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(-) Description

Title :  CRYSTAL STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE DOMAIN FROM MYCOBACTERIUM TUBERCULOSIS AT PH 6.00
 
Authors :  M. Singh, S. Karthikeyan
Date :  11 Apr 10  (Deposition) - 23 Feb 11  (Release) - 07 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Dhbps, Riboflavin, Phosphate, Ribulose-5-Phosphate, Fad, Fmn, 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
    Chains: A, B
    EC Number: 4.1.99.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28(C)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RIBA2
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 419947
    Strain: H37RA
    Synonym: DHBP SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): A 
Biological Unit 2 (2x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2K2Ligand/IonPOTASSIUM ION
3PO43Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2K-1Ligand/IonPOTASSIUM ION
3PO44Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 10)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
2K-1Ligand/IonPOTASSIUM ION
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:5 , SER A:6 , ARG A:9 , HOH A:467 , ASP B:5 , SER B:6 , ARG B:9 , HOH B:405BINDING SITE FOR RESIDUE PO4 A 300
02AC2SOFTWAREARG A:141 , GLY A:143 , HIS A:144 , THR A:145 , GOL A:303 , HOH A:516 , HOH A:566 , HOH A:576BINDING SITE FOR RESIDUE PO4 A 301
03AC3SOFTWARETYR A:56 , HIS A:127 , PO4 A:301 , HOH A:457 , HOH A:493 , HOH A:517BINDING SITE FOR RESIDUE GOL A 303
04AC4SOFTWAREGLU A:39 , LYS A:40 , HOH A:417 , HOH A:429BINDING SITE FOR RESIDUE GOL A 306
05AC5SOFTWAREVAL A:50 , ARG A:51 , THR A:53 , HOH A:432 , HOH A:554BINDING SITE FOR RESIDUE K A 309
06AC6SOFTWAREARG B:141 , GLY B:143 , HIS B:144 , THR B:145 , GOL B:308 , HOH B:486 , HOH B:550BINDING SITE FOR RESIDUE PO4 B 302
07AC7SOFTWAREGLU B:39 , LYS B:40 , HOH B:516BINDING SITE FOR RESIDUE GOL B 304
08AC8SOFTWAREASN B:30 , GLU B:31 , THR B:98 , HOH B:420 , HOH B:550BINDING SITE FOR RESIDUE GOL B 305
09AC9SOFTWARETHR B:107 , ARG B:110 , LEU B:111 , HOH B:521 , HOH B:557 , HOH B:558BINDING SITE FOR RESIDUE GOL B 307
10BC1SOFTWARETYR B:56 , HIS B:127 , GLU B:165 , PO4 B:302 , HOH B:508 , HOH B:509 , HOH B:582BINDING SITE FOR RESIDUE GOL B 308
11BC2SOFTWAREVAL B:50 , ARG B:51 , THR B:53 , HOH B:435 , HOH B:478BINDING SITE FOR RESIDUE K B 309

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Arg A:124 -Pro A:125
2Arg B:124 -Pro B:125

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MIO)

(-) 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:195
 aligned with RIBBA_MYCTA | A5U2B7 from UniProtKB/Swiss-Prot  Length:425

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
          RIBBA_MYCTA     1 MTRLDSVERAVADIAAGKAVIVIDDEDRENEGDLIFAAEKATPEMVAFMVRYTSGYLCVPLDGAICDRLGLLPMYAVNQDKHGTAYTVTVDARNGIGTGISASDRATTMRLLADPTSVADDFTRPGHVVPLRAKDGGVLRRPGHTEAAVDLARMAGLQPAGAICEIVSQKDEGSMAHTDELRVFADEHGLALITIADLIEWRRKHE 206
               SCOP domains d3mioa_ A: automated matches                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh...eeee.........eeeee.hhhhhhhhhhhhhhh....eeeehhhhhhhh.....-----------....eee........hhhhhhhhhhhhhh...hhh.eeeeeeeeeee...hhhhh..hhhhhhhhhhhhh.....eeeee...........hhhhhhhhhhhhh.eeeehhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mio A   1 MTRLDSVERAVADIAAGKAVIVIDDEDRENEGDLIFAAEKATPEMVAFMVRYTSGYLCVPLDGAICDRLGLLPM-----------YTVTVDARNGIGTGISASDRATTMRLLADPTSVADDFTRPGHVVPLRAKDGGVLRRPGHTEAAVDLARMAGLQPAGAICEIVSQKDEGSMAHTDELRVFADEHGLALITIADLIEWRRKHE 206
                                    10        20        30        40        50        60        70   |     -     |  90       100       110       120       130       140       150       160       170       180       190       200      
                                                                                                    74          86                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:194
 aligned with RIBBA_MYCTA | A5U2B7 from UniProtKB/Swiss-Prot  Length:425

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
          RIBBA_MYCTA     1 MTRLDSVERAVADIAAGKAVIVIDDEDRENEGDLIFAAEKATPEMVAFMVRYTSGYLCVPLDGAICDRLGLLPMYAVNQDKHGTAYTVTVDARNGIGTGISASDRATTMRLLADPTSVADDFTRPGHVVPLRAKDGGVLRRPGHTEAAVDLARMAGLQPAGAICEIVSQKDEGSMAHTDELRVFADEHGLALITIADLIEWRRKHE 206
               SCOP domains d3miob_ B: automated matches                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------DHBP_synthase-3mioB01 B:7-202                                                                                                                                                                       ---- Pfam domains (1)
           Pfam domains (2) ------DHBP_synthase-3mioB02 B:7-202                                                                                                                                                                       ---- Pfam domains (2)
         Sec.struct. author .....hhhhhhhhhhh...eeee.........eeeee.hhhhhhhhhhhhhhh....eeeehhhhhhhh.....------------...eee........hhhhhhhhhhhhhh...hhh.eeeeeeeeeee...hhhhh..hhhhhhhhhhhhh.....eeeee...........hhhhhhhhhhhhh.eeeehhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mio B   1 MTRLDSVERAVADIAAGKAVIVIDDEDRENEGDLIFAAEKATPEMVAFMVRYTSGYLCVPLDGAICDRLGLLPM------------TVTVDARNGIGTGISASDRATTMRLLADPTSVADDFTRPGHVVPLRAKDGGVLRRPGHTEAAVDLARMAGLQPAGAICEIVSQKDEGSMAHTDELRVFADEHGLALITIADLIEWRRKHE 206
                                    10        20        30        40        50        60        70   |     -      | 90       100       110       120       130       140       150       160       170       180       190       200      
                                                                                                    74           87
   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, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: DHBP_synthase] (17)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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 | A5U2B7: 3mgz 3mk5 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
3mk5 CRYSTAL STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE DOMAIN FROM MYCOBACTERIUM TUBERCULOSIS WITH SULFATE AND ZINC AT ACTIVE SITE AT PH 4.00