2YW2 - JenaLib

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Title :   CRYSTAL STRUCTURE OF GAR SYNTHETASE FROM AQUIFEX AEOLICUS IN COMPLEX WITH ATP

Authors :   S. Baba, M. Kanagawa, S. Kuramitsu, S. Yokoyama, G. Kawai, G. Sampei, Ri Structural Genomics/Proteomics Initiative (Rsgi)

Date :   19 Apr 07 (Deposition) - 23 Oct 07 (Release) - 08 Dec 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Glycinamide Ribonucleotide Synthetase, Gar Synthetase, Atp Binding, Purine Nucleotide Biosynthetic Pathway, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Sampei, S. Baba, M. Kanagawa, H. Yanai, T. Ishii, H. Kawai, Y. Fukai, A. Ebihara, N. Nakagawa, G. Kawai
Crystal Structures Of Glycinamide Ribonucleotide Synthetase Purd, From Thermophilic Eubacteria
J. Biochem. V. 148 429 2010
PubMed-ID: 20716513 | Reference-DOI: 10.1093/JB/MVQ088

Molecule 1 - PHOSPHORIBOSYLAMINE--GLYCINE LIGASE
	Chains	:	A, B
	EC Number	:	6.3.4.13
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-21A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363
	Synonym	:	GARS, GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE, PHOSPHORIBOSYLGLYCINAMIDE SYNTHETASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:11 , GLU A:71 , ARG A:287 , ASP A:290 , ARG A:378 , HOH A:666 , HOH A:754	BINDING SITE FOR RESIDUE PO4 A 645
2	AC2	SOFTWARE	ARG B:11 , GLU B:71 , ARG B:287 , ASP B:290 , ARG B:378 , HOH B:670 , HOH B:746 , HOH B:760 , HOH B:809 , HOH B:811	BINDING SITE FOR RESIDUE PO4 B 646
3	AC3	SOFTWARE	LYS A:103 , VAL A:141 , LYS A:143 , ALA A:148 , GLY A:150 , LYS A:151 , GLY A:152 , ALA A:153 , GLU A:185 , GLU A:186 , PHE A:187 , LEU A:188 , GLU A:192 , LYS A:214 , ASN A:224 , GLU A:283 , HOH A:676 , HOH A:702 , HOH A:720	BINDING SITE FOR RESIDUE ATP A 646
4	AC4	SOFTWARE	LYS B:103 , LYS B:143 , GLY B:150 , LYS B:151 , GLY B:152 , ALA B:153 , GLU B:185 , GLU B:186 , PHE B:187 , LEU B:188 , GLU B:192 , LYS B:214 , ASN B:224 , HOH B:679 , HOH B:699 , HOH B:700 , HOH B:743 , HOH B:773 , HOH B:777 , HOH B:792	BINDING SITE FOR RESIDUE ATP B 647

Asymmetric Unit

No.	Residues
1	A:404	-	B:404

Asymmetric Unit

No.	Residues
1	Ala A:31	-	Lys A:32
2	Ala A:138	-	Pro A:139
3	Ser A:232	-	Pro A:233
4	Asp A:290	-	Pro A:291
5	Tyr A:336	-	Pro A:337
6	Ala B:31	-	Lys B:32
7	Ala B:138	-	Pro B:139
8	Ser B:232	-	Pro B:233
9	Asp B:290	-	Pro B:291
10	Tyr B:336	-	Pro B:337

(no "SAP(SNP)/Variant" information available for 2YW2)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GARS	PS00184	Phosphoribosylglycinamide synthetase signature.	PUR2_AQUAE	287-294	2	A:287-294 B:287-294

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GARS	PS00184	Phosphoribosylglycinamide synthetase signature.	PUR2_AQUAE	287-294	1	A:287-294 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GARS	PS00184	Phosphoribosylglycinamide synthetase signature.	PUR2_AQUAE	287-294	1	- B:287-294

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GARS	PS00184	Phosphoribosylglycinamide synthetase signature.	PUR2_AQUAE	287-294	2	A:287-294 B:287-294

(no "Exon" information available for 2YW2)

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:423
 aligned with PUR2_AQUAE | O66949 from UniProtKB/Swiss-Prot  Length:424

