4FOG - JenaLib

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Title :   CRYSTAL STRUCTURE OF MTB THYA IN COMPLEX WITH 5-FLUORO-DUMP AND 5-METHYLTETRAHYDROFOLIC ACID

Authors :   M. C. M. Reddy, J. B. Bruning, W. Harshbarger, J. C. Sacchettini, Tb Str Genomics Consortium (Tbsgc)

Date :   20 Jun 12 (Deposition) - 07 Aug 13 (Release) - 07 Aug 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,D  (1x)
Biol. Unit 2: B,C  (1x)

Keywords :   Structural Genomics, Tb Structural Genomics Consortium, Tbsgc, Transferase, Thymidylate Synthase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. C. M. Reddy, J. B. Bruning, J. C. Sacchettini
Crystal Structure Of Binary And Ternary Complexes Of Thymidylate Synthase (Thya) From Mycobacterium Tuberculosis Insights Into The Selectivity And Mode Of Inhibition
To Be Published
PubMed: search

Molecule 1 - THYMIDYLATE SYNTHASE
	Chains	:	A, B, C, D
	EC Number	:	2.1.1.45
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	MT2834, MTV002.29C, RV2764C, THYA
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	83332
	Strain	:	H37RV
	Synonym	:	TS, TSASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A			D
Biological Unit 2 (1x)	:		B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 7)

No.	Name	Count	Type	Full Name
1	C2F	3	Ligand/Ion	5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID
2	UFP	4	Ligand/Ion	5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	C2F	2	Ligand/Ion	5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID
2	UFP	2	Ligand/Ion	5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	C2F	1	Ligand/Ion	5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID
2	UFP	2	Ligand/Ion	5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:94 , CYS A:146 , HIS A:147 , GLN A:165 , ARG A:166 , SER A:167 , ASP A:169 , ASN A:177 , HIS A:207 , TYR A:209 , C2F A:302 , HOH A:420 , ARG D:126 , ARG D:127	BINDING SITE FOR RESIDUE UFP A 301
2	AC2	SOFTWARE	HIS A:51 , SER A:54 , ILE A:79 , TRP A:83 , LEU A:143 , ASP A:169 , GLY A:173 , PHE A:176 , TYR A:209 , UFP A:301	BINDING SITE FOR RESIDUE C2F A 302
3	AC3	SOFTWARE	TYR B:94 , CYS B:146 , HIS B:147 , GLN B:165 , ARG B:166 , SER B:167 , ALA B:168 , ASP B:169 , GLY B:173 , ASN B:177 , HIS B:207 , TYR B:209 , HOH B:439 , HOH B:440 , ARG C:126	BINDING SITE FOR RESIDUE UFP B 301
4	AC4	SOFTWARE	ARG B:126 , ARG B:127 , ARG C:21 , TYR C:94 , CYS C:146 , HIS C:147 , GLN C:165 , ARG C:166 , SER C:167 , ASP C:169 , ASN C:177 , HIS C:207 , TYR C:209 , C2F C:302 , HOH C:416	BINDING SITE FOR RESIDUE UFP C 301
5	AC5	SOFTWARE	HIS C:51 , SER C:54 , ILE C:79 , TRP C:83 , LEU C:143 , ASP C:169 , GLY C:173 , PHE C:176 , VAL C:261 , ALA C:262 , UFP C:301 , HOH C:452 , HOH C:456 , HOH C:459	BINDING SITE FOR RESIDUE C2F C 302
6	AC6	SOFTWARE	ARG A:126 , ARG A:127 , HOH A:440 , ARG D:21 , TYR D:94 , CYS D:146 , HIS D:147 , GLN D:165 , ARG D:166 , SER D:167 , ALA D:168 , ASP D:169 , ASN D:177 , HIS D:207 , TYR D:209 , C2F D:302 , HOH D:484	BINDING SITE FOR RESIDUE UFP D 301
7	AC7	SOFTWARE	ILE D:79 , TRP D:80 , TRP D:83 , LEU D:143 , ASP D:169 , LEU D:172 , GLY D:173 , ILE D:257 , ALA D:262 , UFP D:301 , HOH D:425 , HOH D:467 , HOH D:477 , HOH D:484	BINDING SITE FOR RESIDUE C2F D 302

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

Asymmetric Unit

No.	Residues
1	Arg A:21	-	Thr A:22

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

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

(no "Exon" information available for 4FOG)

