1JKX - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   UNEXPECTED FORMATION OF AN EPOXIDE-DERIVED MULTISUBSTRATE ADDUCT INHIBITOR ON THE ACTIVE SITE OF GAR TRANSFORMYLASE

Authors :   S. E. Greasley, T. H. Marsilje, H. Cai, S. Baker, S. J. Benkovic, D. L. Boger, I. A. Wilson

Date :   13 Jul 01 (Deposition) - 30 Nov 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Purine Biosynthesis, Anti-Cancer Agent, Enzyme-Assembled Multisubstrate Adduct Inhibitor Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. E. Greasley, T. H. Marsilje, H. Cai, S. Baker, S. J. Benkovic, D. L. Boger, I. A. Wilson
Unexpected Formation Of An Epoxide-Derived Multisubstrate Adduct Inhibitor On The Active Site Of Gar Transformylase.
Biochemistry V. 40 13538 2001
PubMed-ID: 11695901 | Reference-DOI: 10.1021/BI011482+
(for further references see the PDB file header)

Molecule 1 - PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
	Chains	:	A, B, C, D
	EC Number	:	2.1.2.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PJS167
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	TRANSFERASE
	Gene	:	PURN
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE; GART

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	138	4	Ligand/Ion	N-[5'-O-PHOSPHONO-RIBOFURANOSYL]-2-[2-HYDROXY-2-[4-[GLUTAMIC ACID]-N-CARBONYLPHENYL]-3-[2-AMINO-4-HYDROXY-QUINAZOLIN-6-YL]-PROPANYLAMINO]-ACETAMIDE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	138	2	Ligand/Ion	N-[5'-O-PHOSPHONO-RIBOFURANOSYL]-2-[2-HYDROXY-2-[4-[GLUTAMIC ACID]-N-CARBONYLPHENYL]-3-[2-AMINO-4-HYDROXY-QUINAZOLIN-6-YL]-PROPANYLAMINO]-ACETAMIDE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	138	2	Ligand/Ion	N-[5'-O-PHOSPHONO-RIBOFURANOSYL]-2-[2-HYDROXY-2-[4-[GLUTAMIC ACID]-N-CARBONYLPHENYL]-3-[2-AMINO-4-HYDROXY-QUINAZOLIN-6-YL]-PROPANYLAMINO]-ACETAMIDE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:10 , GLY A:11 , SER A:12 , ASN A:13 , ARG A:64 , GLY A:87 , PHE A:88 , MET A:89 , ARG A:90 , ILE A:91 , LEU A:92 , VAL A:97 , ILE A:107 , HIS A:108 , PRO A:109 , VAL A:139 , GLN A:170 , GLU A:173 , HOH A:1222 , HOH A:1223 , HOH A:1230 , HOH A:1233 , HOH A:1236 , HOH A:1238 , HOH A:1240 , HOH A:1241 , HOH A:1242 , HOH A:1308 , HOH A:1320 , HOH A:1330 , HOH A:1344 , HOH A:1387 , LYS C:153	BINDING SITE FOR RESIDUE 138 A 1221
2	AC2	SOFTWARE	ASN B:10 , GLY B:11 , SER B:12 , ASN B:13 , LYS B:37 , ARG B:64 , GLY B:87 , PHE B:88 , MET B:89 , ARG B:90 , ILE B:91 , LEU B:92 , VAL B:97 , ILE B:107 , HIS B:108 , PRO B:109 , VAL B:139 , GLU B:173 , HOH B:2227 , HOH B:2231 , HOH B:2233 , HOH B:2240 , HOH B:2246 , HOH B:2251 , HOH B:2255 , HOH B:2266 , HOH B:2278 , HOH B:2288 , HOH B:2307 , HOH B:2342 , HOH B:2384 , GLU D:131 , LYS D:153	BINDING SITE FOR RESIDUE 138 B 2221
3	AC3	SOFTWARE	ASN C:10 , GLY C:11 , SER C:12 , ASN C:13 , ARG C:64 , GLY C:87 , PHE C:88 , MET C:89 , ARG C:90 , ILE C:91 , LEU C:92 , VAL C:97 , ILE C:107 , HIS C:108 , PRO C:109 , VAL C:139 , GLN C:170 , GLU C:173 , HOH C:3224 , HOH C:3234 , HOH C:3248 , HOH C:3259 , HOH C:3266 , HOH C:3270 , HOH C:3280 , HOH C:3286 , HOH C:3292 , HOH C:3319 , HOH C:3339 , HOH C:3365 , HOH C:3366	BINDING SITE FOR RESIDUE 138 C 3221
4	AC4	SOFTWARE	GLU B:131 , ASN D:10 , GLY D:11 , SER D:12 , ASN D:13 , ARG D:64 , GLY D:87 , PHE D:88 , MET D:89 , ARG D:90 , ILE D:91 , LEU D:92 , VAL D:97 , ILE D:107 , HIS D:108 , PRO D:109 , VAL D:139 , GLU D:173 , HOH D:4224 , HOH D:4227 , HOH D:4230 , HOH D:4237 , HOH D:4261 , HOH D:4262 , HOH D:4277 , HOH D:4283 , HOH D:4326 , HOH D:4327 , HOH D:4328	BINDING SITE FOR RESIDUE 138 D 4221

