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(-) Description

Title :  CRYSTAL STRUCTURE OF CAULOBACTER CRESCENTUS THIC COMPLEXED WITH IMIDAZOLE RIBONUCLEOTIDE
 
Authors :  S. Li, A. Chatterjee, Y. Zhang, T. L. Grove, M. Lee, C. Krebs, S. J. Booker, T. P. Begley, S. E. Ealick
Date :  29 Sep 08  (Deposition) - 28 Oct 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.11
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha-Beta Barrel, Sam Superfamily, Thiamine Biosynthesis, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Chatterjee, Y. Li, Y. Zhang, T. L. Grove, M. Lee, C. Krebs, S. J. Booker, T. P. Begley, S. E. Ealick
Reconstitution Of Thic In Thiamine Pyrimidine Biosynthesis Expands The Radical Sam Superfamily
Nat. Chem. Biol. V. 4 758 2008
PubMed-ID: 18953358  |  Reference-DOI: 10.1038/NCHEMBIO.121
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THIAMINE BIOSYNTHESIS PROTEIN THIC
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDESTF1
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: THIC
    Organism Scientific: CAULOBACTER CRESCENTUS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1IRN2Ligand/Ion1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-1H-IMIDAZOLE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:219 , MET A:248 , TYR A:277 , HIS A:313 , SER A:333 , ARG A:334 , GLY A:335 , ASP A:374 , ARG A:377 , GLU A:413 , GLY A:414 , TYR A:440BINDING SITE FOR RESIDUE IRN A1001
2AC2SOFTWAREASN B:219 , MET B:248 , TYR B:277 , HIS B:313 , SER B:333 , ARG B:334 , GLY B:335 , ASP B:374 , ARG B:377 , GLU B:413 , GLY B:414 , TYR B:440BINDING SITE FOR RESIDUE IRN A1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Pro A:415 -Gly A:416
2Gly A:443 -Pro A:444
3Pro B:415 -Gly B:416
4Gly B:443 -Pro B:444

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EPN)

(-) Exons   (0, 0)

(no "Exon" information available for 3EPN)

(-) 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:523
 aligned with THIC_CAUCR | Q9A6Q5 from UniProtKB/Swiss-Prot  Length:612

    Alignment length:542
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544  
           THIC_CAUCR     5 STIKAVAETISTGPIPGSRKVYQAGELFPELRVPFREVAVHPSANEPPVTIYDPSGPYSDPAIQIDIEKGLPRTREALVVARGDVEEVADPRQVKPEDNGFAQGKHLAPEFPDTGRKIYRAKPGKLVTQLEYARAGIITAEMEYVAIRENLRREQDRPCVRDGEDFGASIPDFVTPEFVRQEIARGRAIIPANINHGELEPMAIGRNFLVKINANIGNSAVLSTVADEVDKLVWATRWGADTVMDLSTGRNIHNIRDWIIRNSSVPIGTVPIYQALEKVNGVAEDLNWEVFRDTLIEQCEQGVDYFTIHAGVRLPFIPMTAKRVTGIVSRGGSIMAKWCLAHHKENFLYERFDEICEIMRAYDVSFSLGDGLRPGSTADANDEAQFSELRTLGELTKVAWKHGVQVMIEGPGHVAMHKIKANMDEQLKHCHEAPFYTLGPLTTDIAPGYDHITSAIGAAMIGWFGTAMLCYVTPKEHLGLPDRDDVKTGVITYKLAAHAADLAKGHPGAAMWDDAISRARFEFRWEDQFNLGLDPETARKFH 546
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh........eeeeee.......eeeeeee..hhhhh...eeee..hhhhhh..............hhhhhhhh..eee.......--------------..........eee......hhhhhhhh...hhhhhhhhhhhh........................hhhhhhhhhhh..ee..............ee.....eeeeee..-----hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhh.....eee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....eeee.......hhhhh.hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh....eeee..........hhhhhhhhhhhhhhhhh..eee...........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3epn A   5 STIKAVAETISTGPIPGSRKVYQAGELFPELRVPFREVAVHPSANEPPVTIYDPSGPYSDPAIQIDIEKGLPRTREALVVARGDVEEVADPRQV--------------PEFPDTGRKIYRAKPGKLVTQLEYARAGIITAEMEYVAIRENLRREQDRPCVRDGEDFGASIPDFVTPEFVRQEIARGRAIIPANINHGELEPMAIGRNFLVKINANIGN-----TVADEVDKLVWATRWGADTVMDLSTGRNIHNIRDWIIRNSSVPIGTVPIYQALEKVNGVAEDLNWEVFRDTLIEQCEQGVDYFTIHAGVRLPFIPMTAKRVTGIVSRGGSIMAKWCLAHHKENFLYERFDEICEIMRAYDVSFSLGDGLRPGSTADANDEAQFSELRTLGELTKVAWKHGVQVMIEGPGHVAMHKIKANMDEQLKHCHEAPFYTLGPLTTDIAPGYDHITSAIGAAMIGWFGTAMLCYVTPKEHLGLPDRDDVKTGVITYKLAAHAADLAKGHPGAAMWDDAISRARFEFRWEDQFNLGLDPETARKFH 546
                                    14        24        34        44        54        64        74        84        94   |     -       114       124       134       144       154       164       174       184       194       204       214       | -   |   234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544  
                                                                                                                        98            113                                                                                                          222   228                                                                                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:519
 aligned with THIC_CAUCR | Q9A6Q5 from UniProtKB/Swiss-Prot  Length:612

