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(-) Description

Title :  CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE COMPLEMENTING PROTEIN (TM0449) FROM THERMOTOGA MARITIMA WITH FAD AND BRDUMP AT 2.3 A RESOLUTION
 
Authors :  I. I. Mathews, A. M. Deacon, J. M. Canaves, D. Mcmullan, S. A. Lesley, S. Agarwalla, P. Kuhn, Joint Center For Structural Genomics (Jcsg)
Date :  18 Feb 03  (Deposition) - 24 Jun 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tm0449, Thymidylate Synthase Complementing Protein, Structural Genomics, Jcsg, Joint Center For Structural Genomics, Psi, Protein Structure Initiative, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. I. Mathews, A. M. Deacon, J. M. Canaves, D. Mcmullan, S. A. Lesley, S. Agarwalla, P. Kuhn
Functional Analysis Of Substrate And Cofactor Complex Structures Of A Thymidylate Synthase-Complementing Protein
Structure V. 11 677 2003
PubMed-ID: 12791256  |  Reference-DOI: 10.1016/S0969-2126(03)00097-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THYMIDYLATE SYNTHASE THYX
    Chains: A, B, C, D
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM0449
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: TS, TSASE, THYMIDYLATE SYNTHASE COMPLEMENTING PROTEIN

 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
1BRU4Mod. Residue5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:83 , ASN A:85 , GLU A:86 , TYR A:91 , HOH A:325 , BRU A:603 , SER B:30 , THR B:55 , GLU B:58 , ASN B:163 , ARG B:165 , HOH B:396 , FAD B:610 , ARG D:78 , HIS D:79 , ARG D:80 , ILE D:81 , ASN D:169 , LEU D:173 , ARG D:174 , HIS D:178 , HOH D:303 , HOH D:366BINDING SITE FOR RESIDUE FAD D 600
2AC2SOFTWAREGLU A:86 , LEU A:87 , SER A:88 , GLY A:89 , ARG A:90 , TYR A:91 , ARG A:147 , HOH A:368 , HOH A:390 , GLN D:75 , ARG D:78 , ARG D:174 , FAD D:600BINDING SITE FOR RESIDUE BRU A 603
3AC3SOFTWARESER A:30 , THR A:55 , GLU A:58 , ILE A:81 , ASN A:163 , ARG A:165 , FAD A:615 , ASN B:85 , GLU B:86 , TYR B:91 , BRU B:608 , ARG C:78 , HIS C:79 , ARG C:80 , ILE C:81 , ASN C:169 , LEU C:173 , HIS C:178 , HOH C:304 , HOH C:323 , HOH C:418 , HOH C:456BINDING SITE FOR RESIDUE FAD C 605
4AC4SOFTWAREGLU B:86 , LEU B:87 , SER B:88 , GLY B:89 , ARG B:90 , TYR B:91 , ARG B:147 , HOH B:305 , HOH B:393 , ARG C:74 , GLN C:75 , ARG C:78 , ARG C:174 , HOH C:329 , FAD C:605BINDING SITE FOR RESIDUE BRU B 608
5AC5SOFTWAREARG B:78 , HIS B:79 , ARG B:80 , ILE B:81 , ASN B:169 , LEU B:173 , ARG B:174 , HIS B:178 , HOH B:302 , HOH B:319 , HOH B:410 , ASN C:85 , GLU C:86 , BRU C:613 , SER D:30 , THR D:55 , GLU D:58 , ILE D:81 , ASN D:163 , ARG D:165 , FAD D:600BINDING SITE FOR RESIDUE FAD B 610
6AC6SOFTWAREARG B:74 , GLN B:75 , ARG B:78 , ARG B:174 , FAD B:610 , GLU C:86 , LEU C:87 , SER C:88 , GLY C:89 , ARG C:90 , ARG C:147 , HOH C:309 , HOH C:376BINDING SITE FOR RESIDUE BRU C 613
7AC7SOFTWAREARG A:78 , HIS A:79 , ARG A:80 , ILE A:81 , ASN A:169 , LEU A:173 , HIS A:178 , HOH A:342 , HOH A:472 , THR C:55 , GLU C:58 , ILE C:81 , ASN C:163 , ARG C:165 , FAD C:605 , ASN D:85 , GLU D:86 , TYR D:91 , HOH D:443 , BRU D:618BINDING SITE FOR RESIDUE FAD A 615
8AC8SOFTWAREARG A:74 , GLN A:75 , ARG A:78 , ARG A:174 , HOH A:335 , FAD A:615 , GLU D:86 , LEU D:87 , SER D:88 , GLY D:89 , ARG D:90 , ARG D:147 , HOH D:301BINDING SITE FOR RESIDUE BRU D 618

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O27)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1O27)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O27)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYXPS51331 Flavin-dependent thymidylate synthase (thyX) domain profile.THYX_THEMA1-208
 
 
 		  4A:1-208
B:1-208
C:1-208
D:1-208

(-) Exons   (0, 0)

(no "Exon" information available for 1O27)

(-) 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:216
 aligned with THYX_THEMA | Q9WYT0 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:216
                             1                                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209      
           THYX_THEMA     - -MKIDILDKGFVELVDVMGNDLSAVRAARVSFDMGLKDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDIL 215
               SCOP domains d1o27a_ A: Thy1 homologue                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee...eeeeeeeee.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhh.eeeeeeeeehhhhhhhh.....eeee...............hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -THYX  PDB: A:1-208 UniProt: 1-208                                                                                                                                                                               ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1o27 A   0 HMKIDILDKGFVELVDVMGNDLSAVRAARVSFDMGLKDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDIL 215
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209      


