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(-) Description

Title :  CRYSTAL STRUCTURE OF RFFH
 
Authors :  J. Sivaraman, V. Sauve, A. Matte, M. Cygler, Montreal-Kingston Bacterial Structural Genomics Initiative (Bsgi)
Date :  05 Aug 02  (Deposition) - 20 Nov 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Crystal Structure, Glucose-1-Phosphate Thymidylytransferase, Rffh, Montreal-Kingston Bacterial Structural Genomics Initiative, Bsgi, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Sivaraman, V. Sauve, A. Matte, M. Cygler
Crystal Structure Of Escherichia Coli Glucose-1-Phosphate Thymidylyltransferase (Rffh) Complexed With Dttp And Mg2+
J. Biol. Chem. V. 277 44214 2002
PubMed-ID: 12171937  |  Reference-DOI: 10.1074/JBC.M206932200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
    Chains: A, B
    EC Number: 2.7.7.24
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: DL41
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: RFFH, DTDP-GLUCOSE SYNTHASE, DTDP-GLUCOSE PYROPHOSPHORYLASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2MSE10Mod. Amino AcidSELENOMETHIONINE
3TTP2Ligand/IonTHYMIDINE-5'-TRIPHOSPHATE
Biological Unit 1 (2, 24)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MSE20Mod. Amino AcidSELENOMETHIONINE
3TTP4Ligand/IonTHYMIDINE-5'-TRIPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:108 , ASP A:223 , TTP A:294BINDING SITE FOR RESIDUE MG A 301
2AC2SOFTWAREASP B:108 , ASP B:223 , TTP B:295 , HOH B:326 , HOH B:380BINDING SITE FOR RESIDUE MG B 302
3AC3SOFTWARELEU A:6 , GLY A:8 , GLY A:9 , SER A:10 , GLY A:11 , THR A:12 , ARG A:13 , LYS A:23 , GLN A:24 , GLN A:80 , PRO A:83 , ASP A:84 , GLY A:85 , LEU A:86 , GLY A:107 , ASP A:108 , GLU A:194 , MG A:301 , HOH A:346 , HOH A:379 , HOH A:466BINDING SITE FOR RESIDUE TTP A 294
4AC4SOFTWARELEU B:6 , GLY B:8 , GLY B:9 , SER B:10 , GLY B:11 , THR B:12 , ARG B:13 , LYS B:23 , GLN B:24 , GLN B:80 , PRO B:83 , ASP B:84 , GLY B:85 , LEU B:86 , GLY B:107 , ASP B:108 , MG B:302 , HOH B:326 , HOH B:378 , HOH B:380 , HOH B:441BINDING SITE FOR RESIDUE TTP B 295

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1MC3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1MC3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MC3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1MC3)

(-) Exons   (0, 0)

(no "Exon" information available for 1MC3)