Asymmetric 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:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains d4foga_ A: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhheee.......eeeee..eeeee.hhh.........hhhhhhhhhhhhhh....hhhhhhh....hhhhh........hhhhhhhhee.....eehhhhhhhhhhhhh......eee.....hhhhh.....eeeeeeee...eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeee..hhhhhhhhhhhh......eeeee...hhhhhhhh.eeee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fog A   1 MTPYEDLLRFVLETGTPKSDRTGTGTRSLFGQQMRYDLSAGFPLLTTKKVHFKSVAYELLWFLRGDSNIGWLHEHGVTIWDEWASDTGELGPIYGVQWRSWPAPSGEHIDQISAALDLLRTDPDSRRIIVSAWNVGEIERMALPPCHAFFQFYVADGRLSCQLYQRSADLFLGVPFNIASYALLTHMMAAQAGLSVGEFIWTGGDCHIYDNHVEQVRLQLSREPRPYPKLLLADRDSIFEYTYEDIVVKNYDPHPAIKAP 260
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

Chain B from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains d4fogb_ B: automated matches                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhheeee...eeeeeeeeeeeee.hhh.........hhhhhhhhhhhhhh....hhhhhhh....hhhhh........hhhhhhhhee.....eehhhhhhhhhhhhh......eee.....hhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee....hhhhhhhh.eeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4fog B   1 MTPYEDLLRFVLETGTPKSDGTGTRSLFGQQMRYDLSAGFPLLTTKKVHFKSVAYELLWFLRGDSNIGWLHEHGVTIWDEWASDTGELGPIYGVQWRSWPAPSGEHIDQISAALDLLRTDPDSRRIIVSAWNVGEIERMALPPCHAFFQFYVADGRLSCQLYQRSADLFLGVPFNIASYALLTHMMAAQAGLSVGEFIWTGGDCHIYDNHVEQVRLQLSREPRPYPKLLLADRDSIFEYTYEDIVVKNYDPHPAIKAP 260
                                    10        20|       32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252        
                                              20|                                                                                                                                                                                                                                             
                                               23

Chain C from PDB  Type:PROTEIN  Length:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains d4fogc_ C: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhee.........eeee..eeeee.hhh.........hhhhhhhhhhhhhhh...hhhhhh.....hhhhh........hhhhhhhhee.....eehhhhhhhhhhhhh......eee..hhhhhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeehhhhhhhhhhhhh.......eeeee...hhhhhhhh.eeee............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fog C   1 MTPYEDLLRFVLETGTPKSDRTGTGTRSLFGQQMRYDLSAGFPLLTTKKVHFKSVAYELLWFLRGDSNIGWLHEHGVTIWDEWASDTGELGPIYGVQWRSWPAPSGEHIDQISAALDLLRTDPDSRRIIVSAWNVGEIERMALPPCHAFFQFYVADGRLSCQLYQRSADLFLGVPFNIASYALLTHMMAAQAGLSVGEFIWTGGDCHIYDNHVEQVRLQLSREPRPYPKLLLADRDSIFEYTYEDIVVKNYDPHPAIKAPVA 262
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

Chain D from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains d4fogd_ D: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhheee.......eeeeeeeeeeee.hhh.........hhhhhhhhhhhhhh....hhhhhh.....hhhhh........hhhhhhhhee.....eehhhhhhhhhhhhh......eee..hhhhhhhh.....eeeeeeeee..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee....hhhhhhhh.eeee.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fog D   1 MTPYEDLLRFVLETGTPKSDRTGTGTRSLFGQQMRYDLSAGFPLLTTKKVHFKSVAYELLWFLRGDSNIGWLHEHGVTIWDEWASDTGELGPIYGVQWRSWPAPSGEHIDQISAALDLLRTDPDSRRIIVSAWNVGEIERMALPPCHAFFQFYVADGRLSCQLYQRSADLFLGVPFNIASYALLTHMMAAQAGLSVGEFIWTGGDCHIYDNHVEQVRLQLSREPRPYPKLLLADRDSIFEYTYEDIVVKNYDPHPAIKAPVAV 263
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Thymidylate synthase/dCMP hydroxymethylase (193)

Superfamily: Thymidylate synthase/dCMP hydroxymethylase (193)

Family: Thymidylate synthase/dCMP hydroxymethylase (183)

Protein domain: automated matches (38)

Mycobacterium tuberculosis [TaxId: 83332] (3)

1a	d4foga_	A:
1b	d4fogb_	B:
1c	d4fogc_	C:
1d	d4fogd_	D:

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Arg A:21 - Thr A:22	[ RasMol ]

Biological Units
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	2.1.1.45
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UniProtKB/Swiss-Prot
	TYSY_MYCTO \| P9WFR8	:	3qj7 4foa 4fox 4fqs
	TYSY_MYCTU \| P9WFR9	:	3qj7 4foa 4fox 4fqs

3qj7	THYA BOUND TO DUMP
4foa	THYA BOUND TO 5-FLUORO-DUMP
4fox	THYA IN COMPLEX WITH UMP AND RALTITREXED

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 17)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File