Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF ISPD FROM MYCOBACTERIUM SMEGMATIS IN COMPLEX WITH CTP AND MG
 
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 :  1.49
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
    ChainsA, B
    EC Number2.7.7.60
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPEXP5CT/TOPO
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VariantAI
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-219
    Organism ScientificMYCOBACTERIUM SMEGMATIS
    Organism Taxid1772
    StrainMC2
    Synonym4-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  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CTP2Ligand/IonCYTIDINE-5'-TRIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECTP A:301 , HOH A:2259 , HOH A:2260 , HOH A:2264BINDING SITE FOR RESIDUE MG A 300
2AC2SOFTWAREPRO A:8 , ALA A:9 , ALA A:10 , GLY A:11 , SER A:12 , GLY A:13 , GLU A:14 , ARG A:15 , 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 , MG A:300 , HOH A:2044 , HOH A:2122 , HOH A:2259 , HOH A:2260 , HOH A:2261 , HOH A:2262 , HOH A:2263 , HOH A:2264 , HOH A:2265 , HOH A:2266BINDING SITE FOR RESIDUE CTP A 301
3AC3SOFTWARECTP B:301 , HOH B:2198 , HOH B:2201 , HOH B:2203BINDING SITE FOR RESIDUE MG B 300
4AC4SOFTWAREPRO B:8 , ALA B:9 , ALA B:10 , GLY B:11 , SER B:12 , GLY B:13 , GLU B:14 , ARG B:15 , LYS B:22 , GLY B:76 , VAL B:77 , ASP B:78 , ARG B:79 , SER B:82 , ASP B:100 , ALA B:101 , ALA B:102 , LYS B:204 , MG B:300 , HOH B:2195 , HOH B:2197 , HOH B:2198 , HOH B:2199 , HOH B:2200 , HOH B:2201 , HOH B:2202 , HOH B:2203BINDING SITE FOR RESIDUE CTP B 301

(-) SS Bonds  (0, 0)

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

(-) 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 2XWL)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XWL)

(-) 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:221
 aligned with A0R560_MYCS2 | A0R560 from UniProtKB/TrEMBL  Length:222

    Alignment length:221
                                    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 222
               SCOP domains d2xwla_ A: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhh...hhhh.ee..eehhhhhhhhhhhhh...eeeeeehhhhhhhhhhhh....eeeee...hhhhhhhhhhh......eeee........hhhhhhhhhhhhhhh..eeeeee.....eeee.....eee..hhh.eeee...eeeehhhhhhhhh........hhhhhhhh.....eeee.hhhhh...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xwl A   2 ATVAVVPAAGSGERLRAGRPKAFVTLGGTPLLEHALSGLRASGVIDRIVIAVPPALTDESKLVFGGEDSVIVSGGVDRTESVALALEAAGDAEFVLVHDAARALTPPALIARVVAALKEGHSAVVPGLAPADTIKAVDANGAVLGTPERAGLRAVQTPQGFHADVLRRAYARATAGGVTDDASLVEQLGTPVQIVDGDPLAFKITTPLDLVLAEAVLAHHH 222
                                    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 d2xwlb_ B: automated matches                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -IspD-2xwlB01 B:3-219                                                                                                                                                                                                     ---- Pfam domains (1)
           Pfam domains (2) -IspD-2xwlB02 B:3-219                                                                                                                                                                                                     ---- Pfam domains (2)
         Sec.struct. author .eeeeee............hhhh.ee..eehhhhhhhhhhhh....eeeeeehhhhhhhhhhhhh...eeeee...hhhhhhhhhhh......eeee........hhhhhhhhhhhhhhh..eeeeee.....eeee.....eee..hhh.eeee...eeeehhhhhhhhh........hhhhhhhh.....eeee.hhhhh...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xwl 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

(-) CATH Domains  (0, 0)

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

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CTP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Thr A:158 - Pro A:159   [ RasMol ]  
    Thr B:158 - Pro B:159   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2xwl
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  A0R560_MYCS2 | A0R560
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  2.7.7.60
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  A0R560_MYCS2 | A0R560
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A0R560_MYCS2 | A0R5602xwm

(-) Related Entries Specified in the PDB File

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