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(-) Description

Title :  THYMIDYLYLTRANSFERASE COMPLEXED WITH THYMIDYLYLDIPHOSPHATE-GLUCOSE
 
Authors :  C. Rosano, S. Zuccotti, M. Bolognesi
Date :  25 May 01  (Deposition) - 23 Nov 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transferase, Pyrophosphatase, Nucleotide Sugar Methabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Zuccotti, D. Zanardi, C. Rosano, L. Sturla, M. Tonetti, M. Bolognesi
Kinetic And Crystallographic Analyses Support A Sequential-Ordered Bi Bi Catalytic Mechanism For Escherichia Coli Glucose-1-Phosphate Thymidylyltransferase
J. Mol. Biol. V. 313 831 2001
PubMed-ID: 11697907  |  Reference-DOI: 10.1006/JMBI.2001.5073

(-) Compounds

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

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1DAU4Ligand/Ion2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE
2SO41Ligand/IonSULFATE ION
3TYD4Ligand/IonTHYMIDINE-5'-DIPHOSPHATE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS D:81 , VAL D:82BINDING SITE FOR RESIDUE SO4 D1294
2AC2SOFTWARELEU A:46 , TYR A:115 , GLY A:116 , HIS A:117 , ASP A:118 , PRO A:120 , VAL A:251 , SER A:252 , GLU A:256 , ILE A:257 , HOH A:2125 , HOH A:2143 , GLY D:219 , ARG D:220 , GLY D:221BINDING SITE FOR RESIDUE TYD A1292
3AC3SOFTWARELEU A:9 , GLY A:11 , GLY A:12 , GLN A:83 , PRO A:86 , ASP A:87 , GLY A:88 , LEU A:109 , ASP A:111 , TYR A:146 , GLY A:147 , GLU A:162 , LYS A:163 , VAL A:173 , ARG A:195 , GLU A:197 , THR A:201 , HOH A:2090 , HOH A:2091 , HOH A:2144 , HOH A:2145 , HOH A:2146BINDING SITE FOR RESIDUE DAU A1293
4AC4SOFTWARELEU B:46 , TYR B:115 , GLY B:116 , HIS B:117 , ASP B:118 , VAL B:251 , SER B:252 , GLU B:256 , ILE B:257 , HOH B:2096 , HOH B:2097 , GLY C:219 , ARG C:220 , GLY C:221BINDING SITE FOR RESIDUE TYD B1292
5AC5SOFTWARELEU B:9 , GLY B:11 , GLN B:83 , PRO B:86 , ASP B:87 , GLY B:88 , LEU B:109 , ASP B:111 , TYR B:146 , GLY B:147 , GLU B:162 , LYS B:163 , VAL B:173 , ARG B:195 , GLU B:197 , THR B:201 , HOH B:2058 , HOH B:2063 , HOH B:2098 , HOH B:2099BINDING SITE FOR RESIDUE DAU B1293
6AC6SOFTWAREGLY B:219 , ARG B:220 , GLY B:221 , LEU C:46 , TYR C:115 , GLY C:116 , HIS C:117 , ASP C:118 , LYS C:250 , VAL C:251 , SER C:252 , GLU C:256 , HOH C:2118 , HOH C:2119BINDING SITE FOR RESIDUE TYD C1292
7AC7SOFTWARELEU C:9 , GLY C:11 , GLY C:12 , GLN C:27 , GLN C:83 , PRO C:86 , ASP C:87 , GLY C:88 , LEU C:89 , LEU C:109 , ASP C:111 , TYR C:146 , GLY C:147 , GLU C:162 , LYS C:163 , VAL C:173 , ARG C:195 , GLU C:197 , THR C:201 , TRP C:224 , HOH C:2069 , HOH C:2077BINDING SITE FOR RESIDUE DAU C1293
8AC8SOFTWAREGLY A:219 , ARG A:220 , GLY A:221 , LEU D:46 , TYR D:115 , GLY D:116 , HIS D:117 , ASP D:118 , VAL D:251 , SER D:252 , GLU D:256 , ILE D:257 , HOH D:2134 , HOH D:2135 , HOH D:2136BINDING SITE FOR RESIDUE TYD D1292
9AC9SOFTWARELEU D:9 , GLY D:11 , GLY D:12 , GLN D:27 , GLN D:83 , PRO D:86 , ASP D:87 , GLY D:88 , LEU D:89 , LEU D:109 , GLY D:110 , ASP D:111 , ASN D:112 , TYR D:146 , GLY D:147 , GLU D:162 , LYS D:163 , VAL D:173 , GLU D:197 , HOH D:2090 , HOH D:2137BINDING SITE FOR RESIDUE DAU D1293

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1H5T)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:18 -Pro A:19
2Tyr B:18 -Pro B:19
3Tyr C:18 -Pro C:19
4Tyr D:18 -Pro D:19

