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(-) Description

Title :  3.0 A RESOLUTION CRYSTAL STRUCTURE OF GLYCOSOMAL PYRUVATE PHOSPHATE DIKINASE FROM TRYPANOSOMA BRUCEI
 
Authors :  L. W. Cosenza, F. Bringaud, T. Baltz, F. M. D. Vellieux
Date :  17 Dec 09  (Deposition) - 29 Dec 09  (Release) - 29 Dec 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Kinase, Transferase, Tropical Parasite (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. W. Cosenza, F. Bringaud, T. Baltz, F. M. D. Vellieux
The 3. 0 A Resolution Crystal Structure Of Glycosomal Pyruvate Phosphate Dikinase From Trypanosoma Brucei
J. Mol. Biol. V. 318 1417 2001
PubMed-ID: 12083528  |  Reference-DOI: 10.1016/S0022-2836(02)00113-4
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PYRUVATE PHOSPHATE DIKINASE
    Chains: A
    EC Number: 2.7.9.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 5691
    Strain: ANTAT1

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2X0S)

(-) Sites  (0, 0)

(no "Site" information available for 2X0S)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X0S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2X0S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2X0S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2X0S)

(-) Exons   (0, 0)

(no "Exon" information available for 2X0S)

(-) 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:899
 aligned with O76283_9TRYP | O76283 from UniProtKB/TrEMBL  Length:913

