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(-) Description

Title :  CRYSTAL STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE DOMAIN FROM MYCOBACTERIUM TUBERCULOSIS WITH SULFATE AND ZINC AT PH 4.00
 
Authors :  M. Singh, S. Karthikeyan
Date :  14 Apr 10  (Deposition) - 23 Feb 11  (Release) - 07 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.06
Chains :  Asym./Biol. Unit :  A
Keywords :  Riboflavin, Fmn, Fad, Dhbps, Sulfate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Singh, P. Kumar, S. Karthikeyan
Structural Basis For Ph Dependent Monomer-Dimer Transition Of 3, 4-Dihydroxy 2-Butanone-4-Phosphate Synthase Domain Fro Mycobacterium Tuberculosis
J. Struct. Biol. V. 174 374 2011
PubMed-ID: 21296160  |  Reference-DOI: 10.1016/J.JSB.2011.01.013

(-) Compounds

Molecule 1 - 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE
    ChainsA
    EC Number4.1.99.12
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-28(C)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneRIBA2
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid419947
    StrainH37RA
    SynonymDHBP SYNTHASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
2ZN2Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:141 , GLY A:143 , HIS A:144 , THR A:145 , ZN A:210 , HOH A:285BINDING SITE FOR RESIDUE SO4 A 207
2AC2SOFTWARELYS A:18 , LYS A:134 , ARG A:140 , HOH A:216 , HOH A:241BINDING SITE FOR RESIDUE SO4 A 208
3AC3SOFTWAREASN A:94 , GLY A:95 , HOH A:237BINDING SITE FOR RESIDUE SO4 A 209
4AC4SOFTWAREHIS A:144 , SO4 A:207BINDING SITE FOR RESIDUE ZN A 210
5AC5SOFTWAREARG A:140 , HIS A:188 , HOH A:286BINDING SITE FOR RESIDUE ZN A 211

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MK5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Arg A:124 -Pro A:125

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MK5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MK5)

(-) Exons   (0, 0)

(no "Exon" information available for 3MK5)

(-) Sequences/Alignments

Asymmetric/Biological 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:191
 aligned with RIBBA_MYCTA | A5U2B7 from UniProtKB/Swiss-Prot  Length:425

    Alignment length:207
                             1                                                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       
          RIBBA_MYCTA     - -MTRLDSVERAVADIAAGKAVIVIDDEDRENEGDLIFAAEKATPEMVAFMVRYTSGYLCVPLDGAICDRLGLLPMYAVNQDKHGTAYTVTVDARNGIGTGISASDRATTMRLLADPTSVADDFTRPGHVVPLRAKDGGVLRRPGHTEAAVDLARMAGLQPAGAICEIVSQKDEGSMAHTDELRVFADEHGLALITIADLIEWRRKHE 206
               SCOP domains d3mk5a_ A: automated matches                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------DHBP_synthase-3mk5A01    A:7-202                                                                                                                                                                    ---- Pfam domains
         Sec.struct. author ......hhhhhhhhhhh...eeee....---.eeeeee.hhhhhhhhhhhhhhh....eeeehhhhhhhhh....-----------....eee........hhhhhhhhhhhhhh...hhh.eeeeeeeeeee...hhhhh..hhhhhhhhhhhhh.....eeeee...--..hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mk5 A   0 HMTRLDSVERAVADIAAGKAVIVIDDED---EGDLIFAAEKATPEMVAFMVRYTSGYLCVPLDGAICDRLGLLPM-----------YTVTVDARNGIGTGISASDRATTMRLLADPTSVADDFTRPGHVVPLRAKDGGVLRRPGHTEAAVDLARMAGLQPAGAICEIVS--DEGSMAHTDELRVFADEHGLALITIADLIEWRRKHE 206
                                     9        19       | - |      39        49        59        69    |    -      | 89        99       109       119       129       139       149       159        |- |     179       189       199       
                                                      27  31                                         74          86                                                                               168  |                                   
                                                                                                                                                                                                     171                                   

   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/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MK5)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RIBBA_MYCTA | A5U2B7)
molecular function
    GO:0008686    3,4-dihydroxy-2-butanone-4-phosphate synthase activity    Catalysis of the reaction: D-ribulose 5-phosphate = (2S)-2-hydroxy-3-oxobutyl phosphate + formate + H(+).
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003935    GTP cyclohydrolase II activity    Catalysis of the reaction: GTP + 3 H(2)O = 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine + diphosphate + formate + 3 H(+).
    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: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: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:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0009231    riboflavin biosynthetic process    The chemical reactions and pathways resulting in the formation of riboflavin (vitamin B2), the precursor for the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD).

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 Related Entries

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

UniProtKB/Swiss-Prot
        RIBBA_MYCTA | A5U2B73mgz 3mio 4i14

(-) Related Entries Specified in the PDB File

3mgz CRYSTAL STRUCTURE OF DHBPS DOMAIN OF BI-FUNCTIONAL DHBPS/ GTP CYCLOHYDROLASE II FROM MYCOBACTERIUM TUBERCULOSIS AT PH 4.0
3mio CRYSTAL STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE DOMAIN FROM MYCOBACTERIUM TUBERCULOSIS AT PH 6.00