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(-) Description

Title :  HYDROLYSIS OF GTP TO GDP BY AN MCM-ASSOCIATED AND MEAB- AND MMAA-LIKE G-PROTEIN FROM MYCOBACTERIUM TUBERCULOSIS
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  04 Oct 10  (Deposition) - 10 Nov 10  (Release) - 03 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Meab, Mmaa, Methylmalonic Aciduria Protein A, Gtpase, G-Protein, Mcm, Methylmalonyl-Coa Mutase, Incorrectly Assigned As An Arginine/Ornithine Transport System Atpase, Methylmaolonyl Pathway, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. E. Edwards, L. Baugh, J. Bullen, R. O. Baydo, P. Witte, K. Thompkins, I. Q. Phan, J. Abendroth, M. C. Clifton, B. Sankaran, W. C. Van Voorhis P. J. Myler, B. L. Staker, C. Grundner, D. D. Lorimer
Crystal Structures Of Mycobacterial Meab And Mmaa-Like Gtpases.
J. Struct. Funct. Genom. V. 16 91 2015
PubMed-ID: 25832174  |  Reference-DOI: 10.1007/S10969-015-9197-2

(-) Compounds

Molecule 1 - PROBABLE GTPASE RV1496/MT1543
    Chains: A
    EC Number: 3.6.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: AVA0421
    Gene: MT1543, MTCY277.18, RV1496
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2PGE2Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2PGE4Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:68 , VAL A:69 , GLY A:70 , LYS A:71 , SER A:72 , THR A:73 , ASN A:204 , LYS A:205 , ASP A:207 , SER A:243 , ALA A:244 , VAL A:245 , HOH A:415 , HOH A:460 , HOH A:461BINDING SITE FOR RESIDUE GDP A 335
2AC2SOFTWAREGLU A:232 , ALA A:233 , LEU A:234 , TRP A:235 , ARG A:236 , HOH A:475 , HOH A:476BINDING SITE FOR RESIDUE PGE A 336
3AC3SOFTWARELYS A:192 , GLU A:196 , LEU A:197 , ALA A:198 , ASP A:199 , TYR A:229 , GLU A:232 , TRP A:235 , ARG A:273 , HOH A:382 , HOH A:474BINDING SITE FOR RESIDUE PGE A 337

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P32)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3P32)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P32)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P32)

(-) Exons   (0, 0)

(no "Exon" information available for 3P32)

(-) 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:306
 aligned with Y1496_MYCTO | P9WPZ0 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:324
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329    
          Y1496_MYCTO    10 TVDGLATAVRGGDRAALPRAITLVESTRPDHREQAQQLLLRLLPDSGNAHRVGITGVPGVGKSTAIEALGMHLIERGHRVAVLAVDPSSTRTGGSILGDKTRMARLAVHPNAYIRPSPTSGTLGGVTRATRETVVLLEAAGFDVILIETVGVGQSEVAVANMVDTFVLLTLARTGDQLQGIKKGVLELADIVVVNKADGEHHKEARLAARELSAAIRLIYPREALWRPPVLTMSAVEGRGLAELWDTVERHRQVLTGAGEFDARRRDQQVDWTWQLVRDAVLDRVWSNPTVRKVRSELERRVRAGELTPALAAQQILEIANLTD 333
               SCOP domains d3p32a_ A: automated matches                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ----------------ArgK-3p32A01 A:26-299                                                                                                                                                                                                                                                             ---------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhh....eeeeee.----------------hhhhhh...eeee...--.hhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhh...eeeeeee.............hhhhh.eeeee..hhhhhhhhhhhhhhhhhhhhhhh.........eeeehhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p32 A  10 TVDGLATAVRGGDRAALPRAITLVESTRPDHREQAQQLLLRLLPDSGNAHRVGITGVPGVGKSTAIEALGMHLIERGHRVAVLAVD----------------MARLAVHPNAYIRPSP--GTLGGVTRATRETVVLLEAAGFDVILIETVGVGQSEVAVANMVDTFVLLTLARTGDQLQGIKKGVLELADIVVVNKADGEHHKEARLAARELSAAIRLIYPREALWRPPVLTMSAVEGRGLAELWDTVERHRQVLTGAGEFDARRRDQQVDWTWQLVRDAVLDRVWSNPTVRKVRSELERRVRAGELTPALAAQQILEIANLTD 333
                                    19        29        39        49        59        69        79        89     |   -         -  |    119       | -|      139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329    
                                                                                                                95              112            127  |                                                                                                                                                                                                           
                                                                                                                                                  130                                                                                                                                                                                                           


Chain A from PDB  Type:PROTEIN  Length:306
 aligned with Y1496_MYCTU | P9WPZ1 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:324
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329    
          Y1496_MYCTU    10 TVDGLATAVRGGDRAALPRAITLVESTRPDHREQAQQLLLRLLPDSGNAHRVGITGVPGVGKSTAIEALGMHLIERGHRVAVLAVDPSSTRTGGSILGDKTRMARLAVHPNAYIRPSPTSGTLGGVTRATRETVVLLEAAGFDVILIETVGVGQSEVAVANMVDTFVLLTLARTGDQLQGIKKGVLELADIVVVNKADGEHHKEARLAARELSAAIRLIYPREALWRPPVLTMSAVEGRGLAELWDTVERHRQVLTGAGEFDARRRDQQVDWTWQLVRDAVLDRVWSNPTVRKVRSELERRVRAGELTPALAAQQILEIANLTD 333
               SCOP domains d3p32a_ A: automated matches                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ----------------ArgK-3p32A01 A:26-299                                                                                                                                                                                                                                                             ---------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhh....eeeeee.----------------hhhhhh...eeee...--.hhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhh...eeeeeee.............hhhhh.eeeee..hhhhhhhhhhhhhhhhhhhhhhh.........eeeehhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p32 A  10 TVDGLATAVRGGDRAALPRAITLVESTRPDHREQAQQLLLRLLPDSGNAHRVGITGVPGVGKSTAIEALGMHLIERGHRVAVLAVD----------------MARLAVHPNAYIRPSP--GTLGGVTRATRETVVLLEAAGFDVILIETVGVGQSEVAVANMVDTFVLLTLARTGDQLQGIKKGVLELADIVVVNKADGEHHKEARLAARELSAAIRLIYPREALWRPPVLTMSAVEGRGLAELWDTVERHRQVLTGAGEFDARRRDQQVDWTWQLVRDAVLDRVWSNPTVRKVRSELERRVRAGELTPALAAQQILEIANLTD 333
                                    19        29        39        49        59        69        79        89     |   -         -  |    119       | -|      139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329    
                                                                                                                95              112            127  |                                                                                                                                                                                                           
                                                                                                                                                  130
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P32)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (5, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (Y1496_MYCTU | P9WPZ1)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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.

Chain A   (Y1496_MYCTO | P9WPZ0)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        Y1496_MYCTO | P9WPZ0: 3md0 4gt1
        Y1496_MYCTU | P9WPZ1: 3md0 4gt1

(-) Related Entries Specified in the PDB File

2gm7 MEAB, A BACTERIAL HOMOLOG OF MMAA, BOUND TO GDP
2www HUMAN METHYLMALONIC ACIDEMIA TYPE A PROTEIN MMAA RELATED ID: MYTUD.00200.A RELATED DB: TARGETDB
3mdo STRUCTURE CRYSTALLIZED IN THE PRESENCE OF GDP
3nxs STRUCTURE OF SAME PROTEIN FROM MYCOBACTERIUM SMEGATIS BOUND TO GDP