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(-) Description

Title :  E. COLI THYMIDYLATE SYNTHASE Y209W VARIANT IN COMPLEX WITH SUBSTRATE AND A COFACTOR ANALOG
 
Authors :  Z. Newby, T. T. Lee, J. Finer-Moore, R. M. Stroud
Date :  02 Aug 12  (Deposition) - 29 Aug 12  (Release) - 07 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta Sheet, Alpha/Beta Protein, Methylase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Wang, T. Abeysinghe, J. S. Finer-Moore, R. M. Stroud, A. Kohen
A Remote Mutation Affects The Hydride Transfer By Disruptin Concerted Protein Motions In Thymidylate Synthase.
J. Am. Chem. Soc. V. 134 17722 2012
PubMed-ID: 23034004  |  Reference-DOI: 10.1021/JA307859M
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THYMIDYLATE SYNTHASE
    Chains: A, B
    EC Number: 2.1.1.45
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: B2827, JW2795, THYA
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: TS, TSASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CB32Ligand/Ion10-PROPARGYL-5,8-DIDEAZAFOLIC ACID
2CXM2Mod. Amino AcidN-CARBOXYMETHIONINE
3UMC2Ligand/Ion2'-DEOXY-5'-URIDYLIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:21 , CYS A:146 , HIS A:147 , GLN A:165 , ARG A:166 , SER A:167 , CYS A:168 , ASP A:169 , ASN A:177 , HIS A:207 , TRP A:209 , CB3 A:702 , HOH A:820 , HOH A:859 , ARG B:126 , ARG B:127BINDING SITE FOR RESIDUE UMC A 701
2AC2SOFTWAREGLU A:58 , ILE A:79 , TRP A:80 , TRP A:83 , LEU A:143 , ASP A:169 , GLY A:173 , PHE A:176 , ASN A:177 , VAL A:262 , ALA A:263 , UMC A:701 , HOH A:814 , HOH A:831 , HOH A:854 , HOH A:861 , HOH A:864 , HOH A:880 , HOH A:925 , HOH A:941 , HOH A:957 , HOH A:1145 , HOH A:1183BINDING SITE FOR RESIDUE CB3 A 702
3AC3SOFTWAREARG A:126 , ARG A:127 , ARG B:21 , CYS B:146 , HIS B:147 , GLN B:165 , ARG B:166 , SER B:167 , CYS B:168 , ASP B:169 , ASN B:177 , HIS B:207 , TRP B:209 , CB3 B:802 , HOH B:911 , HOH B:915BINDING SITE FOR RESIDUE UMC B 801
4AC4SOFTWAREGLU B:58 , ILE B:79 , TRP B:80 , TRP B:83 , ASP B:169 , GLY B:173 , PHE B:176 , ASN B:177 , VAL B:262 , ALA B:263 , UMC B:801 , HOH B:922 , HOH B:931 , HOH B:961 , HOH B:963 , HOH B:967 , HOH B:969 , HOH B:992 , HOH B:1025 , HOH B:1110BINDING SITE FOR RESIDUE CB3 B 802

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GEV)

(-) 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:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains d4geva_ A: Thymidylate synthase                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhheee.......eeeeeeeeeeee.hhh.........hhhhhhhhhhhhhhh...hhhhhhh....hhhhh........hhhhhhhhee.....eehhhhhhhhhhhhh......eee..hhhhhhhh.....eeeeeeeee..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee..........hhh.eeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gev A   1 mKQYLELMQKVLDEGTQKNDRTGTGTLSIFGHQMRFNLQDGFPLVTTKRCHLRSIIHELLWFLQGDTNIAYLHENNVTIWDEWADENGDLGPVYGKQWRAWPTPDGRHIDQITTVLNQLKNDPDSRRIIVSAWNVGELDKMALAPCHAFFQFYVADGKLSCQLYQRSCDVFLGLPFNIASYALLVHMMAQQCDLEVGDFVWTGGDTHLWSNHMDQTHLQLSREPRPLPKLIIKRKPESIFDYRFEDFEIEGYDPHPGIKAPVAI 264
                            |       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    
                            |                                                                                                                                                                                                                                                                       
                            1-CXM                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains d4gevb_ B: Thymidylate synthase                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhheee.......eeeeeeeeeeee.hhh.........hhhhhhhhhhhhhhh...hhhhhhh....hhhhh........hhhhhhhhee.....eehhhhhhhhhhhhh......eee..hhhhhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee..........hhh.eeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gev B   1 mKQYLELMQKVLDEGTQKNDRTGTGTLSIFGHQMRFNLQDGFPLVTTKRCHLRSIIHELLWFLQGDTNIAYLHENNVTIWDEWADENGDLGPVYGKQWRAWPTPDGRHIDQITTVLNQLKNDPDSRRIIVSAWNVGELDKMALAPCHAFFQFYVADGKLSCQLYQRSCDVFLGLPFNIASYALLVHMMAQQCDLEVGDFVWTGGDTHLWSNHMDQTHLQLSREPRPLPKLIIKRKPESIFDYRFEDFEIEGYDPHPGIKAPVAI 264
                            |       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    
                            1-CXM
   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 ; only for superseded entry 2G8M: 1,2)

(no "CATH Domain" information available for 4GEV, only for superseded entry 2G8M replaced by 4GEV)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

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
        TYSY_ECOLI | P0A884: 1aiq 1ajm 1an5 1aob 1axw 1bdu 1bid 1bjg 1bq1 1bq2 1ddu 1dna 1ev5 1ev8 1evf 1evg 1f4b 1f4c 1f4d 1f4e 1f4f 1f4g 1ffl 1fwm 1jg0 1jtq 1jtu 1jut 1kce 1kzi 1kzj 1nce 1qqq 1syn 1tdu 1tjs 1tlc 1tls 1trg 1tsd 1tsn 1tys 1zpr 2a9w 2bbq 2ftn 2fto 2ftq 2g8x 2kce 2tsc 2vet 2vf0 3b5b 3b9h 3bfi 3bgx 3bhl 3bhr 3tms 4f2v 4isk 4knz

(-) Related Entries Specified in the PDB File

2g86 L. CASEI THYMIDYLATE SYNTHASE Y261F-DUMP
2g89 L. CASEI THYMIDYLATE SYNTHASE Y261A-DUMP
2g8a L. CASEI THYMIDYLATE SYNTHASE Y261M-DUMP
2g8d L. CASEI THYMIDYLATE SYNTHASE Y261A-DUMP
2g8o WILD TYPE E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH DUMP AND CB3717
2g8x E. COLI Y209W THYMIDYLATE SYNTHASE APO ENZYME