    Alignment length:423
                                    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       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420   
           PUR2_AQUAE     1 MKVLVVGNGGREHAIAWKVAQSPLVKELYVAKGNAGIWEIAKRVDISPTDVEKLAEFAKNEGVDFTIVGPEAPLVEGIVDEFEKRGLKIFGPNKEAAKLEGSKAFAKTFMKKYGIPTARYEVFTDFEKAKEYVEKVGAPIVVKADGLAAGKGAVVCETVEKAIETLDRFLNKKIFGKSSERVVIEEFLEGEEASYIVMINGDRYVPLPTSQDHKRLLDEDKGPNTGGMGAYSPTPVINEEVEKRIREEIVERVIKGLKEEGIYYRGFLYAGLMITKEGPKVLEFNVRLGDPEAQPILMRVKNDFLETLLNFYEGKDVHIKEDERYALDVVLASRGYPEKPETGKIIHGLDYLKSMEDVVVFHAGTKKEGNFTVTSGGRVLNVCAYGKTLKEAKERAYEAIRYVCFEGMHYRKDIGDKAFKYLS 423
               SCOP domains d2yw2a1 A:1-101 automated matches                                                                    d2yw2a2 A:102-322 automated matches                                                                                                                                                                                          d2yw2a3 A:323-423 automated matches                                                                   SCOP domains
               CATH domains -2yw2A01 A:2-93  [code=3.40.50.20, no name defined]                                          -------------------------2yw2A02 A:119-188 ATP-grasp fold, A domain                            2yw2A03 A:189-324 ATP-grasp fold, B domain                                                                                              2yw2A04 A:325-420 Glycinamide Ribonucleotide Synthetase; Chain A, domain 4                      --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhhh......eeeeee...hhhhh.eee.....hhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhh...ee......hhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhh..eeeee........eeee.hhhhhhhhhhhhhh...hhhhhh.eeeee....eeeeeeeeee..eeee....ee..eee...eeee....eeee.....hhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee..eeeeeeee......hhhhhhhh...hhhhhhhhhhh...........eeeeeeee...............hhhhhhh...eeeee..eeee..eeee...eeeeeeeee.hhhhhhhhhhhhhh................hhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GARS    --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yw2 A   1 MKVLVVGNGGREHAIAWKVAQSPLVKELYVAKGNAGIWEIAKRVDISPTDVEKLAEFAKNEGVDFTIVGPEAPLVEGIVDEFEKRGLKIFGPNKEAAKLEGSKAFAKTFMKKYGIPTARYEVFTDFEKAKEYVEKVGAPIVVKADGLAAGKGAVVCETVEKAIETLDRFLNKKIFGKSSERVVIEEFLEGEEASYIVMINGDRYVPLPTSQDHKRLLDEDKGPNTGGMGAYSPTPVINEEVEKRIREEIVERVIKGLKEEGIYYRGFLYAGLMITKEGPKVLEFNVRLGDPEAQPILMRVKNDFLETLLNFYEGKDVHIKEDERYALDVVLASRGYPEKPETGKIIHGLDYLKSMEDVVVFHAGTKKEGNFTVTSGGRVLNVCAYGKTLKEAKERAYEAIRYVCFEGMHYRKDIGDKAFKYLS 423
                                    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       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420

Chain B from PDB  Type:PROTEIN  Length:423
 aligned with PUR2_AQUAE | O66949 from UniProtKB/Swiss-Prot  Length:424

