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(-) Description

Title :  THE STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND REGULATION OF GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE (RMLA). TDP-L-RHAMNOSE COMPLEX.
 
Authors :  W. Blankenfeldt, M. Asuncion, J. S. Lam, J. H. Naismith
Date :  24 Oct 00  (Deposition) - 27 Dec 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  L-Rhamnose, Nucleotidyltransferase, Pyrophosphorylase, Thymidylyltransferase, Allostery (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Blankenfeldt, M. Asuncion, J. S. Lam, J. H. Naismith
The Structural Basis Of The Catalytic Mechanism And Regulation Of Glucose-1-Phosphate Thymidylyltransferase (Rmla).
Embo J. V. 19 6652 2000
PubMed-ID: 11118200  |  Reference-DOI: 10.1093/EMBOJ/19.24.6652
(for further references see the PDB file header)

(-) 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 Plasmid: PET23A(+)
    Expression System Strain: BL21(LAMBDA DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE (RMLA)

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric/Biological Unit (2, 13)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
2TRH8Ligand/Ion2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:62 , PRO B:61 , ARG B:62BINDING SITE FOR RESIDUE SO4 B 700
02AC2SOFTWAREARG A:128 , GLU A:215 , ASP D:151 , GLN D:152BINDING SITE FOR RESIDUE SO4 A 701
03AC3SOFTWAREARG B:128 , GLU B:215 , ASP C:151 , GLN C:152BINDING SITE FOR RESIDUE SO4 B 702
04AC4SOFTWAREARG C:128 , GLN C:129 , THR C:130BINDING SITE FOR RESIDUE SO4 C 703
05AC5SOFTWAREARG D:128 , GLN D:129 , THR D:130BINDING SITE FOR RESIDUE SO4 D 704
06AC6SOFTWARELEU A:8 , ALA A:9 , GLY A:10 , GLY A:11 , GLN A:82 , PRO A:85 , ASP A:86 , GLY A:87 , ASP A:110 , TYR A:145 , GLY A:146 , GLU A:161 , LYS A:162 , VAL A:172 , THR A:173 , GLY A:174 , TYR A:176 , ARG A:194 , GLU A:196 , THR A:200BINDING SITE FOR RESIDUE TRH A 500
07AC7SOFTWARETYR A:114 , GLY A:115 , HIS A:116 , ASP A:117 , PHE A:118 , HIS A:119 , GLU A:120 , VAL A:250 , ALA A:251 , GLU A:255 , ILE A:256 , ARG A:259 , TYR A:293 , GLY C:218 , ARG C:219 , GLY C:220BINDING SITE FOR RESIDUE TRH A 501
08AC8SOFTWARELEU B:8 , GLY B:10 , GLY B:11 , GLN B:82 , PRO B:85 , ASP B:86 , GLY B:87 , ASP B:110 , TYR B:145 , GLY B:146 , GLU B:161 , LYS B:162 , VAL B:172 , THR B:173 , TYR B:176 , ARG B:194 , GLU B:196 , THR B:200BINDING SITE FOR RESIDUE TRH B 502
09AC9SOFTWARELEU B:45 , TYR B:114 , GLY B:115 , HIS B:116 , ASP B:117 , PHE B:118 , HIS B:119 , GLU B:120 , ALA B:251 , GLU B:255 , ILE B:256 , ARG B:259 , GLY D:218 , ARG D:219 , GLY D:220BINDING SITE FOR RESIDUE TRH B 503
10BC1SOFTWARELEU C:8 , GLY C:10 , GLY C:11 , GLN C:82 , PRO C:85 , ASP C:86 , GLY C:87 , LEU C:108 , ASP C:110 , TYR C:145 , GLY C:146 , GLU C:161 , LYS C:162 , VAL C:172 , TYR C:176 , ARG C:194 , GLU C:196 , THR C:200BINDING SITE FOR RESIDUE TRH C 504
11BC2SOFTWAREGLY A:218 , ARG A:219 , GLY A:220 , LEU C:45 , TYR C:114 , GLY C:115 , HIS C:116 , ASP C:117 , PHE C:118 , HIS C:119 , GLU C:120 , VAL C:250 , ALA C:251 , GLU C:255 , ARG C:259 , TYR C:293BINDING SITE FOR RESIDUE TRH C 505
12BC3SOFTWARELEU D:8 , GLY D:10 , GLY D:11 , GLN D:26 , GLN D:82 , PRO D:85 , ASP D:86 , GLY D:87 , ASP D:110 , GLY D:146 , GLU D:161 , LYS D:162 , VAL D:172 , THR D:173 , TYR D:176 , ARG D:194 , GLU D:196 , THR D:200BINDING SITE FOR RESIDUE TRH D 506
13BC4SOFTWAREILE B:216 , GLY B:218 , ARG B:219 , GLY B:220 , LEU D:45 , TYR D:114 , GLY D:115 , HIS D:116 , ASP D:117 , PHE D:118 , HIS D:119 , ALA D:251 , GLU D:255 , ILE D:256 , ARG D:259 , TYR D:293BINDING SITE FOR RESIDUE TRH D 507

