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(-) Description

Title :  CRYSTAL STRUCTURE OF FDTS FROM T. MARITIMA MUTANT (R174K) WITH FAD AND DUMP
 
Authors :  I. I. Mathews
Date :  22 Apr 13  (Deposition) - 26 Mar 14  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.14
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Thyx, Fdts, Fad, Dump, Novel Fdts Fold, Convertion Of Dump To Dtmp Using Tetrahydrofolate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. I. Mathews
Flavin-Dependent Thymidylate Synthase As A Drug Target For Deadly Microbes: Mutational Study And A Strategy For Inhibitor Design.
J Bioterror Biodef V. L 12 004 2013
PubMed-ID: 24563811  |  Reference-DOI: 10.4172/2157-2526.S12-004

(-) Compounds

Molecule 1 - THYMIDYLATE SYNTHASE
    Chains: A, B, C, D
    EC Number: 2.1.1.148
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMH1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: TM0449 (UNP RESIDUES 1-220)
    Gene: THY1, THYX, TM0449, TM_0449
    Mutation: YES
    Organism Scientific: THERMOTOGA MARITIMA MSB8
    Organism Taxid: 243274
    Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099
    Synonym: TS, TSASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1DU4Ligand/Ion2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2FDA4Ligand/IonDIHYDROFLAVINE-ADENINE DINUCLEOTIDE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:86 , LEU A:87 , SER A:88 , GLY A:89 , ARG A:90 , ARG A:147 , HOH A:409 , HOH A:426 , ARG D:74 , GLN D:75 , ARG D:78 , FDA D:301BINDING SITE FOR RESIDUE DU A 301
2AC2SOFTWAREARG A:78 , HIS A:79 , ARG A:80 , ILE A:81 , ASN A:169 , LEU A:173 , LYS A:174 , HIS A:178 , THR C:55 , GLU C:58 , ILE C:81 , ASN C:163 , ARG C:165 , FDA C:301 , ASN D:85 , GLU D:86 , SER D:88 , DU D:302BINDING SITE FOR RESIDUE FDA A 302
3AC3SOFTWAREGLU B:86 , LEU B:87 , SER B:88 , GLY B:89 , ARG B:90 , ARG B:147 , GLN C:75 , ARG C:78 , FDA C:301 , HOH C:402BINDING SITE FOR RESIDUE DU B 301
4AC4SOFTWAREARG B:78 , HIS B:79 , ARG B:80 , ILE B:81 , ASN B:169 , LEU B:173 , HIS B:178 , ALA B:179 , HOH B:413 , ASN C:85 , GLU C:86 , SER C:88 , DU C:302 , HOH C:401 , THR D:55 , GLU D:58 , ILE D:81 , ASN D:163 , ARG D:165 , FDA D:301BINDING SITE FOR RESIDUE FDA B 302
5AC5SOFTWARESER A:30 , THR A:55 , GLU A:58 , ILE A:81 , ASN A:163 , ARG A:165 , FDA A:302 , ASN B:85 , GLU B:86 , SER B:88 , TYR B:91 , DU B:301 , ARG C:78 , HIS C:79 , ARG C:80 , ILE C:81 , ASN C:169 , LEU C:173 , HIS C:178 , ALA C:179 , HOH C:414BINDING SITE FOR RESIDUE FDA C 301
6AC6SOFTWAREGLN B:75 , ARG B:78 , LYS B:174 , FDA B:302 , GLU C:86 , LEU C:87 , SER C:88 , GLY C:89 , ARG C:90 , ARG C:147 , HOH C:406 , HOH C:431BINDING SITE FOR RESIDUE DU C 302
7AC7SOFTWAREASN A:85 , GLU A:86 , SER A:88 , DU A:301 , SER B:30 , THR B:55 , GLU B:58 , ILE B:81 , ASN B:163 , ARG B:165 , FDA B:302 , ARG D:78 , HIS D:79 , ARG D:80 , ILE D:81 , ASN D:169 , LEU D:173 , HIS D:178 , HOH D:412 , HOH D:419BINDING SITE FOR RESIDUE FDA D 301
8AC8SOFTWAREGLN A:75 , ARG A:78 , LYS A:174 , FDA A:302 , HOH A:417 , GLU D:86 , LEU D:87 , SER D:88 , GLY D:89 , ARG D:90 , ARG D:147 , HOH D:402BINDING SITE FOR RESIDUE DU D 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KAT)

(-) 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:218
                                                                                                                                                                                                                                                          
               SCOP domains d4kata_ A: Thy1 homologue                                                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeeeeeee.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhh.....eeee...............hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kat A  -1 HHMKIDILDKGFVELVDVMGNDLSAVRAARVSFDMGLKDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLKADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILK 216
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208        


Chain B from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains d4katb_ B: Thy1 homologue                                                                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeeeeeee.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhh.....eeee...............hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kat B   0 HMKIDILDKGFVELVDVMGNDLSAVRAARVSFDMGLKDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLKADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEVQ 219
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219


Chain C from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d4katc_ C: Thy1 homologue                                                                                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eeeeeeeee.hhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhh.....eeee...............hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kat C   1 MKIDILDKGFVELVDVMGNDLSAVRAARVSKDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLKADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEV 218
                                    10        20        30|       45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215   
                                                        30|                                                                                                                                                                                      
                                                         36                                                                                                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains d4katd_ D: Thy1 homologue                                                                                                                                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eeeeeeeee.hhhhhhhhhhh...hhhhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhh.....eeee...........hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kat D   0 HMKIDILDKGFVELVDVMGNDLSAVRAARVSFEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLKADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEV 218
                                     9        19        29 ||     45        55        65        75        85     || 99       109       119       129       139       149       159       169       179       189       199       209         
                                                          31|                                                   91|                                                                                                                          
                                                           38                                                    96
   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  (1, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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  4kat
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  THYX_THEMA | Q9WYT0
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  2.1.1.148
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 Related Entries

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

UniProtKB/Swiss-Prot
        THYX_THEMA | Q9WYT0: 1kq4 1o24 1o25 1o26 1o27 1o28 1o29 1o2a 1o2b 3g4a 3g4c 3n0b 3n0c 4gt9 4gta 4gtb 4gtc 4gtd 4gte 4gtf 4gtl 4kar 4kas 5chp 5ioq 5ior 5ios 5iot 5jfe

(-) Related Entries Specified in the PDB File

4kar 4kas