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H5T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1H5T)

(-) Exons   (0, 0)

(no "Exon" information available for 1H5T)

(-) 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:290
 aligned with RMLA1_ECOLI | P37744 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:290
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291
          RMLA1_ECOLI     2 KMRKGIILAGGSGTRLYPVTMAVSKQLLPIYDKPMIYYPLSTLMLAGIRDILIISTPQDTPRFQQLLGDGSQWGLNLQYKVQPSPDGLAQAFIIGEEFIGGDDCALVLGDNIFYGHDLPKLMEAAVNKESGATVFAYHVNDPERYGVVEFDKNGTAISLEEKPLEPKSNYAVTGLYFYDNDVVQMAKNLKPSARGELEITDINRIYLEQGRLSVAMMGRGYAWLDTGTHQSLIEASNFIATIEERQGLKVSCPEEIAFRKGFIDVEQVRKLAVPLIKNNYGQYLYKMTKD 291
               SCOP domains d1h5ta_ A: RmlA (RfbA)                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1h5tA00 A:2-291 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhh......hhhh.ee..ee.hhhhhhhhhhh.eeeeeeee...hhhhhhhhhh.hhhhh.eeeeee.......hhhhhhhhhhhh...eeeee...eee..hhhhhhhhhhhh...eeeeeee..hhhh.eeeee.....eeeeee........eeeeeeeee..hhhhhhhh.........hhhhhhhhhhhh..eeeee.....eee...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h5t A   2 KMRKGIILAGGSGTRLYPVTMAVSKQLLPIYDKPMIYYPLSTLMLAGIRDILIISTPQDTPRFQQLLGDGSQWGLNLQYKVQPSPDGLAQAFIIGEEFIGGDDCALVLGDNIFYGHDLPKLMEAAVNKESGATVFAYHVNDPERYGVVEFDKNGTAISLEEKPLEPKSNYAVTGLYFYDNDVVQMAKNLKPSARGELEITDINRIYLEQGRLSVAMMGRGYAWLDTGTHQSLIEASNFIATIEERQGLKVSCPEEIAFRKGFIDVEQVRKLAVPLIKNNYGQYLYKMTKD 291
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291


Chain B from PDB  Type:PROTEIN  Length:290
 aligned with RMLA1_ECOLI | P37744 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:290
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291
          RMLA1_ECOLI     2 KMRKGIILAGGSGTRLYPVTMAVSKQLLPIYDKPMIYYPLSTLMLAGIRDILIISTPQDTPRFQQLLGDGSQWGLNLQYKVQPSPDGLAQAFIIGEEFIGGDDCALVLGDNIFYGHDLPKLMEAAVNKESGATVFAYHVNDPERYGVVEFDKNGTAISLEEKPLEPKSNYAVTGLYFYDNDVVQMAKNLKPSARGELEITDINRIYLEQGRLSVAMMGRGYAWLDTGTHQSLIEASNFIATIEERQGLKVSCPEEIAFRKGFIDVEQVRKLAVPLIKNNYGQYLYKMTKD 291
               SCOP domains d1h5tb_ B: RmlA (RfbA)                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1h5tB00 B:2-291 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhh.ee..ee.hhhhhhhhhhh...eeeeee...hhhhhhhhhh.hhhhh.eeeeee.......hhhhhhhhhhhh..eeeeee...eee..hhhhhhhhhhhh...eeeeeee..hhhh.eeeee.....eeeeee........eeeeeeeee..hhhhhhhh.........hhhhhhhhhhhh..eeeee.....eee...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h5t B   2 KMRKGIILAGGSGTRLYPVTMAVSKQLLPIYDKPMIYYPLSTLMLAGIRDILIISTPQDTPRFQQLLGDGSQWGLNLQYKVQPSPDGLAQAFIIGEEFIGGDDCALVLGDNIFYGHDLPKLMEAAVNKESGATVFAYHVNDPERYGVVEFDKNGTAISLEEKPLEPKSNYAVTGLYFYDNDVVQMAKNLKPSARGELEITDINRIYLEQGRLSVALMGRGYAWLDTGTHQSLIEASNFIATIEERQGLKVSCPEEIAFRKGFIDVEQVRKLAVPLIKNNYGQYLYKQTKD 291
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291