    Alignment length:903
                                    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       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901   
         O76283_9TRYP     2 VAKKWVYYFGGGNADGNKNMKELLGGKGANLAEMVNLGIPVPPGFTITTEACKTYQETETIPQEVADQVRENVSRVEKEMGAKFGDPANPLLFSVRSGAAASMPGMMDTVLNLGLNKVTVDAWVRRAPRLERFVYDSYRRFITMYADIVMQVGREDFEEALSRMKERRGTKFDTDLTASDLKELCDGYLELFELKTGCSFPQDPVMQLFAAIKAVFRSWGNPRATIYRRMNNITGLLGTAVNVQAMVFGNINDRSATGVAFSRSPSTGENFFFGEYLVNAQGEDVVAGIRTPQQINHSLSLRWAKAHGVGEEERRKRYPSMEEAMPENYRLLCDVRKRLENHYRDMQDLEFTVQDGRLWLLQCRNGKRTIHAAVRIAIDMVNEGLISREEAVLRIDPYQVDHLMHPNLEPGAEKANKPIGRGLAASPGAAVGQVVFDAESAKEWSGRGKKVIMVRLETSPEDLAGMDAACGILTARGGMTSHAAVVARGMGKCCVSGCGDMVIRGKSFKLNGSVFREGDYITIDGSKGLIYAGKLKLRSPDLKGSFQTILQWCQEMKRLGVRTNADTPADAAKARSFGAEGVGLCRTEHMFFEGSRINFIREMILADSASGRKAALDKLLPIQRADFVGILRAMRGLPVTIRLLDPPLHEFVPHDAAAQFELAQKLGMPAEKVRNRVNALHELNPMLGHRGCRLGITYPEIYNMQVRAIIEAAIAVSEEGSSVIPEIMVPLVGKKEELSLIREEVVKTAEAVITKSGKRVHYTVGTMIEVPRAAVTADSIAQKADFFSFGTNDLTQMGCGFSRDDAGPFLRHYGNLGIYAQDPFQSIDQEGIGELVRIAVTKGRRVKPMLKMGICGEHGGDPATIGFCHKVGLDYVSCSPFRVPVAIVAAAHASIKDRRAAMK 904
               SCOP domains d2x0sa3 A:1-405 Pyruvate phosphate dikinase, N-terminal domain                                                                                                                                                                                                                                                                                                                                                       d2x0sa2 A:406-537 Pyruvate phosphate dikinase, central domain                                                                       d2x0sa1 A:538-903 Pyruvate phosphate dikinase, C-terminal domain                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------2x0sA01 A:8-111,A:207-247 ATP-grasp fold, A domain                                                      2x0sA02 A:112-206  [code=1.20.80.30, no name defined]                                          2x0sA01 A:8-111,A:207-247                2x0sA03 A:248-368 ATP-grasp fold, B domain                                                                               2x0sA04 A:369-409,A:533-556              2x0sA05 A:410-530 Phosphohistidine domains of PEP-utilising enzymes                                                      --2x0sA04                 2x0sA06 A:557-897 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                                                                                ------ CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..........hhhhhhhhhhhhhhhhhh......eeeehhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...........eeeeee....----..eeeee..hhhhhh........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeee..........eeeeee...........eeeeee....hhhhhh.......hhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeeeee...hhhhhhhhhhhhhhh...hhhhhhhh....hhhhhh.ee...............eeee..eeeeeee.hhhhhhhhh.....eeeee......hhhhhh...eeee......hhhhhhhhh....eee.....ee....eee..eee...eeeee............ee..hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhh.....eeeee.hhhh...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhh......hhhhhh..........hhhhhh....hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhh.eeee..hhhhhhhhh.hhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x0s A   1 VAKKWVYYFGGGNADGNKNMKELLGGKGANLAEMVNLGIPVPPGFTITTEACKTYQETETIPQEVADQVRENVSRVEKEMGAKFGDPANPLLFSVRSGAAAS----MDTVLNLGLNKVTVDAWVRRAPRLERFVYDSYRRFITMYADIVMQVGREDFEEALSRMKERRGTKFDTDLTASDLKELCDGYLELFELKTGCSFPQDPVMQLFAAIKAVFRSWGNPRATIYRRMNNITGLLGTAVNVQAMVFGNINDRSATGVAFSRSPSTGENFFFGEYLVNAQGEDVVAGIRTPQQINHSLSLRWAKAHGVGEEERRKRYPSMEEAMPENYRLLCDVRKRLENHYRDMQDLEFTVQDGRLWLLQCRNGKRTIHAAVRIAIDMVNEGLISREEAVLRIDPYQVDHLMHPNLEPGAEKANKPIGRGLAASPGAAVGQVVFDAESAKEWSGRGKKVIMVRLETSPEDLAGMDAACGILTARGGMTSHAAVVARGMGKCCVSGCGDMVIRGKSFKLNGSVFREGDYITIDGSKGLIYAGKLKLRSPDLKGSFQTILQWCQEMKRLGVRTNADTPADAAKARSFGAEGVGLCRTEHMFFEGSRINFIREMILADSASGRKAALDKLLPIQRADFVGILRAMRGLPVTIRLLDPPLHEFVPHDAAAQFELAQKLGMPAEKVRNRVNALHELNPMLGHRGCRLGITYPEIYNMQVRAIIEAAIAVSEEGSSVIPEIMVPLVGKKEELSLIREEVVKTAEAVITKSGKRVHYTVGTMIEVPRAAVTADSIAQKADFFSFGTNDLTQMGCGFSRDDAGPFLRHYGNLGIYAQDPFQSIDQEGIGELVRIAVTKGRRVKPMLKMGICGEHGGDPATIGFCHKVGLDYVSCSPFRVPVAIVAAAHASIKDRRAAMK 903
                                    10        20        30        40        50        60        70        80        90       100 |    |110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900   
                                                                                                                               102  107
   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  (3, 3)

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

(-) CATH Domains  (6, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2X0S)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (O76283_9TRYP | O76283)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0050242    pyruvate, phosphate dikinase activity    Catalysis of the reaction: ATP + phosphate + pyruvate = AMP + diphosphate + 2 H(+) + phosphoenolpyruvate.
    GO:0016772    transferase activity, transferring phosphorus-containing groups    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
biological process
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006090    pyruvate metabolic process    The chemical reactions and pathways involving pyruvate, 2-oxopropanoate.
cellular component
    GO:0020015    glycosome    A membrane-bounded organelle found in organisms from the order Kinetoplastida that houses the enzymes of glycolysis.

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