALHILTPPSATWTPPVVTISGLHGKGLDSLWSRIEDHRSKLTATGEIAGKRREQDVKWMWALVHERLHQRLVGSAEVRQATAEAERAVAGGEHSPAAGADAIATLIGL 329
                                    15        25    |   35        45        55        65        75        85        95 |       -  |    115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325    
                                                   30  34                                                             97        108
   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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8RPA0_METEX | Q8RPA0)
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.

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    Arg A:97 - Thr A:98   [ RasMol ]  
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 Related Entries

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

UniProtKB/TrEMBL
        Q8RPA0_METEX | Q8RPA0: 2qm8

(-) Related Entries Specified in the PDB File

2hf8 HYPB - A DISTANTLY RELATED G3E GTPASE
2hf9 HYPB - A DISTANTLY RELATED G3E GTPASE
2qm8 MEAB IN THE NUCLEOTIDE FREE FORM