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(-) Description

Title :  CRYSTAL STRUCTURE OF ARGININE/ORNITHINE TRANSPORT SYSTEM ATPASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO GDP (A RAS-LIKE GTPASE SUPERFAMILY PROTEIN)
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  29 Mar 10  (Deposition) - 21 Apr 10  (Release) - 03 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Seattle Structural Genomics Center For Infectious Disease, Ras, Ras- Like Gtpase, Allosteric Modulator, Tuberculosis, Atp-Binding, Nucleotide-Binding, Ssgcid, Transport Protein (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
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ARGININE/ORNITHINE TRANSPORT SYSTEM ATPASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RV1496
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV

 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, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2UNX4Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2UNX8Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:68 , 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:245BINDING SITE FOR RESIDUE GDP A 335

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MD0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MD0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MD0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MD0)

(-) Exons   (0, 0)

(no "Exon" information available for 3MD0)

(-) 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:301
 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 d3md0a_ A: automated matches                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ----------------ArgK-3md0A01 A:26-299                                                                                                                                                                                                                                                             ---------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhh....eeeee.----------------.hhhhhh...eeee..----hhhhhhhhhhhhhhhhhhh...eeeee.---.hhhhhhhh...eeeeeee............hhhhhh.eeeee..hhhhhhhhhhhhhhhhhhhhhhh.........eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3md0 A  10 TVDGLATAVRGGDRAALPRAITLVESTRPDHREQAQQLLLRLLPDSGNAHRVGITGVPGVGKSTAIEALGMHLIERGHRVAVLAV----------------RMARLAVHPNAYIRPS----TLGGVTRATRETVVLLEAAGFDVILIET---GQSEVAVANMVDTFVLLTLARTGDQLQGIKKGVLELADIVVVNKADGEHHKEARLAARELSAAIRLIYPREALWRPPVLTMSAVEGRGLAELWDTVERHRQVLTGAGEFDARRRDQQVDWTWQLVRDAVLDRVWSNPTVRKVRSELERRVRAGELTPALAAQQILEIANLTD 333
                                    19        29        39        49        59        69        79        89    |    -         - |     119      |  - |     139       149        |-  |    169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329    
                                                                                                               94              111            126  131                        158 162                                                                                                                                                                           


Chain A from PDB  Type:PROTEIN  Length:301
 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 d3md0a_ A: automated matches                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ----------------ArgK-3md0A01 A:26-299                                                                                                                                                                                                                                                             ---------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhh....eeeee.----------------.hhhhhh...eeee..----hhhhhhhhhhhhhhhhhhh...eeeee.---.hhhhhhhh...eeeeeee............hhhhhh.eeeee..hhhhhhhhhhhhhhhhhhhhhhh.........eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3md0 A  10 TVDGLATAVRGGDRAALPRAITLVESTRPDHREQAQQLLLRLLPDSGNAHRVGITGVPGVGKSTAIEALGMHLIERGHRVAVLAV----------------RMARLAVHPNAYIRPS----TLGGVTRATRETVVLLEAAGFDVILIET---GQSEVAVANMVDTFVLLTLARTGDQLQGIKKGVLELADIVVVNKADGEHHKEARLAARELSAAIRLIYPREALWRPPVLTMSAVEGRGLAELWDTVERHRQVLTGAGEFDARRRDQQVDWTWQLVRDAVLDRVWSNPTVRKVRSELERRVRAGELTPALAAQQILEIANLTD 333
                                    19        29        39        49        59        69        79        89    |    -         - |     119      |  - |     139       149        |-  |    169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329    
                                                                                                               94              111            126  131                        158 162
   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 3MD0)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (5, 10)

Asymmetric Unit(hide GO term definitions)
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.

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.

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 Related Entries

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

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        Y1496_MYCTO | P9WPZ0: 3p32 4gt1
        Y1496_MYCTU | P9WPZ1: 3p32 4gt1

(-) Related Entries Specified in the PDB File

3nxs 3p32 3tk1 4gt1