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(-) Description

Title :  MYCOBACTERIUM SMEGMATIS 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE (ISPF)
 
Authors :  L. Buetow, A. C. Brown, T. Parish, W. N. Hunter
Date :  27 Apr 07  (Deposition) - 06 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Ispf, Lyase, Mycobacteria, Complex With Cdp, Non-Mevalonate Pathway Of Isoprenoid Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Buetow, A. C. Brown, T. Parish, W. N. Hunter
The Structure Of Mycobacteria 2C-Methyl-D- Erythritol-2, 4-Cyclodiphosphate Synthase, An Essential Enzyme, Provides A Platform For Drug Discovery.
Bmc Struct. Biol. V. 7 68 2007
PubMed-ID: 17956607  |  Reference-DOI: 10.1186/1472-6807-7-68

(-) Compounds

Molecule 1 - 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE
    Atcc: 700084
    Chains: A, B, C
    EC Number: 4.6.1.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15TEV (VARIANT OF PET15B FROM NOVAGEN)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: MYCOBACTERIUM SMEGMATIS
    Organism Taxid: 1772
    Other Details: EACH CONTAINS A ZN CATION, WHICH IS REQUIRED FOR ACTIVITY, AND CDP, A FRAGMENT OF SUBSTRATE.
    Strain: MC(2)155

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 15)

Asymmetric/Biological Unit (7, 15)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CDP3Ligand/IonCYTIDINE-5'-DIPHOSPHATE
3EDO2Ligand/Ion1,2-ETHANEDIOL
4GOL3Ligand/IonGLYCEROL
5IPE1Ligand/Ion3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
6PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
7ZN3Ligand/IonZINC ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:11 , HIS A:13 , HIS A:45 , CDP C:1158BINDING SITE FOR RESIDUE ZN A1157
02AC2SOFTWAREGLY A:103 , ASN A:104 , PRO A:106 , LYS A:107 , VAL A:108 , GLY A:109 , ALA A:131 , THR A:132 , THR A:133 , HOH A:2072 , HOH A:2073 , HOH A:2074 , HOH A:2075 , HOH A:2076 , HOH A:2077 , HOH A:2078 , ASP B:11 , VAL B:12 , HIS B:13 , HIS B:45 , ASP B:59 , LEU B:60 , GLY B:61 , HOH B:2037 , ZN C:1157BINDING SITE FOR RESIDUE CDP A1158
03AC3SOFTWARECDP B:1158 , ASP C:11 , HIS C:13 , HIS C:45BINDING SITE FOR RESIDUE ZN B1157
04AC4SOFTWAREARG B:72 , GLY B:103 , ASN B:104 , PRO B:106 , LYS B:107 , VAL B:108 , GLY B:109 , ALA B:131 , THR B:132 , THR B:133 , ZN B:1157 , HOH B:2102 , HOH B:2103 , HOH B:2104 , HOH B:2105 , HOH B:2106 , ASP C:11 , VAL C:12 , HIS C:13 , ASP C:59 , LEU C:60 , GLY C:61 , HOH C:2028BINDING SITE FOR RESIDUE CDP B1158
05AC5SOFTWARECDP A:1158 , ASP B:11 , HIS B:13 , HIS B:45BINDING SITE FOR RESIDUE ZN C1157
06AC6SOFTWAREASP A:11 , VAL A:12 , HIS A:13 , ASP A:59 , GLY A:61 , ZN A:1157 , HOH A:2020 , GLY C:103 , ASN C:104 , PRO C:106 , LYS C:107 , VAL C:108 , GLY C:109 , ALA C:131 , THR C:132 , THR C:133 , ASP C:135 , HOH C:2075 , HOH C:2076 , HOH C:2078 , HOH C:2079 , HOH C:2080BINDING SITE FOR RESIDUE CDP C1158
07AC7SOFTWARESER A:53 , GLY A:56 , LEU A:57 , GLY A:58 , ARG C:112 , GLN C:116 , SER C:128 , VAL C:129 , SER C:130 , HOH C:2071BINDING SITE FOR RESIDUE EDO C1160
08AC8SOFTWAREARG A:112 , GLN A:116 , SER A:128 , VAL A:129 , SER A:130 , HOH A:2079 , LEU B:52 , SER B:53 , GLY B:56 , LEU B:57 , GLY B:58BINDING SITE FOR RESIDUE EDO A1160
09AC9SOFTWAREGLY A:138 , LEU A:139 , ARG A:142 , GLY B:138 , LEU B:139 , ARG B:142 , ALA B:147 , GLY C:138 , LEU C:139BINDING SITE FOR RESIDUE IPE B1160
10BC1SOFTWAREGLY A:85 , ASN A:89 , GLY C:124 , ACT C:1162 , HOH C:2068 , HOH C:2081BINDING SITE FOR RESIDUE GOL C1161
11BC2SOFTWAREGLN A:116 , VAL A:127 , SER A:128 , HOH A:2080 , ARG B:5 , HOH B:2004BINDING SITE FOR RESIDUE GOL A1161
12BC3SOFTWAREPRO B:14 , ILE B:15 , GLU B:16 , GLU B:121 , PEG B:1162 , HOH B:2107 , HOH B:2108BINDING SITE FOR RESIDUE GOL B1161
13BC4SOFTWAREHIS A:82 , GLY A:85 , ASN A:89 , ARG C:84 , GLU C:121 , GLY C:124 , GOL C:1161BINDING SITE FOR RESIDUE ACT C1162
14BC5SOFTWAREILE B:15 , CYS B:25 , ALA B:77 , ARG B:81 , VAL B:118 , ARG B:142 , GLU B:144 , GOL B:1161 , HOH B:2038 , HOH B:2088BINDING SITE FOR RESIDUE PEG B1162
15BC6SOFTWAREARG B:19 , ASP B:30 , ALA B:31 , ASP B:32 , ARG B:81 , HIS B:82 , HOH B:2109 , ARG C:142BINDING SITE FOR RESIDUE PEG B1163