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1G3L)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1His A:17 -Pro A:18
2His B:17 -Pro B:18
3His C:17 -Pro C:18
4His D:17 -Pro D:18

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1G3L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1G3L)

(-) Exons   (0, 0)

(no "Exon" information available for 1G3L)

(-) 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:292
 aligned with Q9HU22_PSEAE | Q9HU22 from UniProtKB/TrEMBL  Length:293

    Alignment length:292
                                    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  
         Q9HU22_PSEAE     2 KRKGIILAGGSGTRLHPATLAISKQLLPVYDKPMIYYPLSTLMLAGIREILIISTPQDTPRFQQLLGDGSNWGLDLQYAVQPSPDGLAQAFLIGESFIGNDLSALVLGDNLYYGHDFHELLGSASQRQTGASVFAYHVLDPERYGVVEFDQGGKAISLEEKPLEPKSNYAVTGLYFYDQQVVDIARDLKPSPRGELEITDVNRAYLERGQLSVEIMGRGYAWLDTGTHDSLLEAGQFIATLENRQGLKVACPEEIAYRQKWIDAAQLEKLAAPLAKNGYGQYLKRLLTETVY 293
               SCOP domains d1g3la_ A: RmlA (RfbA)                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1g3lA00 A:2-293 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...............hhhh.ee..ee.hhhhhhhhhhh...eeeeee...hhhhhhhhhh.hhhhh.eeeeee.......hhhhhhhhhhhh..eeeeee..eeee..hhhhhhhhhhhh...eeeeeee..hhhh.eeeee.....eeeeee........eee..eeee..hhhhhhhh.........hhhhhhhhhhhh..eeeee.....eeee..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g3l A   2 KRKGIILAGGSGTRLHPATLAISKQLLPVYDKPMIYYPLSTLMLAGIREILIISTPQDTPRFQQLLGDGSNWGLDLQYAVQPSPDGLAQAFLIGESFIGNDLSALVLGDNLYYGHDFHELLGSASQRQTGASVFAYHVLDPERYGVVEFDQGGKAISLEEKPLEPKSNYAVTGLYFYDQQVVDIARDLKPSPRGELEITDVNRAYLERGQLSVEIMGRGYAWLDTGTHDSLLEAGQFIATLENRQGLKVACPEEIAYRQKWIDAAQLEKLAAPLAKNGYGQYLKRLLTETVY 293
                                    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:292
 aligned with Q9HU22_PSEAE | Q9HU22 from UniProtKB/TrEMBL  Length:293

    Alignment length:292
                                    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  
         Q9HU22_PSEAE     2 KRKGIILAGGSGTRLHPATLAISKQLLPVYDKPMIYYPLSTLMLAGIREILIISTPQDTPRFQQLLGDGSNWGLDLQYAVQPSPDGLAQAFLIGESFIGNDLSALVLGDNLYYGHDFHELLGSASQRQTGASVFAYHVLDPERYGVVEFDQGGKAISLEEKPLEPKSNYAVTGLYFYDQQVVDIARDLKPSPRGELEITDVNRAYLERGQLSVEIMGRGYAWLDTGTHDSLLEAGQFIATLENRQGLKVACPEEIAYRQKWIDAAQLEKLAAPLAKNGYGQYLKRLLTETVY 293
               SCOP domains d1g3lb_ B: RmlA (RfbA)                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1g3lB00 B:2-293 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..............hhhh.ee..ee.hhhhhhhhhhh...eeeeee...hhhhhhhhhh.hhhhh.eeeeee.......hhhhhhhhhhhh..eeeeee..eeee..hhhhhhhhhhhh...eeeeeee..hhhh.eeeee.....eeeeee........eeeeeeeee..hhhhhhhh.........hhhhhhhhhhhh..eeeee.....eeee..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g3l B   2 KRKGIILAGGSGTRLHPATLAISKQLLPVYDKPMIYYPLSTLMLAGIREILIISTPQDTPRFQQLLGDGSNWGLDLQYAVQPSPDGLAQAFLIGESFIGNDLSALVLGDNLYYGHDFHELLGSASQRQTGASVFAYHVLDPERYGVVEFDQGGKAISLEEKPLEPKSNYAVTGLYFYDQQVVDIARDLKPSPRGELEITDVNRAYLERGQLSVEIMGRGYAWLDTGTHDSLLEAGQFIATLENRQGLKVACPEEIAYRQKWIDAAQLEKLAAPLAKNGYGQYLKRLLTETVY 293
                                    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:292
 aligned with Q9HU22_PSEAE | Q9HU22 from UniProtKB/TrEMBL  Length:293

