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(-) Description

Title :  CRYSTAL STRUCTURE OF ISPD FROM MYCOBACTERIUM SMEGMATIS IN COMPLEX WITH CMP
 
Authors :  C. Bjorkelid, T. Bergfors, T. Unge, T. A. Jones
Date :  04 Nov 10  (Deposition) - 27 Apr 11  (Release) - 01 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Mep Pathway (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Bjorkelid, T. Bergfors, L. M. Henriksson, A. L. Stern, T. Unge, S. L. Mowbray, T. A. Jones
Structural And Functional Studies On Mycobacterial Ispd Enzymes
Acta Crystallogr. , Sect. D V. 67 403 2011
PubMed-ID: 21543842  |  Reference-DOI: 10.1107/S0907444911006160

(-) Compounds

Molecule 1 - 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE
    Chains: A, B
    EC Number: 2.7.7.60
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEXP5CT/TOPO
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: AI
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-219
    Organism Scientific: MYCOBACTERIUM SMEGMATIS
    Organism Taxid: 246196
    Strain: MC2
    Synonym: 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL SYNTHASE, MEP CYTIDYLYL TRANSFERASE, CDP-ME SYNTHETASE, ISPD

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1C5P2Ligand/IonCYTIDINE-5'-MONOPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:8 , ALA A:9 , ALA A:10 , GLY A:11 , LYS A:22 , GLY A:76 , VAL A:77 , ASP A:78 , ARG A:79 , SER A:82 , ASP A:100 , ALA A:101 , ALA A:102 , LYS A:204 , HOH A:2154 , HOH A:2156 , HOH A:2157 , HOH A:2158 , HOH A:2160BINDING SITE FOR RESIDUE C5P A 301
2AC2SOFTWAREPRO B:8 , ALA B:9 , ALA B:10 , GLY B:11 , SER B:12 , GLY B:13 , LYS B:22 , GLY B:76 , VAL B:77 , ASP B:78 , ARG B:79 , SER B:82 , ASP B:100 , HOH B:2005 , HOH B:2038 , HOH B:2045 , HOH B:2113 , HOH B:2114BINDING SITE FOR RESIDUE C5P B 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:158 -Pro A:159
2Thr B:158 -Pro B:159

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XWM)

(-) 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:220
 aligned with A0R560_MYCS2 | A0R560 from UniProtKB/TrEMBL  Length:222

    Alignment length:220
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221
         A0R560_MYCS2     2 ATVAVVPAAGSGERLRAGRPKAFVTLGGTPLLEHALSGLRASGVIDRIVIAVPPALTDESKLVFGGEDSVIVSGGVDRTESVALALEAAGDAEFVLVHDAARALTPPALIARVVAALKEGHSAVVPGLAPADTIKAVDANGAVLGTPERAGLRAVQTPQGFHADVLRRAYARATAGGVTDDASLVEQLGTPVQIVDGDPLAFKITTPLDLVLAEAVLARG 221
               SCOP domains d2xwma_ A: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee............hhhh.ee..eehhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhh...eeeee...hhhhhhhhhhh......eeee........hhhhhhhhhhhhhhh..eeeeee.....eeee.....eee..hhh.eeee...eeeehhhhhhhhhh.......hhhhhhhh.....eeee.hhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xwm A   2 ATVAVVPAAGSGERLRAGRPKAFVTLGGTPLLEHALSGLRASGVIDRIVIAVPPALTDESKLVFGGEDSVIVSGGVDRTESVALALEAAGDAEFVLVHDAARALTPPALIARVVAALKEGHSAVVPGLAPADTIKAVDANGAVLGTPERAGLRAVQTPQGFHADVLRRAYARATAGGVTDDASLVEQLGTPVQIVDGDPLAFKITTPLDLVLAEAVLAHH 221
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221


Chain B from PDB  Type:PROTEIN  Length:222
 aligned with A0R560_MYCS2 | A0R560 from UniProtKB/TrEMBL  Length:222

    Alignment length:222
                                                                                                                                                                                                                                                      222 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221| 
         A0R560_MYCS2     2 ATVAVVPAAGSGERLRAGRPKAFVTLGGTPLLEHALSGLRASGVIDRIVIAVPPALTDESKLVFGGEDSVIVSGGVDRTESVALALEAAGDAEFVLVHDAARALTPPALIARVVAALKEGHSAVVPGLAPADTIKAVDANGAVLGTPERAGLRAVQTPQGFHADVLRRAYARATAGGVTDDASLVEQLGTPVQIVDGDPLAFKITTPLDLVLAEAVLARGA-   -
               SCOP domains d2xwmb_ B: automated matches                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -IspD-2xwmB01 B:3-219                                                                                                                                                                                                     ---- Pfam domains (1)
           Pfam domains (2) -IspD-2xwmB02 B:3-219                                                                                                                                                                                                     ---- Pfam domains (2)
         Sec.struct. author .eeeeee.....hhhhh..hhhh.ee..eehhhhhhhhhhhh....eeeeeehhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh.....eeee........hhhhhhhhhhhhhh...eeeeee.....eeee.....eee..hhh.eeee...eeeehhhhhhhhhh.......hhhhhhhh.....eeee.hhhhh...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xwm B   2 ATVAVVPAAGSGERLRAGRPKAFVTLGGTPLLEHALSGLRASGVIDRIVIAVPPALTDESKLVFGGEDSVIVSGGVDRTESVALALEAAGDAEFVLVHDAARALTPPALIARVVAALKEGHSAVVPGLAPADTIKAVDANGAVLGTPERAGLRAVQTPQGFHADVLRRAYARATAGGVTDDASLVEQLGTPVQIVDGDPLAFKITTPLDLVLAEAVLAHHHH 223
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XWM)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: GT-A (172)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A0R560_MYCS2 | A0R560)
molecular function
    GO:0050518    2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity    Catalysis of the reaction: 2-C-methyl-D-erythritol 4-phosphate + CTP = 4-CDP-2-C-methyl-D-erythritol + diphosphate.
    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: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:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
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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 Related Entries

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

UniProtKB/TrEMBL
        A0R560_MYCS2 | A0R560: 2xwl

(-) Related Entries Specified in the PDB File

2xwl CRYSTAL STRUCTURE OF ISPD FROM MYCOBACTERIUM SMEGMATIS IN COMPLEX WITH CTP AND MG
2xwn CRYSTAL STRUCTURE OF ISPD FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH CTP AND MG