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(-) Description

Title :  CRYSTAL STRUCTURE OF DEOXYGUANOSINETRIPHOSPHATE TRIPHOSPHOHYDROLASE FROM FLAVOBACTERIUM SP. MED217
 
Authors :  A. A. Fedorov, E. V. Fedorov, R. Toro, A. J. Meyer, J. M. Sauder, S. K. Burl S. C. Almo, New York Sgx Research Center For Structural Genomi (Nysgxrc)
Date :  25 Nov 07  (Deposition) - 04 Dec 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Structural Genomics, Nysgxrc, Target 10395N, Triphosphohydrolase, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Fedorov, E. V. Fedorov, R. Toro, A. J. Meyer, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of The Deoxyguanosinetriphosphate Triphosphohydrolase From Flavobacterium Sp. Med217.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DGTP TRIPHOSPHOHYDROLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MED217_16760
    Organism Scientific: LEEUWENHOEKIELLA BLANDENSIS
    Organism Taxid: 398720
    Strain: MED217

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3BG2)

(-) Sites  (0, 0)

(no "Site" information available for 3BG2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BG2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3BG2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BG2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BG2)

(-) Exons   (0, 0)

(no "Exon" information available for 3BG2)

(-) 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:397
 aligned with A3XHN1_LEEBM | A3XHN1 from UniProtKB/TrEMBL  Length:444

    Alignment length:440
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441
         A3XHN1_LEEBM     2 MNWEHLLSLKRQGDTAKRLRIEQDDTRLGFEVDYDRIIFSAPFRSLQDKTQVIPLSKTDFVHTRLTHSLEVSVVGRSLGRMVGKKLLEKYPHLEQVYGYKFNDFGAIVAAAALAHDIGNPPFGHSGEKAIGEFFKNGYGKRYKDSLTAKEYQDLIKFEGNANGFKVLSQSKPGAQGGLRLSYATLGAFMKYPKESLPHKPSDHIADKKYGFFQSERALFEDVAQELGLLKRSTTDDVSWSRHPLAYLVEAADDICYTIIDFEDGINLGLIPEEYALEYMVKLVGQTIDRNKYNALQETSDRVSYLRALAIGTLINESVDTFMKYEEEILAGTFDQSLIDKSNYQAQITDIINLSIERIYNSREVIEKEIAGYEILSTLLEARCRALDNNDTHYNQLIQQLLAPNDHSEKSLYENLIQICAEVSTMTDGKALRNYKKIKGL 441
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3bg2A01 A:2-120,A:157-244 Hypothetical protein af1432                                                                  3bg2A02 A:121-156,A:360-441         3bg2A01 A:2-120,A:157-244 Hypothetical pr           otein af1432                        3bg2A03 A:245-359 putative de                   oxyguanosinetriphosphate triphosphohydrolase like domain           3bg2A02 A:121-156,A:360-441                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....---.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...........hhhhhhhhh.......-----------....hhhhhhhhhhhhhhhh....----........hhhhhhhhhhhhhhhhhhhhhhhhh....-------------------.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bg2 A   2 MNWEHLLSLKRQGDTAKRLRIEQDDTRLGFEVDYDRIIFSAPFRSLQDKTQVIP---TDFVHTRLTHSLEVSVVGRSLGRMVGKKLLEKYPHLEQVYGYKFNDFGAIVAAAALAHDIGNPPFGHSGEKAIGEFFKNGYGKRYKDSLTAKEYQDLIKFEGNANGFKVLSQSKPGAQGGLRLSYATLGAFMKYPKESL-----------KYGFFQSERALFEDVAQELGLLKR----DVSWSRHPLAYLVEAADDICYTIIDFEDGINLGLIPE-------------------YNALQETSDRVSYLRALAIGTLINESVDTFMKYEEEILAGTFDQSLIDKSNYQAQITDIINLSIERIYNSREVIEKEIAGYEILSTLLEARCRALDNNDTHYNQLIQQLLA------KSLYENLIQICAEVSTMTDGKALRNYKKIKGL 441
                                    11        21        31        41        51   |   |61        71        81        91       101       111       121       131       141       151       161       171       181       191     |   -       211       221       231|    | 241       251       261       271 |       -         - |     301       311       321       331       341       351       361       371       381       391       401 |     411       421       431       441
                                                                                55  59                                                                                                                                       197         209                    232  237                                 273                 293                                                                                                           403    410                               


