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(-) Description

Title :  STRUCTURE OF TRYPANOSOMA BRUCEI ENOLASE REVEALS THE INHIBITORY DIVALENT METAL SITE
 
Authors :  M. T. Da Silva Giotto, M. V. A. S. Navarro, R. C. Garratt, D. J. Rigden
Date :  28 Mar 03  (Deposition) - 02 Apr 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Lyase, Glycolysis, His-Tag (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. T. Da Silva Giotto, V. Hannaert, D. Vertommen, M. V. A. S. Navarro, M. H. Rider, P. A. M. Michels, R. C. Garratt, D. J. Rigden
The Crystal Structure Of Trypanosoma Brucei Enolase: Visualisation Of The Inhibitory Metal Binding Site Iii And Potential As Target For Selective, Irreversible Inhibition
J. Mol. Biol. V. 331 653 2003
PubMed-ID: 12899835  |  Reference-DOI: 10.1016/S0022-2836(03)00752-6

(-) Compounds

Molecule 1 - ENOLASE
    Chains: A
    EC Number: 4.2.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28A
    Organism Scientific: TRYPANOSOMA BRUCEI BRUCEI
    Organism Taxid: 5702
    Other Details: CHAIN A HAS COVALENTLY LINKED 2 VISIBLE RESIDUES IN AN ARTEFACTUAL N-TERMINAL EXTENSION RESULTING FROM CLEAVAGE OF HIS-TAG, RESIDUES -3 TO -1
    Synonym: 2-PHOSPHOGLYCERATE DEHYDRATASE, 2-PHOSPHO-D- GLYCERATE HYDRO-LYASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2SO41Ligand/IonSULFATE ION
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2SO42Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:243 , GLU A:291 , ASP A:292 , ASP A:318 , HOH A:2234BINDING SITE FOR RESIDUE ZN A 500
2AC2SOFTWAREHIS A:156 , GLN A:164 , GLU A:165 , GLU A:208BINDING SITE FOR RESIDUE ZN A 501
3AC3SOFTWAREGLY A:38 , LYS A:343 , ARG A:372 , SER A:373 , HOH A:2234 , HOH A:2235BINDING SITE FOR RESIDUE SO4 A 600
4AC4SOFTWAREARG A:32 , TYR A:129 , GLN A:409 , GLU A:416 , HOH A:2236BINDING SITE FOR RESIDUE EDO A 700
5AC5SOFTWAREGLU A:10 , SER A:177 , LEU A:411 , GLU A:414 , GLU A:415BINDING SITE FOR RESIDUE EDO A 701
6AC6SOFTWAREARG A:130 , LYS A:139 , GLU A:140 , LEU A:141 , HOH A:2238 , HOH A:2239BINDING SITE FOR RESIDUE EDO A 702

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OEP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OEP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OEP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OEP)

(-) Exons   (0, 0)

(no "Exon" information available for 1OEP)

(-) 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:422
 aligned with Q9NDH8_TRYBB | Q9NDH8 from UniProtKB/TrEMBL  Length:429

    Alignment length:431
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                            
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428 
         Q9NDH8_TRYBB     - --MTIQKVHGREVLDSRGNPTVEVEVTTERGVFRSAVPSGASTGVYEACELRDGDKKRYVGKGCLQAVKNVNEVIGPALIGRDELKQEELDTLMLRLDGTPNKGKLGANAILGCSMAISKAAAAAKGVPLYRYLASLAGTKELRLPVPCFNVINGGKHAGNALPFQEFMIAPVKATSFSEALRMGSEVYHSLRGIIKKKYGQDAVNVGDEGGFAPPIKDINEPLPILMEAIEEAGHRGKFAICMDCAASETYDEKKQQYNLTFKSPEPTWVTAEQLRETYCKWAHDYPIVSIEDPYDQDDFAGFAGITEALKGKTQIVGDDLTVTNTERIKMAIEKKACNSLLLKINQIGTISEAIASSKLCMENGWSVMVSHRSGETEDTYIADLVVALGSGQIKTGAPCRGERTAKLNQLLRIEEELGAHAKFGFPGWS 429
               SCOP domains d1oepa2 A:-2-138 Enolase                                                                                                                    d1oepa1 A:139-429 Enolase                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---1oepA01 A:2-125 Enolase-like, N-termina  l domain                                                                           1oepA02 A:126-427 Enolase superfamily                                                                                                                                                                                                                                                                         -- CATH domains
               Pfam domains ---Enolase_N-1oepA01 A:2-132                                                                                                          -------Enolase_C-1oepA02 A:140-426                                                                                                                                                                                                                                                                    --- Pfam domains
         Sec.struct. author ......eeeeeeee.....eeeeeeeee..eeeeee......--.............hhhhh.hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.......ee.eeeee.hhhh.......eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhh.....eeeee.hhhhh..........-------.......hhhhhhhhhhhh.eeeee......hhhhhhhhhh......eeee......hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhh..eeeee........hhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oep A  -2 SHMTIQKVHGREVLDSRGNPTVEVEVTTEKGVFRSAVPSGAS--VYEACELRDGDKKRYVGKGCLQAVKNVNEVIGPALIGRDELKQEELDTLMLRLDGTPNKGKLGANAILGCSMAISKAAAAAKGVPLYRYLASLAGTKELRLPVPCFNVINGGKHAGNALPFQEFMIAPVKATSFSEALRMGSEVYHSLKGIIKKKYGQDAVNVGDEGGFAPPIKDINEPLPILMEAIEEAGHRGKFAICMDCAASETYDEKKQQYNL-------TWVTAEQLRETYCKWAHDYPIVSIEDPYDQDDFAGFAGITEALKGKTQIVGDDLTVTNTERIKMAIEKKACNSLLLKINQIGTISEAIASSKLCMENGWSVMVSHRSGETEDTYIADLVVALGSGQIKTGAPCRGERTAKLNQLLRIEEELGAHAKFGFPGWS 429
                             ||      8        18        28        38 |  |   48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258|      268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428 
                             ||                                     40 43                                                                                                                                                                                                                     259     267                                                                                                                                                                  
                            -1|                                                                                                                                                                                                                                                                                                                                                                                                                                            
                              1
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: Enolase_N (69)
(-)
Clan: Enolase_TIM (82)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9NDH8_TRYBB | Q9NDH8)
molecular function
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004634    phosphopyruvate hydratase activity    Catalysis of the reaction: 2-phospho-D-glycerate = phosphoenolpyruvate + H2O.
biological process
    GO:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
cellular component
    GO:0000015    phosphopyruvate hydratase complex    A multimeric enzyme complex, usually a dimer or an octamer, that catalyzes the conversion of 2-phospho-D-glycerate to phosphoenolpyruvate and water.

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  1oep
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 Related Entries

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        Q9NDH8_TRYBB | Q9NDH8: 2pu1

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