Chain C from PDB  Type:PROTEIN  Length:290
 aligned with RMLA1_ECOLI | P37744 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:290
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291
          RMLA1_ECOLI     2 KMRKGIILAGGSGTRLYPVTMAVSKQLLPIYDKPMIYYPLSTLMLAGIRDILIISTPQDTPRFQQLLGDGSQWGLNLQYKVQPSPDGLAQAFIIGEEFIGGDDCALVLGDNIFYGHDLPKLMEAAVNKESGATVFAYHVNDPERYGVVEFDKNGTAISLEEKPLEPKSNYAVTGLYFYDNDVVQMAKNLKPSARGELEITDINRIYLEQGRLSVAMMGRGYAWLDTGTHQSLIEASNFIATIEERQGLKVSCPEEIAFRKGFIDVEQVRKLAVPLIKNNYGQYLYKMTKD 291
               SCOP domains d1h5tc_ C: RmlA (RfbA)                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1h5tC00 C:2-291 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhh.ee..ee.hhhhhhhhhhh.eeeeeeee...hhhhhhhhhh.hhhhh.eeeeee.......hhhhhhhhhhhh...eeeee...eee..hhhhhhhhhhhh...eeeeeee..hhhh.eeeee.....eeeeee........eee..eeee..hhhhhhhhh........hhhhhhhhhhhh..eeeee.....eee...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h5t C   2 KMRKGIILAGGSGTRLYPVTMAVSKQLLPIYDKPMIYYPLSTLMLAGIRDILIISTPQDTPRFQQLLGDGSQWGLNLQYKVQPSPDGLAQAFIIGEEFIGGDDCALVLGDNIFYGHDLPKLMEAAVNKESGATVFAYHVNDPERYGVVEFDKNGTAISLEEKPLEPKSNYAVTGLYFYDNDVVQMAKNLKPSARGELEITDINRIYLEQGRLSVAMMGRGYAWLDTGTHQSLIEASNFIATIEERQGLKVSCPEEIAFRKGFIDVEQVRKLAVPLIKNNYGQYLYKMTKD 291
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291


Chain D from PDB  Type:PROTEIN  Length:290
 aligned with RMLA1_ECOLI | P37744 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:290
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291
          RMLA1_ECOLI     2 KMRKGIILAGGSGTRLYPVTMAVSKQLLPIYDKPMIYYPLSTLMLAGIRDILIISTPQDTPRFQQLLGDGSQWGLNLQYKVQPSPDGLAQAFIIGEEFIGGDDCALVLGDNIFYGHDLPKLMEAAVNKESGATVFAYHVNDPERYGVVEFDKNGTAISLEEKPLEPKSNYAVTGLYFYDNDVVQMAKNLKPSARGELEITDINRIYLEQGRLSVAMMGRGYAWLDTGTHQSLIEASNFIATIEERQGLKVSCPEEIAFRKGFIDVEQVRKLAVPLIKNNYGQYLYKMTKD 291
               SCOP domains d1h5td_ D: RmlA (RfbA)                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1h5tD00 D:2-291 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....hhhhh......hhhh.ee..ee.hhhhhhhhhhh...eeeeee...hhhhhhhhhh.hhhhh.eeeeee.......hhhhhhhhhhhh...eeeee...eee..hhhhhhhhhhh....eeeeeee..hhhh.eeeee.....eeeeee........eeeeeeeee..hhhhhhhh.........hhhhhhhhhhhh..eeeee.....eee...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h5t D   2 KMRKGIILAGGSGTRLYPVTMAVSKQLLPIYDKPMIYYPLSTLMLAGIRDILIISTPQDTPRFQQLLGDGSQWGLNLQYKVQPSPDGLAQAFIIGEEFIGGDDCALVLGDNIFYGHDLPKLMEAAVNKESGATVFAYHVNDPERYGVVEFDKNGTAISLEEKPLEPKSNYAVTGLYFYDNDVVQMAKNLKPSARGELEITDINRIYLEQGRLSVAMMGRGYAWLDTGTHQSLIEASNFIATIEERQGLKVSCPEEIAFRKGFIDVEQVRKLAVPLIKNNYGQYLYKMTKD 291
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1H5T)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (RMLA1_ECOLI | P37744)
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: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:0009243    O antigen biosynthetic process    The chemical reactions and pathways resulting in the formation of the O side chain of a lipopolysaccharide, which determines the antigenic specificity of the organism. It is made up of about 50 repeating units of a branched tetrasaccharide.
    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:0019305    dTDP-rhamnose biosynthetic process    The chemical reactions and pathways resulting in the formation of dTDP-rhamnose, a substance composed of rhamnose in glycosidic linkage with deoxyribosylthymine diphosphate.
    GO:0045226    extracellular polysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of polysaccharides used in extracellular structures.
    GO:0009103    lipopolysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
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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  1h5t
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  RMLA1_ECOLI | P37744
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  2.7.7.24
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 Related Entries

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

UniProtKB/Swiss-Prot
        RMLA1_ECOLI | P37744: 1h5r 1h5s

(-) Related Entries Specified in the PDB File

1h5r THYMIDYLYLTRANSFERASE COMPLEXED WITH THIMIDINE AND GLUCOSE-1-PHOSPATE
1h5s THYMIDYLYLTRANSFERASE COMPLEXED WITH TMP