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(-) Description

Title :  CRYSTAL STRUCTURE OF CAULOBACTER CRESCENTUS THIC
 
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 :  2.79
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  (4, 28)

Asymmetric/Biological Unit (4, 28)
No.NameCountTypeFull Name
1HMH1Ligand/Ion4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE
2MSE24Mod. Amino AcidSELENOMETHIONINE
3SO41Ligand/IonSULFATE ION
4ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:417 , HIS A:481BINDING SITE FOR RESIDUE ZN A 613
2AC2SOFTWARETYR A:277 , HIS A:313 , VAL A:332 , SER A:333 , ARG A:334 , ARG A:377BINDING SITE FOR RESIDUE HMH A1001
3AC3SOFTWAREARG A:124 , GLY A:128BINDING SITE FOR RESIDUE SO4 A2001
4AC4SOFTWAREHIS B:417 , HIS B:481BINDING SITE FOR RESIDUE ZN B 613

(-) SS Bonds  (0, 0)

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

(-) 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 3EPM)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3EPM)

(-) 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:515
 aligned with THIC_CAUCR | Q9A6Q5 from UniProtKB/Swiss-Prot  Length:612

    Alignment length:534
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542    
           THIC_CAUCR    13 TISTGPIPGSRKVYQAGELFPELRVPFREVAVHPSANEPPVTIYDPSGPYSDPAIQIDIEKGLPRTREALVVARGDVEEVADPRQVKPEDNGFAQGKHLAPEFPDTGRKIYRAKPGKLVTQLEYARAGIITAEMEYVAIRENLRREQDRPCVRDGEDFGASIPDFVTPEFVRQEIARGRAIIPANINHGELEPMAIGRNFLVKINANIGNSAVLSTVADEVDKLVWATRWGADTVMDLSTGRNIHNIRDWIIRNSSVPIGTVPIYQALEKVNGVAEDLNWEVFRDTLIEQCEQGVDYFTIHAGVRLPFIPMTAKRVTGIVSRGGSIMAKWCLAHHKENFLYERFDEICEIMRAYDVSFSLGDGLRPGSTADANDEAQFSELRTLGELTKVAWKHGVQVMIEGPGHVAMHKIKANMDEQLKHCHEAPFYTLGPLTTDIAPGYDHITSAIGAAMIGWFGTAMLCYVTPKEHLGLPDRDDVKTGVITYKLAAHAADLAKGHPGAAMWDDAISRARFEFRWEDQFNLGLDPETARKFH 546
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeeee.......eeeeeee..hhhhh...eee...hhhhhh..............hhhhhhh...eee......--------------...........eee......hhhhhhhh...hhhhhhhhhhhhh.......................hhhhhhhhhhh.........................eeeeee..-----hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh....eeehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....eeee.......hhhhh.hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh....eeee..........hhhhhhhhhhhhhhhhh..eee...........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3epm A  13 TISTGPIPGSRKVYQAGELFPELRVPFREVAVHPSANEPPVTIYDPSGPYSDPAIQIDIEKGLPRTREALVVARGDVEEVADPRQ--------------APEFPDTGRKIYRAKPGKLVTQLEYARAGIITAEmEYVAIRENLRREQDRPCVRDGEDFGASIPDFVTPEFVRQEIARGRAIIPANINHGELEPmAIGRNFLVKINANIGN-----TVADEVDKLVWATRWGADTVmDLSTGRNIHNIRDWIIRNSSVPIGTVPIYQALEKVNGVAEDLNWEVFRDTLIEQCEQGVDYFTIHAGVRLPFIPmTAKRVTGIVSRGGSImAKWCLAHHKENFLYERFDEICEImRAYDVSFSLGDGLRPGSTADANDEAQFSELRTLGELTKVAWKHGVQVmIEGPGHVAmHKIKANmDEQLKHCHEAPFYTLGPLTTDIAPGYDHITSAIGAAmIGWFGTAmLCYVTPKEHLGLPDRDDVKTGVITYKLAAHAADLAKGHPGAAmWDDAISRARFEFRWEDQFNLGLDPETARKFH 546
                                    22        32        42        52        62        72        82        92    |    -       112       122       132       142   |   152       162       172       182       192       202   |   212       222     | 232       242     | 252       262       272       282       292       302       312       322|      332      |342       352       362|      372       382       392       402       412       422    |  432       442       452       462 |     472       482       492       502       512  |    522       532       542    
                                                                                                               97            112                               146-MSE                                                     206-MSE         222   228                 248-MSE                                                                    323-MSE         339-MSE                 363-MSE                                         411-MSE  420-MSE  |                                  464-MSE 472-MSE                                    515-MSE                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                        427-MSE                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:512
 aligned with THIC_CAUCR | Q9A6Q5 from UniProtKB/Swiss-Prot  Length:612

