1CDE - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   STRUCTURES OF APO AND COMPLEXED ESCHERICHIA COLI GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE

Authors :   R. J. Almassy, C. A. Janson, C. -C. Kan, Z. Hostomska

Date :   15 May 92 (Deposition) - 31 Oct 93 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Transferase(Formyl) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. J. Almassy, C. A. Janson, C. C. Kan, Z. Hostomska
Structures Of Apo And Complexed Escherichia Coli Glycinamide Ribonucleotide Transformylase.
Proc. Natl. Acad. Sci. Usa V. 89 6114 1992
PubMed-ID: 1631098 | Reference-DOI: 10.1073/PNAS.89.13.6114
(for further references see the PDB file header)

Molecule 1 - PHOSPHORIBOSYL-GLYCINAMIDE FORMYLTRANSFERASE
	Chains	:	A, B, C, D
	EC Number	:	2.1.2.2
	Engineered	:	YES
	Expression System Strain	:	K12
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	DZF	4	Ligand/Ion	5-DEAZAFOLIC ACID
2	GAR	4	Ligand/Ion	GLYCINAMIDE RIBONUCLEOTIDE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	DZF	1	Ligand/Ion	5-DEAZAFOLIC ACID
2	GAR	1	Ligand/Ion	GLYCINAMIDE RIBONUCLEOTIDE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	DZF	1	Ligand/Ion	5-DEAZAFOLIC ACID
2	GAR	1	Ligand/Ion	GLYCINAMIDE RIBONUCLEOTIDE

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	DZF	1	Ligand/Ion	5-DEAZAFOLIC ACID
2	GAR	1	Ligand/Ion	GLYCINAMIDE RIBONUCLEOTIDE

Biological Unit 4 (2, 2)

No.	Name	Count	Type	Full Name
1	DZF	1	Ligand/Ion	5-DEAZAFOLIC ACID
2	GAR	1	Ligand/Ion	GLYCINAMIDE RIBONUCLEOTIDE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:10 , GLY A:11 , SER A:12 , ASN A:13 , GLY A:87 , MET A:89 , ILE A:107 , HIS A:108 , PRO A:109 , GLN A:170 , GLU A:173 , DZF A:225	BINDING SITE FOR RESIDUE GAR A 222
2	AC2	SOFTWARE	MET A:89 , ARG A:90 , ILE A:91 , LEU A:92 , VAL A:97 , ASN A:106 , VAL A:139 , THR A:140 , ASP A:141 , GLU A:142 , ASP A:144 , GAR A:222	BINDING SITE FOR RESIDUE DZF A 225
3	AC3	SOFTWARE	ASN B:10 , GLY B:11 , SER B:12 , ASN B:13 , GLY B:87 , MET B:89 , ILE B:107 , HIS B:108 , PRO B:109 , GLN B:170 , GLU B:173 , DZF B:225	BINDING SITE FOR RESIDUE GAR B 222
4	AC4	SOFTWARE	MET B:89 , ARG B:90 , ILE B:91 , LEU B:92 , VAL B:97 , ASN B:106 , VAL B:139 , THR B:140 , ASP B:141 , GLU B:142 , ASP B:144 , GAR B:222	BINDING SITE FOR RESIDUE DZF B 225
5	AC5	SOFTWARE	ASN C:10 , GLY C:11 , SER C:12 , ASN C:13 , GLY C:87 , MET C:89 , ILE C:107 , HIS C:108 , PRO C:109 , GLN C:170 , GLU C:173 , DZF C:225	BINDING SITE FOR RESIDUE GAR C 222
6	AC6	SOFTWARE	MET C:89 , ARG C:90 , ILE C:91 , LEU C:92 , VAL C:97 , ASN C:106 , VAL C:139 , THR C:140 , ASP C:141 , GLU C:142 , ASP C:144 , GAR C:222	BINDING SITE FOR RESIDUE DZF C 225
7	AC7	SOFTWARE	ASN D:10 , GLY D:11 , SER D:12 , ASN D:13 , GLY D:87 , MET D:89 , ILE D:107 , HIS D:108 , PRO D:109 , GLN D:170 , GLU D:173 , DZF D:225	BINDING SITE FOR RESIDUE GAR D 222
8	AC8	SOFTWARE	MET D:89 , ARG D:90 , ILE D:91 , LEU D:92 , VAL D:97 , ASN D:106 , VAL D:139 , THR D:140 , ASP D:141 , GLU D:142 , ASP D:144 , GAR D:222	BINDING SITE FOR RESIDUE DZF D 225

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

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 1CDE)

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, 1)

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

Biological Unit 2 (1, 1)

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

Biological Unit 3 (1, 1)

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

Biological Unit 4 (1, 1)

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

(no "Exon" information available for 1CDE)

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 d1cdea_ A: Glycinamide ribonucleotide transformylase, GART                                                                                                                                                        SCOP domains
               CATH domains 1cdeA00 A:1-209  [code=3.40.50.170, no name defined]                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeeeeeee..hhhhhhhhhhhhhh......eeeeee...hhhhhhhhhhh.eeeeeeee...hhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhh.eeeeeee.........hhhhhhhhhh....eeeeee..........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh...................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------GART  PDB: A:133-156    ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cde 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 d1cdeb_ B: Glycinamide ribonucleotide transformylase, GART                                                                                                                                                        SCOP domains
               CATH domains 1cdeB00 B:1-209  [code=3.40.50.170, no name defined]                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeeeeeee..hhhhhhhhhhhhhh......eeeeee...hhhhhhhhhhh.eeeeeeee...hhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhh.eeeeeee.........hhhhhhhhhh....eeeeee..........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh...................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------GART  PDB: B:133-156    ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cde 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 d1cdec_ C: Glycinamide ribonucleotide transformylase, GART                                                                                                                                                        SCOP domains
               CATH domains 1cdeC00 C:1-209  [code=3.40.50.170, no name defined]                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeeeeeee..hhhhhhhhhhhhhh......eeeeee...hhhhhhhhhhh.eeeeeeee...hhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhh.eeeeeee.........hhhhhhhhhh....eeeeee..........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh...................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------GART  PDB: C:133-156    ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cde 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 d1cded_ D: Glycinamide ribonucleotide transformylase, GART                                                                                                                                                        SCOP domains
               CATH domains 1cdeD00 D:1-209  [code=3.40.50.170, no name defined]                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeeeeeee..hhhhhhhhhhhhhh......eeeeee...hhhhhhhhhhh.eeeeeeee...hhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhh.eeeeeee.........hhhhhhhhhh....eeeeee..........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh...................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------GART  PDB: D:133-156    ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cde 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)
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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 Unit

Classes(

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Folds(

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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	d1cdea_	A:
1b	d1cdeb_	B:
1c	d1cdec_	C:
1d	d1cded_	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. (3)

1a	1cdeA00	A:1-209
1b	1cdeB00	B:1-209
1c	1cdeC00	C:1-209
1d	1cdeD00	D:1-209

(no "Pfam Domain" information available for 1CDE)

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.

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

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

1cdd	APOENZYME PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

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