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(-) Description

Title :  CRYSTAL STRUCTURE OF 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE FROM LISTERIA MONOCYTOGENES
 
Authors :  Y. Patskovsky, J. Ho, R. Toro, M. Gilmore, S. Miller, C. Groshong, J. M. S S. K. Burley, New York Sgx Research Center For Structural Geno (Nysgxrc)
Date :  27 Oct 08  (Deposition) - 18 Nov 08  (Release) - 24 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Transferase, Psi-2, Protein Structure Initiative, New York Structural Genomix Research Consortium, Nysgxrc, New York Sgx Research Center For Structural Genomics, Isoprene Biosynthesis, Nucleotidyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, J. Ho, R. Toro, M. Gilmore, S. Miller, C. Groshong, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of 2-C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase From Listeria Monocytogenes
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE 2
    Chains: A, B
    EC Number: 2.7.7.60
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ISPD2, LMOF2365_1100
    Organism Scientific: LISTERIA MONOCYTOGENES STR. 4B F2365
    Organism Taxid: 265669
    Synonym: 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL SYNTHASE 2, MEP CYTIDYLYLTRANSFERASE 2, MCT 2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3F1C)

(-) Sites  (0, 0)

(no "Site" information available for 3F1C)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F1C)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:167 -Pro A:168
2Thr B:167 -Pro B:168

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F1C)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ISPDPS01295 4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature.TARI_LISMF106-113
 		  2A:106-113
B:106-113

(-) Exons   (0, 0)

(no "Exon" information available for 3F1C)

(-) 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:229
 aligned with TARI_LISMF | Q720Y7 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:235
                             1                                                                                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229     
           TARI_LISMF     - -MIYAQILAGGKGTRMGNVSMPKQFLPLNGKPIIVHTVEKFILNTRFDKILISSPKEWMNHAEDNIKKYISDDRIVVIEGGEDRNETIMNGIRFVEKTYGLTDDDIIVTHDAVRPFLTHRIIEENIDAALETGAVDTVIEALDTIVESSNHEVITDIPVRDHMYQGQTPQSFNMKKVFNHYQNLTPEKKQILTDACKICLLAGDDVKLVKGEIFNIKITTPYDLKVANAIIQERI 234
               SCOP domains d3f1ca_ A:       automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..-----.-....hhhh.ee..eehhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhh......eeeeee......hhhhhhhhhhhhhhh.eeeeeee....eee...........hhh.eeeeeeeeeeehhhhhhhhhh.hhhhhhhh.hhhhhhhhh....eeee.........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------ISPD    ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f1c A   0 SLIYAQILAG-----M-NVSMPKQFLPLNGKPIIVHTVEKFILNTRFDKILISSPKEWMNHAEDNIKKYISDDRIVVIEGGEDRNETIMNGIRFVEKTYGLTDDDIIVTHDAVRPFLTHRIIEENIDAALETGAVDTVIEALDTIVESSNHEVITDIPVRDHMYQGQTPQSFNMKKVFNHYQNLTPEKKQILTDACKICLLAGDDVKLVKGEIFNIKITTPYDLKVANAIIQERI 234
                                     9     | |19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229     
                                     9    15 |                                                                                                                                                                                                                         
                                            17                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:230
 aligned with TARI_LISMF | Q720Y7 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:235
                             1                                                                                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229     
           TARI_LISMF     - -MIYAQILAGGKGTRMGNVSMPKQFLPLNGKPIIVHTVEKFILNTRFDKILISSPKEWMNHAEDNIKKYISDDRIVVIEGGEDRNETIMNGIRFVEKTYGLTDDDIIVTHDAVRPFLTHRIIEENIDAALETGAVDTVIEALDTIVESSNHEVITDIPVRDHMYQGQTPQSFNMKKVFNHYQNLTPEKKQILTDACKICLLAGDDVKLVKGEIFNIKITTPYDLKVANAIIQERI 234
               SCOP domains d3f1cb_ B:      automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..-----......hhhh.ee..eehhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhh......eeeeee......hhhhhhhhhhhhhhh.eeeeeee....eee...........hhh.eeeeeeeeeeehhhhhhhhhh.hhhhhhhh.hhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------ISPD    ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f1c B   0 SLIYAQILAG-----MGNVSMPKQFLPLNGKPIIVHTVEKFILNTRFDKILISSPKEWMNHAEDNIKKYISDDRIVVIEGGEDRNETIMNGIRFVEKTYGLTDDDIIVTHDAVRPFLTHRIIEENIDAALETGAVDTVIEALDTIVESSNHEVITDIPVRDHMYQGQTPQSFNMKKVFNHYQNLTPEKKQILTDACKICLLAGDDVKLVKGEIFNIKITTPYDLKVANAIIQERI 234
                                     9     |  19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229     
                                     9    15
   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 3F1C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F1C)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TARI_LISMF | Q720Y7)
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: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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  Cis Peptide Bonds
    Thr A:167 - Pro A:168   [ RasMol ]  
    Thr B:167 - Pro B:168   [ RasMol ]  
 

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