    Alignment length:540
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546
           THIC_CAUCR     7 IKAVAETISTGPIPGSRKVYQAGELFPELRVPFREVAVHPSANEPPVTIYDPSGPYSDPAIQIDIEKGLPRTREALVVARGDVEEVADPRQVKPEDNGFAQGKHLAPEFPDTGRKIYRAKPGKLVTQLEYARAGIITAEMEYVAIRENLRREQDRPCVRDGEDFGASIPDFVTPEFVRQEIARGRAIIPANINHGELEPMAIGRNFLVKINANIGNSAVLSTVADEVDKLVWATRWGADTVMDLSTGRNIHNIRDWIIRNSSVPIGTVPIYQALEKVNGVAEDLNWEVFRDTLIEQCEQGVDYFTIHAGVRLPFIPMTAKRVTGIVSRGGSIMAKWCLAHHKENFLYERFDEICEIMRAYDVSFSLGDGLRPGSTADANDEAQFSELRTLGELTKVAWKHGVQVMIEGPGHVAMHKIKANMDEQLKHCHEAPFYTLGPLTTDIAPGYDHITSAIGAAMIGWFGTAMLCYVTPKEHLGLPDRDDVKTGVITYKLAAHAADLAKGHPGAAMWDDAISRARFEFRWEDQFNLGLDPETARKFH 546
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhh........eeeeee.......eeeeeee..hhhhh...eee...hhhhhh..............hhhhhhh...eee.......--------------....--....eee......hhhhhhhh...hhhhhhhhhhhhh.......................hhhhhhhhhhh..ee..............ee.....eeeeee..-----hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh....eee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....eeee.......hhhhh.hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh....eeee..........hhhhhhhhhhhhhhhhh..eee...........hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3epn B   7 IKAVAETISTGPIPGSRKVYQAGELFPELRVPFREVAVHPSANEPPVTIYDPSGPYSDPAIQIDIEKGLPRTREALVVARGDVEEVADPRQV--------------PEFP--GRKIYRAKPGKLVTQLEYARAGIITAEMEYVAIRENLRREQDRPCVRDGEDFGASIPDFVTPEFVRQEIARGRAIIPANINHGELEPMAIGRNFLVKINANIGN-----TVADEVDKLVWATRWGADTVMDLSTGRNIHNIRDWIIRNSSVPIGTVPIYQALEKVNGVAEDLNWEVFRDTLIEQCEQGVDYFTIHAGVRLPFIPMTAKRVTGIVSRGGSIMAKWCLAHHKENFLYERFDEICEIMRAYDVSFSLGDGLRPGSTADANDEAQFSELRTLGELTKVAWKHGVQVMIEGPGHVAMHKIKANMDEQLKHCHEAPFYTLGPLTTDIAPGYDHITSAIGAAMIGWFGTAMLCYVTPKEHLGLPDRDDVKTGVITYKLAAHAADLAKGHPGAAMWDDAISRARFEFRWEDQFNLGLDPETARKFH 546
                                    16        26        36        46        56        66        76        86        96 |       -      |116  |    126       136       146       156       166       176       186       196       206       216     |   - |     236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546
                                                                                                                      98            113  |  |                                                                                                    222   228                                                                                                                                                                                                                                                                                                                              
                                                                                                                                       116  |                                                                                                                                                                                                                                                                                                                                                                                                                                           
                                                                                                                                          119
   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  (0, 0)

(no "SCOP Domain" information available for 3EPN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3EPN)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (THIC_CAUCR | Q9A6Q5)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0009228    thiamine biosynthetic process    The chemical reactions and pathways resulting in the formation of thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
    GO:0009229    thiamine diphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of thiamine diphosphate, a derivative of thiamine (vitamin B1) which acts as a coenzyme in a range of processes including the Krebs cycle.

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 Related Entries

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UniProtKB/Swiss-Prot
        THIC_CAUCR | Q9A6Q5: 3epm 3epo 4s2a

(-) Related Entries Specified in the PDB File

3epm 3epo