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Asp A:32 -Gly A:33
2Arg A:105 -Pro A:106
3Arg B:105 -Pro B:106
4Asp C:32 -Gly C:33
5Arg C:105 -Pro C:106

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2UZH)

(-) 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:153
 aligned with A0R559_MYCS2 | A0R559 from UniProtKB/TrEMBL  Length:163

    Alignment length:155
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152     
         A0R559_MYCS2     3 LPRVGLGTDVHPIEAGRPCRLLCLEFDDADGCAGHSDGDVAAHALCDALLSAAGLGDLGTIFGTDRPQWRGASGADMIRHVRGLVENAGFVIGNATVQVIGNRPKVGPRREEAQQVLSELVGAPVSVSATTTDGLGLTGRGEGLAAIATALVAAE 157
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2uzhA00 A:3-157  [code=3.30.1330.  50, no name defined]                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.......ee..ee........--...hhhhhhhhhhhhhhh...hhhhhhh..hhhhh..hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhhh..eeeeee....hhhhhh..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uzh A   3 LPRVGLGTDVHPIEAGRPCRLLCLEFDDADGCA--SDGDVAAHALCDALLSAAGLGDLGTIFGTDRPQWRGASGADMIRHVRGLVENAGFVIGNATVQVIGNRPKVGPRREEAQQVLSELVGAPVSVSATTTDGLGLTGRGEGLAAIATALVAAE 157
                                    12        22        32  |  |  42        52        62        72        82        92       102       112       122       132       142       152     
                                                           35 38                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:153
 aligned with A0R559_MYCS2 | A0R559 from UniProtKB/TrEMBL  Length:163

    Alignment length:155
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152     
         A0R559_MYCS2     3 LPRVGLGTDVHPIEAGRPCRLLCLEFDDADGCAGHSDGDVAAHALCDALLSAAGLGDLGTIFGTDRPQWRGASGADMIRHVRGLVENAGFVIGNATVQVIGNRPKVGPRREEAQQVLSELVGAPVSVSATTTDGLGLTGRGEGLAAIATALVAAE 157
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2uzhB00 B:3-157  [code=3.30.1330.  50, no name defined]                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeeeeeee..eeeeeeeee.--...hhhhhhhhhhhhhhh...hhhhhhh..hhhhh..hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhhh..eeeeee....hhhhhh..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uzh B   3 LPRVGLGTDVHPIEAGRPCRLLCLEFDDADGCA--SDGDVAAHALCDALLSAAGLGDLGTIFGTDRPQWRGASGADMIRHVRGLVENAGFVIGNATVQVIGNRPKVGPRREEAQQVLSELVGAPVSVSATTTDGLGLTGRGEGLAAIATALVAAE 157
                                    12        22        32  |  |  42        52        62        72        82        92       102       112       122       132       142       152     
                                                           35 38                                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:155
 aligned with A0R559_MYCS2 | A0R559 from UniProtKB/TrEMBL  Length:163

    Alignment length:155
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152     
         A0R559_MYCS2     3 LPRVGLGTDVHPIEAGRPCRLLCLEFDDADGCAGHSDGDVAAHALCDALLSAAGLGDLGTIFGTDRPQWRGASGADMIRHVRGLVENAGFVIGNATVQVIGNRPKVGPRREEAQQVLSELVGAPVSVSATTTDGLGLTGRGEGLAAIATALVAAE 157
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2uzhC00 C:3-157  [code=3.30.1330.50, no name defined]                                                                                                       CATH domains
           Pfam domains (1) -YgbB-2uzhC01 C:4-157                                                                                                                                       Pfam domains (1)
           Pfam domains (2) -YgbB-2uzhC02 C:4-157                                                                                                                                       Pfam domains (2)
           Pfam domains (3) -YgbB-2uzhC03 C:4-157                                                                                                                                       Pfam domains (3)
         Sec.struct. author ..eeeeeeeeee......eee..eee............hhhhhhhhhhhhhhh...hhhhhhh..hhhhh..hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhhh..eeeeee............eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uzh C   3 LPRVGLGTDVHPIEAGRPCRLLCLEFDDADGCAGHSDGDVAAHALCDALLSAAGLGDLGTIFGTDRPQWRGASGADMIRHVRGLVENAGFVIGNATVQVIGNRPKVGPRREEAQQVLSELVGAPVSVSATTTDGLGLTGRGEGLAAIATALVAAE 157
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152
   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 2UZH)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: YgbB] (24)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (A0R559_MYCS2 | A0R559)
molecular function
    GO:0008685    2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity    Catalysis of the reaction: 4-CDP-2-C-methyl-D-erythritol 2-phosphate = 2-C-methyl-D-erythritol 2,4-cyclic diphosphate + CMP.
    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: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.
biological process
    GO:0019288    isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway    The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.
    GO:0008299    isoprenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
    GO:0016114    terpenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of terpenoids, any member of a class of compounds characterized by an isoprenoid chemical structure.

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