(-) 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:291
 aligned with RMLA2_ECOLI | P61887 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:291
                             1                                                                                                                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289 
          RMLA2_ECOLI     - -MKGIILAGGSGTRLHPITRGVSKQLLPIYDKPMIYYPLSVLMLAGIREILIITTPEDKGYFQRLLGDGSEFGIQLEYAEQPSPDGLAQAFIIGETFLNGEPSCLVLGDNIFFGQGFSPKLRHVAARTEGATVFGYQVMDPERFGVVEFDDNFRAISLEEKPKQPKSNWAVTGLYFYDSKVVEYAKQVKPSERGELEITSINQMYLEAGNLTVELLGRGFAWLDTGTHDSLIEASTFVQTVEKRQGFKIACLEEIAWRNGWLDDEGVKRAASSLAKTGYGQYLLELLRARP 290
               SCOP domains d1mc3a_ A: RffH                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1mc3A00 A:0-290 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhh..hhhh.ee..ee.hhhhhhhhhhh...eeeeee...hhhhhhhhhh.hhhhh.eeeeee.......hhhhhhhhhhhh...eeeee..eeee...hhhhhhhhh.....eeeeeee..........eee..eeeee...........eeeeeeee..hhhhhhhhh.........hhhhhhhhhhhh..eeeee.....eeee..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mc3 A   0 HmKGIILAGGSGTRLHPITRGVSKQLLPIYDKPmIYYPLSVLmLAGIREILIITTPEDKGYFQRLLGDGSEFGIQLEYAEQPSPDGLAQAFIIGETFLNGEPSCLVLGDNIFFGQGFSPKLRHVAARTEGATVFGYQVmDPERFGVVEFDDNFRAISLEEKPKQPKSNWAVTGLYFYDSKVVEYAKQVKPSERGELEITSINQmYLEAGNLTVELLGRGFAWLDTGTHDSLIEASTFVQTVEKRQGFKIACLEEIAWRNGWLDDEGVKRAASSLAKTGYGQYLLELLRARP 290
                             |       9        19        29   |    39  |     49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199   |   209       219       229       239       249       259       269       279       289 
                             |                              33-MSE   42-MSE                                                                                         138-MSE                                                          203-MSE                                                                                   
                             1-MSE                                                                                                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:291
 aligned with RMLA2_ECOLI | P61887 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:291
                             1                                                                                                                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289 
          RMLA2_ECOLI     - -MKGIILAGGSGTRLHPITRGVSKQLLPIYDKPMIYYPLSVLMLAGIREILIITTPEDKGYFQRLLGDGSEFGIQLEYAEQPSPDGLAQAFIIGETFLNGEPSCLVLGDNIFFGQGFSPKLRHVAARTEGATVFGYQVMDPERFGVVEFDDNFRAISLEEKPKQPKSNWAVTGLYFYDSKVVEYAKQVKPSERGELEITSINQMYLEAGNLTVELLGRGFAWLDTGTHDSLIEASTFVQTVEKRQGFKIACLEEIAWRNGWLDDEGVKRAASSLAKTGYGQYLLELLRARP 290
               SCOP domains d1mc3b_ B: RffH                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1mc3B00 B:0-290 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                                                        CATH domains
           Pfam domains (1) --NTP_transferase-1mc3B01 B:2-240                                                                                                                                                                                                                -------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --NTP_transferase-1mc3B02 B:2-240                                                                                                                                                                                                                -------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..eeeee....hhhhhhhhh..hhhh.ee..ee.hhhhhhhhhhh...eeeeee...hhhhhhhhhh.hhhhh.eeeeee.......hhhhhhhhhhhh...eeeee..eeee..hhhhhhhhhhh....eeeeeee........eee........eee.........eeeeeeeee.hhhhhhhhh.........hhhhhhhhhhhh...eeee.....eeee..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mc3 B   0 HmKGIILAGGSGTRLHPITRGVSKQLLPIYDKPmIYYPLSVLmLAGIREILIITTPEDKGYFQRLLGDGSEFGIQLEYAEQPSPDGLAQAFIIGETFLNGEPSCLVLGDNIFFGQGFSPKLRHVAARTEGATVFGYQVmDPERFGVVEFDDNFRAISLEEKPKQPKSNWAVTGLYFYDSKVVEYAKQVKPSERGELEITSINQmYLEAGNLTVELLGRGFAWLDTGTHDSLIEASTFVQTVEKRQGFKIACLEEIAWRNGWLDDEGVKRAASSLAKTGYGQYLLELLRARP 290
                             |       9        19        29   |    39  |     49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199   |   209       219       229       239       249       259       269       279       289 
                             1-MSE                          33-MSE   42-MSE                                                                                         138-MSE                                                          203-MSE
   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) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: GT-A (172)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RMLA2_ECOLI | P61887)
molecular function
    GO:0008879    glucose-1-phosphate thymidylyltransferase activity    Catalysis of the reaction: alpha-D-glucose 1-phosphate + dTTP = diphosphate + dTDP-glucose.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0009246    enterobacterial common antigen biosynthetic process    The chemical reactions and pathways resulting in the formation of the enterobacterial common antigen, an acidic polysaccharide containing N-acetyl-D-glucosamine, N-acetyl-D-mannosaminouronic acid, and 4-acetamido-4,6-dideoxy-D-galactose. A major component of the cell wall outer membrane of Gram-negative bacteria.
    GO:0045226    extracellular polysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of polysaccharides used in extracellular structures.
    GO:0000271    polysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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