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

Asymmetric Unit

No.	Residues
1	Leu A:112	-	Pro A:113
2	Leu B:112	-	Pro B:113
3	Leu C:112	-	Pro C:113
4	Leu D:112	-	Pro D:113

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GART	PS00373	Phosphoribosylglycinamide formyltransferase active site.	PUR3_ECOLI	133-156	4	A:133-156 B:133-156 C:133-156 D:133-156

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GART	PS00373	Phosphoribosylglycinamide formyltransferase active site.	PUR3_ECOLI	133-156	2	A:133-156 B:133-156 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GART	PS00373	Phosphoribosylglycinamide formyltransferase active site.	PUR3_ECOLI	133-156	2	- - C:133-156 D:133-156

(no "Exon" information available for 1JKX)

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:209
 aligned with PUR3_ECOLI | P08179 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200         
           PUR3_ECOLI     1 MNIVVLISGNGSNLQAIIDACKTNKIKGTVRAVFSNKADAFGLERARQAGIATHTLIASAFDSREAYDRELIHEIDMYAPDVVVLAGFMRILSPAFVSHYAGRLLNIHPSLLPKYPGLHTHRQALENGDEEHGTSVHFVTDELDGGPVILQAKVPVFAGDSEDDITARVQTQEHAIYPLVISWFADGRLKMHENAAWLDGQRLPPQGYA 209
               SCOP domains d1jkxa_ A: Glycinamide ribonucleotide transformylase, GART                                                                                                                                                        SCOP domains
               CATH domains 1jkxA00 A:1-209  [code=3.40.50.170, no name defined]                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhh..eeee.hhhhh.hhhhhhhhhhhhhhhhh..eeee.......hhhhhhhh...eeeee..........hhhhhhhhh...eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeee..ee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------GART  PDB: A:133-156    ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jkx A   1 MNIVVLISGNGSNLQAIIDACKTNKIKGTVRAVFSNKADAFGLERARQAGIATHTLIASAFDSREAYDRELIHEIDMYAPDVVVLAGFMRILSPAFVSHYAGRLLNIHPSLLPKYPGLHTHRQALENGDEEHGTSVHFVTDELDGGPVILQAKVPVFAGDSEDDITARVQTQEHAIYPLVISWFADGRLKMHENAAWLDGQRLPPQGYA 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain B from PDB  Type:PROTEIN  Length:209
 aligned with PUR3_ECOLI | P08179 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200         
           PUR3_ECOLI     1 MNIVVLISGNGSNLQAIIDACKTNKIKGTVRAVFSNKADAFGLERARQAGIATHTLIASAFDSREAYDRELIHEIDMYAPDVVVLAGFMRILSPAFVSHYAGRLLNIHPSLLPKYPGLHTHRQALENGDEEHGTSVHFVTDELDGGPVILQAKVPVFAGDSEDDITARVQTQEHAIYPLVISWFADGRLKMHENAAWLDGQRLPPQGYA 209
               SCOP domains d1jkxb_ B: Glycinamide ribonucleotide transformylase, GART                                                                                                                                                        SCOP domains
               CATH domains 1jkxB00 B:1-209  [code=3.40.50.170, no name defined]                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhh..eeee.hhhhh.hhhhhhhhhhhhhhhhh..eeee.......hhhhhhhh...eeeee..........hhhhhhhhh...eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeee..ee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------GART  PDB: B:133-156    ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jkx B   1 MNIVVLISGNGSNLQAIIDACKTNKIKGTVRAVFSNKADAFGLERARQAGIATHTLIASAFDSREAYDRELIHEIDMYAPDVVVLAGFMRILSPAFVSHYAGRLLNIHPSLLPKYPGLHTHRQALENGDEEHGTSVHFVTDELDGGPVILQAKVPVFAGDSEDDITARVQTQEHAIYPLVISWFADGRLKMHENAAWLDGQRLPPQGYA 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain C from PDB  Type:PROTEIN  Length:209
 aligned with PUR3_ECOLI | P08179 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200         
           PUR3_ECOLI     1 MNIVVLISGNGSNLQAIIDACKTNKIKGTVRAVFSNKADAFGLERARQAGIATHTLIASAFDSREAYDRELIHEIDMYAPDVVVLAGFMRILSPAFVSHYAGRLLNIHPSLLPKYPGLHTHRQALENGDEEHGTSVHFVTDELDGGPVILQAKVPVFAGDSEDDITARVQTQEHAIYPLVISWFADGRLKMHENAAWLDGQRLPPQGYA 209
               SCOP domains d1jkxc_ C: Glycinamide ribonucleotide transformylase, GART                                                                                                                                                        SCOP domains
               CATH domains 1jkxC00 C:1-209  [code=3.40.50.170, no name defined]                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhh..eeee.hhhhh.hhhhhhhhhhhhhhhhh..eeee.......hhhhhhhh...eeeee..........hhhhhhhhhh..eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eee..ee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------GART  PDB: C:133-156    ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jkx C   1 MNIVVLISGNGSNLQAIIDACKTNKIKGTVRAVFSNKADAFGLERARQAGIATHTLIASAFDSREAYDRELIHEIDMYAPDVVVLAGFMRILSPAFVSHYAGRLLNIHPSLLPKYPGLHTHRQALENGDEEHGTSVHFVTDELDGGPVILQAKVPVFAGDSEDDITARVQTQEHAIYPLVISWFADGRLKMHENAAWLDGQRLPPQGYA 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain D from PDB  Type:PROTEIN  Length:209
 aligned with PUR3_ECOLI | P08179 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200         
           PUR3_ECOLI     1 MNIVVLISGNGSNLQAIIDACKTNKIKGTVRAVFSNKADAFGLERARQAGIATHTLIASAFDSREAYDRELIHEIDMYAPDVVVLAGFMRILSPAFVSHYAGRLLNIHPSLLPKYPGLHTHRQALENGDEEHGTSVHFVTDELDGGPVILQAKVPVFAGDSEDDITARVQTQEHAIYPLVISWFADGRLKMHENAAWLDGQRLPPQGYA 209
               SCOP domains d1jkxd_ D: Glycinamide ribonucleotide transformylase, GART                                                                                                                                                        SCOP domains
               CATH domains 1jkxD00 D:1-209  [code=3.40.50.170, no name defined]                                                                                                                                                              CATH domains
           Pfam domains (1) Formyl_trans_N-1jkxD01 D:1-181                                                                                                                                                       ---------------------------- Pfam domains (1)
           Pfam domains (2) Formyl_trans_N-1jkxD02 D:1-181                                                                                                                                                       ---------------------------- Pfam domains (2)
           Pfam domains (3) Formyl_trans_N-1jkxD03 D:1-181                                                                                                                                                       ---------------------------- Pfam domains (3)
           Pfam domains (4) Formyl_trans_N-1jkxD04 D:1-181                                                                                                                                                       ---------------------------- Pfam domains (4)
         Sec.struct. author .eeeeee...hhhhhhhhhhhhh.....eeeeeee.....hhhhhhhhh..eeee.hhhhh.hhhhhhhhhhhhhhhhh..eeee.......hhhhhhhh...eeeee..........hhhhhhhhh...eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eee..ee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------GART  PDB: D:133-156    ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jkx D   1 MNIVVLISGNGSNLQAIIDACKTNKIKGTVRAVFSNKADAFGLERARQAGIATHTLIASAFDSREAYDRELIHEIDMYAPDVVVLAGFMRILSPAFVSHYAGRLLNIHPSLLPKYPGLHTHRQALENGDEEHGTSVHFVTDELDGGPVILQAKVPVFAGDSEDDITARVQTQEHAIYPLVISWFADGRLKMHENAAWLDGQRLPPQGYA 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

