1O28 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE COMPLEMENTING PROTEIN (TM0449) FROM THERMOTOGA MARITIMA WITH FDUMP AT 2.1 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 :   2.10

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)

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

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 12)

No.	Name	Count	Type	Full Name
1	EPE	4	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2	PGE	4	Ligand/Ion	TRIETHYLENE GLYCOL
3	UFP	4	Ligand/Ion	5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	UFP A:703 , ARG B:165 , ARG D:78 , ARG D:80 , ASN D:169 , LEU D:173 , HOH D:319	BINDING SITE FOR RESIDUE EPE D 700
02	AC2	SOFTWARE	GLU A:86 , LEU A:87 , SER A:88 , GLY A:89 , ARG A:90 , TYR A:91 , ARG A:147 , HOH A:377 , HOH A:438 , HOH A:463 , HOH A:479 , GLN D:75 , ARG D:78 , ARG D:174 , EPE D:700	BINDING SITE FOR RESIDUE UFP A 703
03	AC3	SOFTWARE	ARG A:165 , UFP B:708 , ARG C:78 , ARG C:80 , ASN C:169 , HOH C:321 , HOH C:548	BINDING SITE FOR RESIDUE EPE C 705
04	AC4	SOFTWARE	GLU B:86 , LEU B:87 , SER B:88 , GLY B:89 , ARG B:90 , TYR B:91 , ARG B:147 , HOH B:318 , HOH B:475 , GLN C:75 , ARG C:78 , ARG C:174 , HOH C:332 , HOH C:392 , EPE C:705	BINDING SITE FOR RESIDUE UFP B 708
05	AC5	SOFTWARE	ARG B:78 , ARG B:80 , ASN B:169 , HOH B:421 , HOH B:496 , UFP C:713 , ARG D:165	BINDING SITE FOR RESIDUE EPE B 710
06	AC6	SOFTWARE	ARG B:74 , GLN B:75 , ARG B:78 , ARG B:174 , EPE B:710 , PHE C:77 , GLU C:86 , LEU C:87 , SER C:88 , GLY C:89 , ARG C:90 , TYR C:91 , ARG C:147 , HOH C:316 , HOH C:346 , HOH C:371	BINDING SITE FOR RESIDUE UFP C 713
07	AC7	SOFTWARE	ARG A:78 , ARG A:80 , ASN A:169 , HOH A:339 , ARG C:165 , UFP D:718	BINDING SITE FOR RESIDUE EPE A 715
08	AC8	SOFTWARE	GLN A:75 , ARG A:78 , ARG A:174 , HOH A:432 , EPE A:715 , GLU D:86 , LEU D:87 , SER D:88 , GLY D:89 , ARG D:90 , TYR D:91 , ARG D:147 , HOH D:433	BINDING SITE FOR RESIDUE UFP D 718
09	AC9	SOFTWARE	ARG A:80 , ALA A:82 , ILE B:81 , ASN B:163 , ARG B:165 , ARG D:80	BINDING SITE FOR RESIDUE PGE B 720
10	BC1	SOFTWARE	ILE A:81 , ARG A:165 , ALA B:82 , ARG C:80 , HOH C:328	BINDING SITE FOR RESIDUE PGE C 725
11	BC2	SOFTWARE	ARG B:80 , ILE B:81 , ALA C:82 , ILE D:81 , ARG D:165	BINDING SITE FOR RESIDUE PGE D 730
12	BC3	SOFTWARE	ARG A:80 , ARG C:165 , ALA D:82 , SER D:83	BINDING SITE FOR RESIDUE PGE D 735

(no "SS Bond" information available for 1O28)

(no "Cis Peptide Bond" information available for 1O28)

(no "SAP(SNP)/Variant" information available for 1O28)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THYX	PS51331	Flavin-dependent thymidylate synthase (thyX) domain profile.	THYX_THEMA	1-208	4	A:1-208 B:1-208 C:1-208 D:1-208

(no "Exon" information available for 1O28)

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

    Alignment length:218
                               1                                                                                                                                                                                                                      
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207        
           THYX_THEMA     - ---MKIDILDKGFVELVDVMGNDLSAVRAARVSFDMGLKDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDIL 215
               SCOP domains d1o28a_ A: Thy1 homologue                                                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...eeeeeeeee.hhhhhhhhhhhh......hhhhhhhhhhhhhhh..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
                 1o28 A  -2 HHHMKIDILDKGFVELVDVMGNDLSAVRAARVSFDMGLKDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDIL 215
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207

Chain B from PDB  Type:PROTEIN  Length:220
 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 d1o28b_ B: Thy1 homologue                                                                                                                                                                                                    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...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE THYX  PDB: B:1-208 UniProt: 1-208                                                                                                                                                                               ------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o28 B   1 MKIDILDKGFVELVDVMGNDLSAVRAARVSFDMGLKDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEVQV 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

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 d1o28c_ C: Thy1 homologue                                                                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eeeeeeeee.hhhhhhhhhhh..----.hhhhhhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhh.....eeee...............hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE THYX  PDB: C:1-208 UniProt: 1-208                                                                                                                                                                               ------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o28 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:214
 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 d1o28d_ D: Thy1 homologue                                                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------Thy1-1o28D01 D:11-201                                                                                                                                                                          ----------------- Pfam domains (1)
           Pfam domains (2) ----------Thy1-1o28D02 D:11-201                                                                                                                                                                          ----------------- Pfam domains (2)
           Pfam domains (3) ----------Thy1-1o28D03 D:11-201                                                                                                                                                                          ----------------- Pfam domains (3)
           Pfam domains (4) ----------Thy1-1o28D04 D:11-201                                                                                                                                                                          ----------------- Pfam domains (4)
         Sec.struct. author .eeee...eeeeeeeee.hhhhhhhhhh...----.hhhhhhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhh.....eeee...............hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE THYX  PDB: D:1-208 UniProt: 1-208                                                                                                                                                                               ---------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o28 D   1 MKIDILDKGFVELVDVMGNDLSAVRAARVSF----KDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEV 218
                                    10        20        30|    |  40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        
                                                         31   36

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Thymidylate synthase-complementing protein Thy1 (24)

Superfamily: Thymidylate synthase-complementing protein Thy1 (24)

Family: Thymidylate synthase-complementing protein Thy1 (24)

Protein domain: Thy1 homologue (22)

Thermotoga maritima [TaxId: 2336] (22)

1a	d1o28a_	A:
1b	d1o28b_	B:
1c	d1o28c_	C:
1d	d1o28d_	D:

(no "CATH Domain" information available for 1O28)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Thy1] (11)

Family: Thy1 (11)

Thermotoga maritima (11)

1a	Thy1-1o28D01	D:11-201
1b	Thy1-1o28D02	D:11-201
1c	Thy1-1o28D03	D:11-201
1d	Thy1-1o28D04	D:11-201

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).

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1o28)

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	1o28
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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
1o27	CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE COMPLEMENTING PROTEIN (TM0449) FROM THERMOTOGA MARITIMA WITH FAD AND BRDUMP AT 2.3 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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (1, 4)

Gene Ontology (7, 7)

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