Chain B from PDB  Type:PROTEIN  Length:397
 aligned with A3XHN1_LEEBM | A3XHN1 from UniProtKB/TrEMBL  Length:444

    Alignment length:440
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441
         A3XHN1_LEEBM     2 MNWEHLLSLKRQGDTAKRLRIEQDDTRLGFEVDYDRIIFSAPFRSLQDKTQVIPLSKTDFVHTRLTHSLEVSVVGRSLGRMVGKKLLEKYPHLEQVYGYKFNDFGAIVAAAALAHDIGNPPFGHSGEKAIGEFFKNGYGKRYKDSLTAKEYQDLIKFEGNANGFKVLSQSKPGAQGGLRLSYATLGAFMKYPKESLPHKPSDHIADKKYGFFQSERALFEDVAQELGLLKRSTTDDVSWSRHPLAYLVEAADDICYTIIDFEDGINLGLIPEEYALEYMVKLVGQTIDRNKYNALQETSDRVSYLRALAIGTLINESVDTFMKYEEEILAGTFDQSLIDKSNYQAQITDIINLSIERIYNSREVIEKEIAGYEILSTLLEARCRALDNNDTHYNQLIQQLLAPNDHSEKSLYENLIQICAEVSTMTDGKALRNYKKIKGL 441
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3bg2B01 B:2-120,B:157-244 Hypothetical protein af1432                                                                  3bg2B02 B:121-156,B:360-441         3bg2B01 B:2-120,B:157-244 Hypothetical pr           otein af1432                        3bg2B03 B:245-359 putative de                   oxyguanosinetriphosphate triphosphohydrolase like domain           3bg2B02 B:121-156,B:360-441                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....---.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...........hhhhhhhhh.......-----------....hhhhhhhhhhhhhhhh....----........hhhhhhhhhhhhhhhhhhhhhhhhh....-------------------.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bg2 B   2 MNWEHLLSLKRQGDTAKRLRIEQDDTRLGFEVDYDRIIFSAPFRSLQDKTQVIP---TDFVHTRLTHSLEVSVVGRSLGRMVGKKLLEKYPHLEQVYGYKFNDFGAIVAAAALAHDIGNPPFGHSGEKAIGEFFKNGYGKRYKDSLTAKEYQDLIKFEGNANGFKVLSQSKPGAQGGLRLSYATLGAFMKYPKESL-----------KYGFFQSERALFEDVAQELGLLKR----DVSWSRHPLAYLVEAADDICYTIIDFEDGINLGLIPE-------------------YNALQETSDRVSYLRALAIGTLINESVDTFMKYEEEILAGTFDQSLIDKSNYQAQITDIINLSIERIYNSREVIEKEIAGYEILSTLLEARCRALDNNDTHYNQLIQQLLA------KSLYENLIQICAEVSTMTDGKALRNYKKIKGL 441
                                    11        21        31        41        51   |   |61        71        81        91       101       111       121       131       141       151       161       171       181       191     |   -       211       221       231|    | 241       251       261       271 |       -         - |     301       311       321       331       341       351       361       371       381       391       401 |     411       421       431       441
                                                                                55  59                                                                                                                                       197         209                    232  237                                 273                 293                                                                                                           403    410
   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  (0, 0)

(no "SCOP Domain" information available for 3BG2)

(-) CATH Domains  (3, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BG2)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A3XHN1_LEEBM | A3XHN1)
molecular function
    GO:0008832    dGTPase activity    Catalysis of the reaction: dGTP + H(2)O = 2'-deoxyguanosine + 2 H(+) + triphosphate.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
biological process
    GO:0046039    GTP metabolic process    The chemical reactions and pathways involving GTP, guanosine triphosphate.

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