    Alignment length:423
                                    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       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420   
           PUR2_AQUAE     1 MKVLVVGNGGREHAIAWKVAQSPLVKELYVAKGNAGIWEIAKRVDISPTDVEKLAEFAKNEGVDFTIVGPEAPLVEGIVDEFEKRGLKIFGPNKEAAKLEGSKAFAKTFMKKYGIPTARYEVFTDFEKAKEYVEKVGAPIVVKADGLAAGKGAVVCETVEKAIETLDRFLNKKIFGKSSERVVIEEFLEGEEASYIVMINGDRYVPLPTSQDHKRLLDEDKGPNTGGMGAYSPTPVINEEVEKRIREEIVERVIKGLKEEGIYYRGFLYAGLMITKEGPKVLEFNVRLGDPEAQPILMRVKNDFLETLLNFYEGKDVHIKEDERYALDVVLASRGYPEKPETGKIIHGLDYLKSMEDVVVFHAGTKKEGNFTVTSGGRVLNVCAYGKTLKEAKERAYEAIRYVCFEGMHYRKDIGDKAFKYLS 423
               SCOP domains d2yw2b1 B:1-101 automated matches                                                                    d2yw2b2 B:102-322 automated matches                                                                                                                                                                                          d2yw2b3 B:323-423 automated matches                                                                   SCOP domains
               CATH domains -2yw2B01 B:2-93  [code=3.40.50.20, no name defined]                                          -------------------------2yw2B02 B:119-188 ATP-grasp fold, A domain                            2yw2B03 B:189-324 ATP-grasp fold, B domain                                                                                              2yw2B04 B:325-420 Glycinamide Ribonucleotide Synthetase; Chain A, domain 4                      --- CATH domains
           Pfam domains (1) GARS_N-2yw2B05 B:1-100                                                                              GARS_A-2yw2B01 B:101-293                                                                                                                                                                         -------------------------------GARS_C-2yw2B03 B:325-419                                                                       ---- Pfam domains (1)
           Pfam domains (2) GARS_N-2yw2B06 B:1-100                                                                              GARS_A-2yw2B02 B:101-293                                                                                                                                                                         -------------------------------GARS_C-2yw2B04 B:325-419                                                                       ---- Pfam domains (2)
         Sec.struct. author .eeeeee.hhhhhhhhhhhh......eeeeee...hhhhh.eee.....hhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhh...ee......hhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhh..eeeee........eeee.hhhhhhhhhhhhhh...hhhhhh.eeeee....eeeeeeeeee..eeee....ee..eeehhheeee....eeee.....hhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee..eeeeeeee......hhhhhhhh...hhhhhhhhhhh...........eeeeeeee...............hhhhhhhh..eeeee..eeee..eeee...eeeeeeeee.hhhhhhhhhhhhhh................hhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GARS    --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yw2 B   1 MKVLVVGNGGREHAIAWKVAQSPLVKELYVAKGNAGIWEIAKRVDISPTDVEKLAEFAKNEGVDFTIVGPEAPLVEGIVDEFEKRGLKIFGPNKEAAKLEGSKAFAKTFMKKYGIPTARYEVFTDFEKAKEYVEKVGAPIVVKADGLAAGKGAVVCETVEKAIETLDRFLNKKIFGKSSERVVIEEFLEGEEASYIVMINGDRYVPLPTSQDHKRLLDEDKGPNTGGMGAYSPTPVINEEVEKRIREEIVERVIKGLKEEGIYYRGFLYAGLMITKEGPKVLEFNVRLGDPEAQPILMRVKNDFLETLLNFYEGKDVHIKEDERYALDVVLASRGYPEKPETGKIIHGLDYLKSMEDVVVFHAGTKKEGNFTVTSGGRVLNVCAYGKTLKEAKERAYEAIRYVCFEGMHYRKDIGDKAFKYLS 423
                                    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       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420

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

Clans(

)

Families(

)

Organisms( (-)

)

Clan: ATP-grasp (83)

Family: GARS_A (12)

Aquifex aeolicus (2)

1a	GARS_A-2yw2B01	B:101-293
1b	GARS_A-2yw2B02	B:101-293

Clan: no clan defined [family: GARS_C] (12)

Family: GARS_C (12)

Aquifex aeolicus (2)

2a	GARS_C-2yw2B03	B:325-419
2b	GARS_C-2yw2B04	B:325-419

Clan: no clan defined [family: GARS_N] (12)

Family: GARS_N (12)

Aquifex aeolicus (2)

3a	GARS_N-2yw2B05	B:1-100
3b	GARS_N-2yw2B06	B:1-100

Asymmetric Unit(hide GO term definitions)

Chain A,B (PUR2_AQUAE | O66949)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0004637	phosphoribosylamine-glycine ligase activity	Catalysis of the reaction: 5-phospho-D-ribosylamine + ATP + glycine = N(1)-(5-phospho-D-ribosyl)glycinamide + ADP + 2 H(+) + phosphate.
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:0009113	purine nucleobase biosynthetic process	The chemical reactions and pathways resulting in the formation of purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.
	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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Ala A:138 - Pro A:139	[ RasMol ]
		Ala A:31 - Lys A:32	[ RasMol ]
		Ala B:138 - Pro B:139	[ RasMol ]
		Ala B:31 - Lys B:32	[ RasMol ]
		Asp A:290 - Pro A:291	[ RasMol ]
		Asp B:290 - Pro B:291	[ RasMol ]
		Ser A:232 - Pro A:233	[ RasMol ]
		Ser B:232 - Pro B:233	[ RasMol ]
		Tyr A:336 - Pro A:337	[ RasMol ]
		Tyr B:336 - Pro B:337	[ RasMol ]

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	PUR2_AQUAE \| O66949	:	2yya

1gso	GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE (GAR-SYN) FROM E. COLI RELATED ID: AAE001000742.1 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (1, 1)

Cis Peptide Bonds (10, 10)

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SAPs(SNPs)/Variants (0, 0)

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