    Alignment length:532
                                    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    15 STGPIPGSRKVYQAGELFPELRVPFREVAVHPSANEPPVTIYDPSGPYSDPAIQIDIEKGLPRTREALVVARGDVEEVADPRQVKPEDNGFAQGKHLAPEFPDTGRKIYRAKPGKLVTQLEYARAGIITAEMEYVAIRENLRREQDRPCVRDGEDFGASIPDFVTPEFVRQEIARGRAIIPANINHGELEPMAIGRNFLVKINANIGNSAVLSTVADEVDKLVWATRWGADTVMDLSTGRNIHNIRDWIIRNSSVPIGTVPIYQALEKVNGVAEDLNWEVFRDTLIEQCEQGVDYFTIHAGVRLPFIPMTAKRVTGIVSRGGSIMAKWCLAHHKENFLYERFDEICEIMRAYDVSFSLGDGLRPGSTADANDEAQFSELRTLGELTKVAWKHGVQVMIEGPGHVAMHKIKANMDEQLKHCHEAPFYTLGPLTTDIAPGYDHITSAIGAAMIGWFGTAMLCYVTPKEHLGLPDRDDVKTGVITYKLAAHAADLAKGHPGAAMWDDAISRARFEFRWEDQFNLGLDPETARKFH 546
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee.......eeeeeee..hhhhh...eee...hhhhhh..............hhhhhhhh..eee.....---------------...........eee......hhhhhhhh...hhhhhhhhhhh.........................hhhhhhhhhhh.........................eeeeee..-----hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh....eeehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..eeee.......hhhhhh.......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
                 3epm B  15 STGPIPGSRKVYQAGELFPELRVPFREVAVHPSANEPPVTIYDPSGPYSDPAIQIDIEKGLPRTREALVVARGDVEEVADPR---------------APEFPDTGRKIYRAKPGKLVTQLEYARAGIITAEmEYVAIRENLRREQDRPCVRDGEDFGASIPDFVTPEFVRQEIARGRAIIPANINHGELEPmAIGRNFLVKINANIGN-----TVADEVDKLVWATRWGADTVmDLSTGRNIHNIRDWIIRNSSVPIGTVPIYQALEKVNGVAEDLNWEVFRDTLIEQCEQGVDYFTIHAGVRLPFIPmTAKRVTGIVSRGGSImAKWCLAHHKENFLYERFDEICEImRAYDVSFSLGDGLRPGSTADANDEAQFSELRTLGELTKVAWKHGVQVmIEGPGHVAmHKIKANmDEQLKHCHEAPFYTLGPLTTDIAPGYDHITSAIGAAmIGWFGTAmLCYVTPKEHLGLPDRDDVKTGVITYKLAAHAADLAKGHPGAAmWDDAISRARFEFRWEDQFNLGLDPETARKFH 546
                                    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  
                                                                                                            96             112                               146-MSE                                                     206-MSE         222   228                 248-MSE                                                                    323-MSE         339-MSE                 363-MSE                                         411-MSE  420-MSE  |                                  464-MSE 472-MSE                                    515-MSE                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                      427-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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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        THIC_CAUCR | Q9A6Q5: 3epn 3epo 4s2a

(-) Related Entries Specified in the PDB File

3epn 3epo