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(-) Description

Title :  CRYSTAL STRUCTURE OF C.ELEGANS THYMIDYLATE SYNTHASE IN COMPLEX WITH DUMP
 
Authors :  P. Wilk, A. Dowiercial, K. Banaszak, A. Jarmula, W. Rypniewski, W. Rode
Date :  15 Jan 13  (Deposition) - 29 Jan 14  (Release) - 29 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.48
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein Dimer, Deoxynucleotide Biosynthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Wilk, A. Dowiercial, K. Banaszak, A. Jarmula, W. Rypniewski, W. Rod
Crystal Structure Of C. Elegans Thymidylate Synthase In Complex With Dump
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - THYMIDYLATE SYNTHASE
    Chains: A, B
    EC Number: 2.1.1.45
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPIGDM4+STOP
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: NEMATODE
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1DTT4Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
2UMP2Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:51 , CYS A:197 , GLN A:216 , ARG A:217 , SER A:218 , GLY A:219 , ASP A:220 , GLY A:224 , ASN A:228 , HIS A:258 , TYR A:260 , HOH A:523 , HOH A:645 , ARG B:177 , ARG B:178BINDING SITE FOR RESIDUE UMP A 401
2AC2SOFTWARESER A:95 , ARG A:142 , HIS A:143 , SER A:156 , HOH A:627BINDING SITE FOR RESIDUE DTT A 402
3AC3SOFTWARELYS A:268BINDING SITE FOR RESIDUE DTT A 403
4AC4SOFTWAREARG A:177 , ARG A:178 , ARG B:51 , CYS B:197 , GLN B:216 , ARG B:217 , SER B:218 , GLY B:219 , ASP B:220 , GLY B:224 , VAL B:225 , ASN B:228 , HIS B:258 , TYR B:260 , DTT B:402 , HOH B:567 , HOH B:578BINDING SITE FOR RESIDUE UMP B 401
5AC5SOFTWAREGLU B:89 , PHE B:227 , UMP B:401 , HOH B:570 , HOH B:622 , HOH B:658BINDING SITE FOR RESIDUE DTT B 402
6AC6SOFTWARETYR A:204 , SER A:211 , THR A:249 , THR B:46 , SER B:58 , PHE B:60 , HOH B:580BINDING SITE FOR RESIDUE DTT B 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4IRR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4IRR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IRR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4IRR)

(-) Exons   (0, 0)

(no "Exon" information available for 4IRR)

(-) 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
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4irra_ A: automated matches                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhheeee.....eeeeeeeeeeeee.hhhh.........hhhhhhhhhhhhhhh..hhhhhhh.....hhhhhhhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee..hhhhhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee..........hhh.eeee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4irr A  23 QQVHLNQDEYKYLKQVEQILREGTRRDDRTGTGTISIFGMQSKYCLRNGTIPLLTTKRVYWKGVLEELLWFISGSTDGKLLMEKNVKIWEKNGDRAFLDNLGFTSREEGDLGPVYGFQWRHFGAKYVDCHTDYSGQGVDQLAEVIRQIKEQPDSRRIIMSAWNPSDLGQMVLPPCHTMCQFYVDNGELSCQLYQRSGDMGLGVPFNLASYGLLTHMIAKVCGLKPGTLVHTLGDAHVYSNHVDALKIQLDREPYAFPKIRFTRDVASIDDFTSDMIALDDYKCHPKIPMD 312
                                    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


Chain B from PDB  Type:PROTEIN  Length:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4irrb_ B: automated matches                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhheeee.....eeeeeeeeeeeee.hhhh.........hhhhhhhhhhhhhh...hhhhhhhh....hhhhhhhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee.....hhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee.....hhhhhhhh.eeee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4irr B  23 QQVHLNQDEYKYLKQVEQILREGTRRDDRTGTGTISIFGMQSKYCLRNGTIPLLTTKRVYWKGVLEELLWFISGSTDGKLLMEKNVKIWEKNGDRAFLDNLGFTSREEGDLGPVYGFQWRHFGAKYVDCHTDYSGQGVDQLAEVIRQIKEQPDSRRIIMSAWNPSDLGQMVLPPCHTMCQFYVDNGELSCQLYQRSGDMGLGVPFNLASYGLLTHMIAKVCGLKPGTLVHTLGDAHVYSNHVDALKIQLDREPYAFPKIRFTRDVASIDDFTSDMIALDDYKCHPKIPMD 312
                                    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
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4IRR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4IRR)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q9Y052_CAEEL | Q9Y052: 5noo
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        Q9Y052_CAEEL | Q9Y052: 4iqb 4iqq 4isw 4psg

(-) Related Entries Specified in the PDB File

3ihi CRYSTAL STRUCTURES OF SUBSTRATE- AND SULFATE-BOUND MOUSE THYMIDYLATE SYNTHASE
4e5o CRYSTAL STRUCTURE OF MOUSE THYMIDYLATE SYNTHASE IN COMPLEX WITH DUMP
4eb4 CRYSTAL STRUCTURE OF MOUSE THYMIDYLATE SYNTHASE IN TERNARY COMPLEX WITH DUMP AND TOMUDEX
4g9u CRYSTAL STRUCTURE OF T.SPIRALIS THYMIDYLATE SYNTHASE COMPLEX WITH DUMP
4iqb HIGH RESOLUTION CRYSTAL STRUCTURE OF C.ELEGANS THYMIDYLATE SYNTHASE
4iqq CRYSTAL STRUCTURE OF C.ELEGANS THYMIDYLATE SYNTHASE IN COMPLEX WITH DUMP AND TOMUDEX
4isw CRYSTAL STRUCTURE OF PHOSPHORYLATED C.ELEGANS THYMIDYLATE SYNTHASE IN COMPLEX WITH DUMP