3G4A - JenaLib

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Title :   CRYSTAL STRUCTURE OF FLAVINE DEPENDANT THYMIDYLATE SYNTHASE S88A MUTANT FROM THERMOTOGA MARITIMA AT 1.95 ANGSTROM RESOLUTION

Authors :   I. I. Mathews, S. A. Lesley, A. Kohen

Date :   03 Feb 09 (Deposition) - 07 Apr 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Fdts, Thyx, S88A Mutation, Dump Complex, Fad, Flavoprotein, Methyltransferase, Nucleotide Biosynthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. M. Koehn, T. Fleischmann, J. A. Conrad, B. A. Palfey, S. A. Lesley, I. I. Mathews, A. Kohen
An Unusual Mechanism Of Thymidylate Biosynthesis In Organisms Containing The Thyx Gene.
Nature V. 458 919 2009
PubMed-ID: 19370033 | Reference-DOI: 10.1038/NATURE07973
(for further references see the PDB file header)

Molecule 1 - THYMIDYLATE SYNTHASE THYX
	Atcc	:	43589
	Chains	:	A, B, C, D
	EC Number	:	2.1.1.148
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	MH1
	Expression System Strain	:	DL41
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	THY1, THYX, TM_0449
	Mutation	:	YES
	Organism Scientific	:	THERMOTOGA MARITIMA MSB8
	Organism Taxid	:	243274
	Strain	:	MSB8 / DSM 3109 / JCM 10099
	Synonym	:	TS, TSASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 8)

No.	Name	Count	Type	Full Name
1	FAD	4	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	UMP	4	Ligand/Ion	2'-DEOXYURIDINE 5'-MONOPHOSPHATE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:83 , ASN A:85 , GLU A:86 , ALA A:88 , TYR A:91 , UMP A:303 , SER B:30 , THR B:55 , GLU B:58 , ILE B:81 , ASN B:163 , ARG B:165 , FAD B:310 , 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:246 , HOH D:264 , HOH D:281	BINDING SITE FOR RESIDUE FAD D 300
2	AC2	SOFTWARE	GLU A:86 , LEU A:87 , ALA A:88 , GLY A:89 , ARG A:90 , ARG A:147 , HOH A:221 , HOH A:254 , GLN D:75 , ARG D:78 , ARG D:174 , FAD D:300	BINDING SITE FOR RESIDUE UMP A 303
3	AC3	SOFTWARE	SER A:30 , THR A:55 , GLU A:58 , ILE A:81 , ASN A:163 , ARG A:165 , FAD A:315 , ASN B:85 , GLU B:86 , ALA B:88 , TYR B:91 , UMP B:308 , ARG C:78 , HIS C:79 , ARG C:80 , ILE C:81 , ASN C:169 , LEU C:173 , ARG C:174 , HIS C:178 , HOH C:234 , HOH C:244 , HOH C:328	BINDING SITE FOR RESIDUE FAD C 305
4	AC4	SOFTWARE	GLU B:86 , LEU B:87 , ALA B:88 , GLY B:89 , ARG B:90 , ARG B:147 , HOH B:223 , HOH B:315 , GLN C:75 , ARG C:78 , ARG C:174 , HOH C:229 , FAD C:305	BINDING SITE FOR RESIDUE UMP B 308
5	AC5	SOFTWARE	ARG 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:232 , HOH B:278 , HOH B:280 , ASN C:85 , GLU C:86 , ALA C:88 , TYR C:91 , UMP C:313 , THR D:55 , GLU D:58 , ILE D:81 , ASN D:163 , ARG D:165 , FAD D:300	BINDING SITE FOR RESIDUE FAD B 310
6	AC6	SOFTWARE	ARG B:74 , GLN B:75 , ARG B:78 , ARG B:174 , FAD B:310 , GLU C:86 , LEU C:87 , ALA C:88 , GLY C:89 , ARG C:90 , ARG C:147 , HOH C:228 , HOH C:294	BINDING SITE FOR RESIDUE UMP C 313
7	AC7	SOFTWARE	ARG A:78 , HIS A:79 , ARG A:80 , ILE A:81 , ASN A:169 , LEU A:173 , ARG A:174 , HIS A:178 , HOH A:263 , HOH A:289 , HOH A:295 , THR C:55 , GLU C:58 , ILE C:81 , ASN C:163 , ARG C:165 , FAD C:305 , ASN D:85 , GLU D:86 , ALA D:88 , TYR D:91 , UMP D:318	BINDING SITE FOR RESIDUE FAD A 315
8	AC8	SOFTWARE	ARG A:74 , GLN A:75 , ARG A:78 , ARG A:174 , FAD A:315 , GLU D:86 , LEU D:87 , ALA D:88 , GLY D:89 , ARG D:90 , ARG D:147 , HOH D:222 , HOH D:269	BINDING SITE FOR RESIDUE UMP D 318

(no "SS Bond" information available for 3G4A)

(no "Cis Peptide Bond" information available for 3G4A)

(no "SAP(SNP)/Variant" information available for 3G4A)

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 3G4A)

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                                                                                                                                                                                                                       
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208        
           THYX_THEMA     - --MKIDILDKGFVELVDVMGNDLSAVRAARVSFDMGLKDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILK 216
               SCOP domains d3g4aa_ A: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeeeeeee.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhh.eeeeeeeeehhhhhhhh.....eeee...............hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --THYX  PDB: A:1-208 UniProt: 1-208                                                                                                                                                                               -------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g4a A  -1 HHMKIDILDKGFVELVDVMGNDLSAVRAARVSFDMGLKDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELAGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILK 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
 aligned with THYX_THEMA | Q9WYT0 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:220
                             1                                                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219
           THYX_THEMA     - -MKIDILDKGFVELVDVMGNDLSAVRAARVSFDMGLKDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEVQ 219
               SCOP domains d3g4ab_ B: automated matches                                                                                                                                                                                                 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...hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -THYX  PDB: B:1-208 UniProt: 1-208                                                                                                                                                                               ----------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g4a B   0 HMKIDILDKGFVELVDVMGNDLSAVRAARVSFDMGLKDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELAGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEVQ 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: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 d3g4ac_ C: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eeeeeeeee.hhhhhhhhhhh..----.hhhhhhhhhhhhhhh..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
                 3g4a C   1 MKIDILDKGFVELVDVMGNDLSAVRAARVSF----KDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELAGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEV 218
                                    10        20        30|    |  40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        
                                                         31   36

Chain D from PDB  Type:PROTEIN  Length:212
 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 d3g4ad_ D: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eeeeeeeee.hhhhhhhhhhh..------hhhhhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhh.....eeee...............hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE THYX  PDB: D:1-208 UniProt: 1-208                                                                                                                                                                               ---------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g4a D   1 MKIDILDKGFVELVDVMGNDLSAVRAARVSF------EERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELAGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEV 218
                                    10        20        30|      |40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        
                                                         31     38

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

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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: automated matches (2)

Thermotoga maritima [TaxId: 243274] (1)

1a	d3g4aa_	A:
1b	d3g4ab_	B:
1c	d3g4ac_	C:
1d	d3g4ad_	D:

(no "CATH Domain" information available for 3G4A)

(no "Pfam Domain" information available for 3G4A)

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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Description

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Ligands, Modified Residues, Ions (2, 8)

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