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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF FDTS (TM0449) MUTANT (H53D) WITH FAD

Authors :   I. I. Mathews

Date :   22 Apr 13 (Deposition) - 26 Mar 14 (Release) - 26 Mar 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.03

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

Keywords :   Thyx, Fdts, H53D Mutant, Fad, Novel Fdts Fold, Convertion Of Dump To Dtmp Using Tetrahydrofolate, And Nad(P)H, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. I. Mathews
Flavin-Dependent Thymidylate Synthase As A Drug Target For Deadly Microbes: Mutational Study And A Strategy For Inhibitor Design.
J Bioterror Biodef V. L 12 004 2013
PubMed-ID: 24563811 | Reference-DOI: 10.4172/2157-2526.S12-004

Molecule 1 - THYMIDYLATE SYNTHASE
	Chains	:	A, B, C, D
	EC Number	:	2.1.1.148
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMH1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	TM0449 (UNP RESIDUES 1-220)
	Gene	:	THY1, THYX, TM0449, TM_0449
	Mutation	:	YES
	Organism Scientific	:	THERMOTOGA MARITIMA MSB8
	Organism Taxid	:	243274
	Strain	:	ATCC 43589 / 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, 5)

No.	Name	Count	Type	Full Name
1	2PE	1	Ligand/Ion	NONAETHYLENE GLYCOL
2	FAD	4	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:78 , HIS A:79 , ARG A:80 , ILE A:81 , ASN A:169 , LEU A:173 , ARG A:174 , HOH A:420 , HOH A:430 , GLU C:58 , ILE C:81 , ASN C:163 , ARG C:165 , FAD C:301 , SER D:83	BINDING SITE FOR RESIDUE FAD A 301
2	AC2	SOFTWARE	ARG B:78 , HIS B:79 , ARG B:80 , ILE B:81 , ASN B:169 , LEU B:173 , ARG B:174 , HOH B:408 , HOH B:424 , GLU D:58 , ILE D:81 , ASN D:163 , ARG D:165 , FAD D:301	BINDING SITE FOR RESIDUE FAD B 301
3	AC3	SOFTWARE	GLU A:58 , ILE A:81 , ASN A:163 , ARG A:165 , FAD A:301 , SER B:83 , ARG C:78 , HIS C:79 , ARG C:80 , ILE C:81 , ASN C:169 , LEU C:173 , HOH C:402 , HOH C:417	BINDING SITE FOR RESIDUE FAD C 301
4	AC4	SOFTWARE	SER A:83 , GLU B:58 , ILE B:81 , ASN B:163 , ARG B:165 , FAD B:301 , ARG D:78 , HIS D:79 , ARG D:80 , ILE D:81 , ASN D:169 , LEU D:173 , HOH D:408 , HOH D:413	BINDING SITE FOR RESIDUE FAD D 301
5	AC5	SOFTWARE	GLU C:203 , LEU C:206 , LEU C:215 , LYS C:216 , GLN C:219 , HIS D:43 , GLU D:46 , TYR D:47 , LYS D:50 , HIS D:51	BINDING SITE FOR RESIDUE 2PE D 302

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

(no "Cis Peptide Bond" information available for 4KAR)

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

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

(no "Exon" information available for 4KAR)

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:214
                                                                                                                                                                                                                                                      
               SCOP domains d4kara_ A: Thy1 homologue                                                                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eeeeeeeee.hhhhhhhhhhh.....hhhhhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhh.....eeee...............hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kar A  -1 HHMKIDILDKGFVELVDVMGNDLSAVRAARVSFDMDEERDRHLIEYLMKHGDETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDIL 215
                                     8        18        28    ||  41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211    
                                                             33|                                                                                                                                                                                  
                                                              37

Chain B from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains d4karb_ B: Thy1 homologue                                                                                                                                                                                            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
                 4kar B   0 HMKIDILDKGFVELVDVMGNDLSAVRAARVSFEERDRHLIEYLMKHGDETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEVQV 220
                                     9        19        29 ||     45        55        65        75        85     || 98       108       118       128       138       148       158       168       178       188       198       208       218  
                                                          31|                                                   91|                                                                                                                             
                                                           38                                                    95

Chain C from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains d4karc_ C: Thy1 homologue                                                                                                                                                                                                  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...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kar C   0 HMKIDILDKGFVELVDVMGNDLSAVRAARVSFDKDEERDRHLIEYLMKHGDETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEVQV 220
                                     9        19        29  ||    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212        
                                                           32|                                                                                                                                                                                        
                                                            36

Chain D from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains d4kard_ D: Thy1 homologue                                                                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eeeeeeeee.hhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhhh....eeee...............hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kar D   1 MKIDILDKGFVELVDVMGNDLSAVRAARVSFDDEERDRHLIEYLMKHGDETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEV 218
                                    10        20        30 ||     44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214    
                                                          32|                                                                                                                                                                                     
                                                           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 '\|'

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	d4kara_	A:
1b	d4karb_	B:
1c	d4karc_	C:
1d	d4kard_	D:

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		2PE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FAD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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		AC2	[ RasMol ]	+environment [ RasMol ]
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		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4kar)

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Access by PDB/NDB ID
	4kar
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
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		Structural Neighbours	:	CE \| VAST
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	THYX_THEMA \| Q9WYT0
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		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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	2.1.1.148
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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		Disease Information	:	OMIM

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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