Chain B from PDB  Type:PROTEIN  Length:217
 aligned with THYX_THEMA | Q9WYT0 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
           THYX_THEMA     1 MKIDILDKGFVELVDVMGNDLSAVRAARVSFDMGLKDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEVQV 220
               SCOP domains d1o27b_ B: Thy1 homologue                                                                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eeeeeeeee.hhhhhhhhhhhhhh...---hhhhhhhhhhhhhh.hhhhhh.eeeeeeeeehhhhhhhh.....eeee...............hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE THYX  PDB: B:1-208 UniProt: 1-208                                                                                                                                                                               ------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o27 B   1 MKIDILDKGFVELVDVMGNDLSAVRAARVSFDMGL---ERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEVQV 220
                                    10        20        30    |   40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
                                                             35  39                                                                                                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:216
 aligned with THYX_THEMA | Q9WYT0 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
           THYX_THEMA     1 MKIDILDKGFVELVDVMGNDLSAVRAARVSFDMGLKDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEVQV 220
               SCOP domains d1o27c_ C: Thy1 homologue                                                                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eeeeeeeee.hhhhhhhhhhh..----.hhhhhhhhhhhhhhhh.hhhhhh.eeeeeeeeehhhhhhhh.....eeee...............hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE THYX  PDB: C:1-208 UniProt: 1-208                                                                                                                                                                               ------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o27 C   1 MKIDILDKGFVELVDVMGNDLSAVRAARVSF----KDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEVQV 220
                                    10        20        30|    |  40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
                                                         31   36                                                                                                                                                                                        


Chain D from PDB  Type:PROTEIN  Length:215
 aligned with THYX_THEMA | Q9WYT0 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        
           THYX_THEMA     1 MKIDILDKGFVELVDVMGNDLSAVRAARVSFDMGLKDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEV 218
               SCOP domains d1o27d_ D: Thy1 homologue                                                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------Thy1-1o27D01 D:11-201                                                                                                                                                                          ----------------- Pfam domains (1)
           Pfam domains (2) ----------Thy1-1o27D02 D:11-201                                                                                                                                                                          ----------------- Pfam domains (2)
           Pfam domains (3) ----------Thy1-1o27D03 D:11-201                                                                                                                                                                          ----------------- Pfam domains (3)
           Pfam domains (4) ----------Thy1-1o27D04 D:11-201                                                                                                                                                                          ----------------- Pfam domains (4)
         Sec.struct. author .eeee...eeeeeeeee.hhhhhhhhhhh....---hhhhhhhhhhhhhhhh.hhhhhh.eeeeeeeeehhhhhhhh.....eeee...............hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE THYX  PDB: D:1-208 UniProt: 1-208                                                                                                                                                                               ---------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o27 D   1 MKIDILDKGFVELVDVMGNDLSAVRAARVSFDM---DEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEV 218
                                    10        20        30  |   | 40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        
                                                           33  37
   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 1O27)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Thy1] (11)
(-)
Family: Thy1 (11)
(-)
Thermotoga maritima (11)
1aThy1-1o27D01D:11-201
1bThy1-1o27D02D:11-201
1cThy1-1o27D03D:11-201
1dThy1-1o27D04D:11-201

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (THYX_THEMA | Q9WYT0)
molecular function
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0050797    thymidylate synthase (FAD) activity    Catalysis of the reaction: 5,10-methylenetetrahydrofolate + dUMP + NADPH + H+ = dTMP + tetrahydrofolate + NADP+.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006231    dTMP biosynthetic process    The chemical reactions and pathways resulting in the formation of dTMP, deoxyribosylthymine monophosphate (2'-deoxyribosylthymine 5'-phosphate).
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0009165    nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).

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  1o27
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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 1o28 1o29 1o2a 1o2b 3g4a 3g4c 3n0b 3n0c 4gt9 4gta 4gtb 4gtc 4gtd 4gte 4gtf 4gtl 4kar 4kas 4kat 5chp 5ioq 5ior 5ios 5iot 5jfe

(-) Related Entries Specified in the PDB File

1o24 CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE COMPLEMENTING PROTEIN (TM0449) FROM THERMOTOGA MARITIMA AT 2.0 A RESOLUTION
1o25 CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE COMPLEMENTING PROTEIN (TM0449) FROM THERMOTOGA MARITIMA WITH DUMP AT 2.4 A RESOLUTION
1o26 CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE COMPLEMENTING PROTEIN (TM0449) FROM THERMOTOGA MARITIMA WITH FAD AND DUMP AT 1.6 A RESOLUTION
1o28 CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE COMPLEMENTING PROTEIN (TM0449) FROM THERMOTOGA MARITIMA WITH FDUMP AT 2.1 A RESOLUTION
1o29 CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE COMPLEMENTING PROTEIN (TM0449) FROM THERMOTOGA MARITIMA WITH FAD AND FDUMP AT 2.0 A RESOLUTION
1o2a CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE COMPLEMENTING PROTEIN (TM0449) FROM THERMOTOGA MARITIMA WITH FAD AT 1.8 A RESOLUTION
1o2b CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE COMPLEMENTING PROTEIN (TM0449) FROM THERMOTOGA MARITIMA WITH FAD AND PO4 AT 2.45 A RESOLUTION