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) (23833)

Fold: Formyltransferase (42)

Superfamily: Formyltransferase (42)

Family: Formyltransferase (34)

Protein domain: Glycinamide ribonucleotide transformylase, GART (24)

Escherichia coli [TaxId: 562] (9)

1a	d1jkxa_	A:
1b	d1jkxb_	B:
1c	d1jkxc_	C:
1d	d1jkxd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.170, no name defined] (28)

Escherichia coli. Organism_taxid: 562. (2)

1a	1jkxA00	A:1-209
1b	1jkxB00	B:1-209
1c	1jkxC00	C:1-209
1d	1jkxD00	D:1-209

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Formyl_trans_N] (25)

Family: Formyl_trans_N (25)

Escherichia coli (strain K12) (3)

1a	Formyl_trans_N-1jkxD01	D:1-181
1b	Formyl_trans_N-1jkxD02	D:1-181
1c	Formyl_trans_N-1jkxD03	D:1-181
1d	Formyl_trans_N-1jkxD04	D:1-181

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (PUR3_ECOLI | P08179)

molecular function
	GO:0016742	hydroxymethyl-, formyl- and related transferase activity	Catalysis of the transfer of a hydroxymethyl- or formyl group from one compound (donor) to another (acceptor).
	GO:0004644	phosphoribosylglycinamide formyltransferase activity	Catalysis of the reaction: 10-formyltetrahydrofolate + N1-(5-phospho-D-ribosyl)glycinamide = tetrahydrofolate + N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide.
	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:0006189	'de novo' IMP biosynthetic process	The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate, by the stepwise assembly of a purine ring on ribose 5-phosphate.
	GO:0009058	biosynthetic process	The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0006164	purine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
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	Cis Peptide Bonds
		Leu A:112 - Pro A:113	[ RasMol ]
		Leu B:112 - Pro B:113	[ RasMol ]
		Leu C:112 - Pro C:113	[ RasMol ]
		Leu D:112 - Pro D:113	[ RasMol ]

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	1jkx
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	PUR3_ECOLI \| P08179	:	1c2t 1c3e 1cdd 1cde 1gar 1grc 2gar 3gar

(no "Related Entries Specified in the PDB File" available for 1JKX)

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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