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(-) Description

Title :  FLAVIN-DEPENDENT THYMIDYLATE SYNTHASE R174A VARIANT IN COMPLEX WITH FAD AND DUMP
 
Authors :  S. M. Bernard, F. W. Stull, J. L. Smith
Date :  08 Mar 16  (Deposition) - 08 Jun 16  (Release) - 22 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Fad-Dependent, Nucleotide Biosynthesis, Reductive Methylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. W. Stull, S. M. Bernard, A. Sapra, J. L. Smith, E. R. Zuiderweg, B. A. Palfey
Deprotonations In The Reaction Of Flavin-Dependent Thymidylate Synthase.
Biochemistry V. 55 3261 2016
PubMed-ID: 27214228  |  Reference-DOI: 10.1021/ACS.BIOCHEM.6B00510

(-) Compounds

Molecule 1 - THYMIDYLATE SYNTHASE THYX
    Chains: A, B, C, D
    EC Number: 2.1.1.148
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: THYX, THY1, TM_0449
    Mutation: YES
    Organism Scientific: THERMOTOGA MARITIMA (STRAIN ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
    Organism Taxid: 243274
    Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099
    Synonym: 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
1FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2UMP4Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:78 , HIS A:79 , ARG A:80 , ILE A:81 , ASN A:169 , LEU A:173 , HIS A:178 , HOH A:412 , HOH A:417 , HOH A:418 , HOH A:425 , HOH A:438 , SER B:83 , ASN B:85 , GLU B:86 , SER B:88 , TYR B:91 , UMP B:302 , SER D:30 , THR D:55 , GLU D:58 , ILE D:81 , ASN D:163 , ARG D:165 , FAD D:301binding site for residue FAD A 301
2AC2SOFTWAREGLU A:86 , LEU A:87 , SER A:88 , GLY A:89 , ARG A:90 , ARG A:147 , HOH A:410 , GLN B:75 , ARG B:78 , FAD B:301 , HOH B:410 , HOH B:421 , HOH B:431binding site for residue UMP A 302
3AC3SOFTWAREASN A:85 , GLU A:86 , SER A:88 , TYR A:91 , UMP A:302 , HOH A:403 , ARG B:78 , HIS B:79 , ARG B:80 , ILE B:81 , ASN B:169 , LEU B:173 , HIS B:178 , HOH B:417 , HOH B:424 , HOH B:434 , HOH B:435 , HOH B:456 , THR C:55 , GLU C:58 , ILE C:81 , ASN C:163 , ARG C:165 , FAD C:301binding site for residue FAD B 301
4AC4SOFTWAREGLN A:75 , ARG A:78 , FAD A:301 , GLU B:86 , LEU B:87 , SER B:88 , GLY B:89 , ARG B:90 , ARG B:147 , HOH B:412 , HOH B:426 , HOH B:439 , HOH B:443 , HOH B:448binding site for residue UMP B 302
5AC5SOFTWARESER B:30 , THR B:55 , GLU B:58 , ILE B:81 , ASN B:163 , ARG B:165 , FAD B:301 , ARG C:78 , HIS C:79 , ARG C:80 , ILE C:81 , ASN C:169 , LEU C:173 , HIS C:178 , HOH C:416 , HOH C:418 , HOH C:420 , HOH C:424 , HOH C:433 , HOH C:437 , HOH C:463 , ASN D:85 , GLU D:86 , SER D:88 , TYR D:91 , UMP D:302binding site for residue FAD C 301
6AC6SOFTWAREGLU C:86 , LEU C:87 , SER C:88 , GLY C:89 , ARG C:90 , ARG C:147 , HOH C:412 , HOH C:414 , HOH C:415 , HOH C:426 , GLN D:75 , ARG D:78 , FAD D:301 , HOH D:428binding site for residue UMP C 302
7AC7SOFTWARETHR A:55 , GLU A:58 , ILE A:81 , ASN A:163 , ARG A:165 , FAD A:301 , ASN C:85 , GLU C:86 , SER C:88 , TYR C:91 , UMP C:302 , HOH C:410 , ARG D:78 , HIS D:79 , ARG D:80 , ILE D:81 , ASN D:169 , LEU D:173 , HIS D:178 , HOH D:406 , HOH D:408 , HOH D:409 , HOH D:431 , HOH D:436 , HOH D:450binding site for residue FAD D 301
8AC8SOFTWAREGLN C:75 , ARG C:78 , FAD C:301 , HOH C:422 , HOH C:432 , HOH C:435 , GLU D:86 , LEU D:87 , SER D:88 , GLY D:89 , ARG D:90 , ARG D:147 , HOH D:413 , HOH D:429binding site for residue UMP D 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5IOT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5IOT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IOT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IOT)

(-) Exons   (0, 0)

(no "Exon" information available for 5IOT)

(-) 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:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eeeeeeeee.hhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhh.....eeee...............hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iot A   1 MKIDILDKGFVELVDVMGNDLSAVRAARVSFDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLAADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEVQV 220
                                    10        20        30||      45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215     
                                                         31|                                                                                                                                                                                       
                                                          37                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeeeeeee.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhh.eeeeeeeeehhhhhhhh.....eeee...............hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iot B   0 HMKIDILDKGFVELVDVMGNDLSAVRAARVSFDMGLKDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLAADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILK 216
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       


Chain C from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 5iot C   1 MKIDILDKGFVELVDVMGNDLSAVRAARVSKDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLAADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEV 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:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eeeeeeeee.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhh.....eeee...............hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iot D   1 MKIDILDKGFVELVDVMGNDLSAVRAARVSFDMGLKDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLAADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEV 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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 5IOT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IOT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IOT)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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  5iot
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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 4kat 5chp 5ioq 5ior 5ios 5jfe

(-) Related Entries Specified in the PDB File

5ioq 5ior 5iot