    Alignment length:292
                                    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  
         Q9HU22_PSEAE     2 KRKGIILAGGSGTRLHPATLAISKQLLPVYDKPMIYYPLSTLMLAGIREILIISTPQDTPRFQQLLGDGSNWGLDLQYAVQPSPDGLAQAFLIGESFIGNDLSALVLGDNLYYGHDFHELLGSASQRQTGASVFAYHVLDPERYGVVEFDQGGKAISLEEKPLEPKSNYAVTGLYFYDQQVVDIARDLKPSPRGELEITDVNRAYLERGQLSVEIMGRGYAWLDTGTHDSLLEAGQFIATLENRQGLKVACPEEIAYRQKWIDAAQLEKLAAPLAKNGYGQYLKRLLTETVY 293
               SCOP domains d1g3lc_ C: RmlA (RfbA)                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1g3lC00 C:2-293 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..............hhhh.ee..ee.hhhhhhhhhhh...eeeeee...hhhhhhhhhh.hhhhh.eeeeee.......hhhhhhhhhhhh..eeeeee..eeee..hhhhhhhhhhh....eeeeeee..hhhh.eeeee.....eeeeee........eee..eeee..hhhhhhhh.........hhhhhhhhhhh...eeeee.....eeee..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g3l C   2 KRKGIILAGGSGTRLHPATLAISKQLLPVYDKPMIYYPLSTLMLAGIREILIISTPQDTPRFQQLLGDGSNWGLDLQYAVQPSPDGLAQAFLIGESFIGNDLSALVLGDNLYYGHDFHELLGSASQRQTGASVFAYHVLDPERYGVVEFDQGGKAISLEEKPLEPKSNYAVTGLYFYDQQVVDIARDLKPSPRGELEITDVNRAYLERGQLSVEIMGRGYAWLDTGTHDSLLEAGQFIATLENRQGLKVACPEEIAYRQKWIDAAQLEKLAAPLAKNGYGQYLKRLLTETVY 293
                                    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:293
 aligned with Q9HU22_PSEAE | Q9HU22 from UniProtKB/TrEMBL  Length:293

    Alignment length:293
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290   
         Q9HU22_PSEAE     1 MKRKGIILAGGSGTRLHPATLAISKQLLPVYDKPMIYYPLSTLMLAGIREILIISTPQDTPRFQQLLGDGSNWGLDLQYAVQPSPDGLAQAFLIGESFIGNDLSALVLGDNLYYGHDFHELLGSASQRQTGASVFAYHVLDPERYGVVEFDQGGKAISLEEKPLEPKSNYAVTGLYFYDQQVVDIARDLKPSPRGELEITDVNRAYLERGQLSVEIMGRGYAWLDTGTHDSLLEAGQFIATLENRQGLKVACPEEIAYRQKWIDAAQLEKLAAPLAKNGYGQYLKRLLTETVY 293
               SCOP domains d1g3ld_ D: RmlA (RfbA)                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1g3lD00 D:1-293 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.........hhhhh.hhhh.ee..ee.hhhhhhhhhhh...eeeeee...hhhhhhhhhh.hhhhh.eeeeee.......hhhhhhhhhhhh..eeeeee..eeee..hhhhhhhhhhhh...eeeeeee..hhhh.eeeee.....eeeeee........eee..eeee..hhhhhhhh.........hhhhhhhhhhh...eeeee.....eeee..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g3l D   1 MKRKGIILAGGSGTRLHPATLAISKQLLPVYDKPMIYYPLSTLMLAGIREILIISTPQDTPRFQQLLGDGSNWGLDLQYAVQPSPDGLAQAFLIGESFIGNDLSALVLGDNLYYGHDFHELLGSASQRQTGASVFAYHVLDPERYGVVEFDQGGKAISLEEKPLEPKSNYAVTGLYFYDQQVVDIARDLKPSPRGELEITDVNRAYLERGQLSVEIMGRGYAWLDTGTHDSLLEAGQFIATLENRQGLKVACPEEIAYRQKWIDAAQLEKLAAPLAKNGYGQYLKRLLTETVY 293
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290
   Legend:   → Mismatch (orange background)
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  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 1G3L)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q9HU22_PSEAE | Q9HU22)
molecular function
    GO:0008879    glucose-1-phosphate thymidylyltransferase activity    Catalysis of the reaction: alpha-D-glucose 1-phosphate + dTTP = diphosphate + dTDP-glucose.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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:0045226    extracellular polysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of polysaccharides used in extracellular structures.

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  1g3l
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  Q9HU22_PSEAE | Q9HU22
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  2.7.7.24
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 Related Entries

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

UniProtKB/TrEMBL
        Q9HU22_PSEAE | Q9HU22: 1fxo 1fzw 1g0r 1g1l 1g23 1g2v 3zlk 3zll 4arw 4asj 4asy 4b2w 4b2x 4b3u 4b42 4b4b 4b4g 4b4m 4b5b 5fts 5ftv 5fu0 5fu8 5fuh 5fye

(-) Related Entries Specified in the PDB File

1fxo 1FXO IS RMLA IN COMPLEX WITH DTMP
1fzw 1FZW IS RMLA APO ENZYME
1g0r 1G0R IS RMLA IN COMPLEX WITH GLUCOSE-1-PHOSPHATE AND THYMIDINE
1g1l 1G1L IS RMLA IN COMPLEX WITH DTDP-D-GLUCOSE
1g23 1G23 IS RMLA IN COMPLEX WITH GLUCOSE-1-PHOSPHATE
1g2v 1G2V IS RMLA IN COMPLEX WITH DTTP