2GQR - JenaLib

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Title :   SAICAR SYNTHETASE COMPLEXED WITH ADP-MG2+

Authors :   N. D. Ginder, R. B. Honzatko

Date :   21 Apr 06 (Deposition) - 16 May 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Purc, Ade2, Ade1, Nucleotide Complex, Octahedral Magnesium Coordination, Alternate Folding, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. D. Ginder, D. J. Binkowski, H. J. Fromm, R. B. Honzatko
Nucleotide Complexes Of Escherichia Coli Phosphoribosylaminoimidazole Succinocarboxamide Synthetase.
J. Biol. Chem. V. 281 20680 2006
PubMed-ID: 16687397 | Reference-DOI: 10.1074/JBC.M602109200
(for further references see the PDB file header)

Molecule 1 - PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE
	Chains	:	A, B
	EC Number	:	6.3.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	PURC
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	SAICAR SYNTHETASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 22)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	MSE	18	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ADP A:238 , HOH A:240 , HOH A:241 , HOH A:242 , HOH A:243	BINDING SITE FOR RESIDUE MG A 239
2	AC2	SOFTWARE	ADP B:238 , HOH B:240 , HOH B:241 , HOH B:242 , HOH B:243	BINDING SITE FOR RESIDUE MG B 239
3	AC3	SOFTWARE	TYR A:8 , GLY A:10 , LYS A:11 , ALA A:12 , LYS A:13 , VAL A:15 , LEU A:24 , GLN A:69 , LYS A:82 , LEU A:84 , MSE A:86 , LYS A:123 , GLU A:179 , ASP A:191 , MG A:239 , HOH A:240 , HOH A:242 , HOH A:243 , HOH A:256 , HOH A:266 , HOH A:291 , HOH A:343 , HOH A:354	BINDING SITE FOR RESIDUE ADP A 238
4	AC4	SOFTWARE	TYR B:8 , GLY B:10 , LYS B:11 , ALA B:12 , LYS B:13 , VAL B:15 , LEU B:24 , GLN B:69 , VAL B:81 , LYS B:82 , LEU B:84 , MSE B:86 , LYS B:123 , GLU B:179 , ASP B:191 , MG B:239 , HOH B:240 , HOH B:242 , HOH B:243 , HOH B:251 , HOH B:311 , HOH B:324 , HOH B:336	BINDING SITE FOR RESIDUE ADP B 238

(no "SS Bond" information available for 2GQR)

Asymmetric/Biological Unit

No.	Residues
1	Asn A:114	-	Pro A:115
2	Asn B:114	-	Pro B:115

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

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAICAR_SYNTHETASE_1	PS01057	SAICAR synthetase signature 1.	PUR7_ECOLI	86-100	2	A:86-100 B:86-100
2	SAICAR_SYNTHETASE_2	PS01058	SAICAR synthetase signature 2.	PUR7_ECOLI	173-181	2	A:173-181 B:173-181

(no "Exon" information available for 2GQR)

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:237
 aligned with PUR7_ECOLI | P0A7D7 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
           PUR7_ECOLI     1 MQKQAELYRGKAKTVYSTENPDLLVLEFRNDTSAGDGARIEQFDRKGMVNNKFNYFIMSKLAEAGIPTQMERLLSDTECLVKKLDMVPVECVVRNRAAGSLVKRLGIEEGIELNPPLFDLFLKNDAMHDPMVNESYCETFGWVSKENLARMKELTYKANDVLKKLFDDAGLILVDFKLEFGLYKGEVVLGDEFSPDGSRLWDKETLEKMDKDRFRQSLGGLIEAYEAVARRLGVQLD 237
               SCOP domains d2gqra_ A: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------2gqrA02 A:85-220 ATP-grasp fold, B domain                                                                                               ----------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...eeeee.....eeeeee..ee........ee..hhhhhhhhhhhhhhhhhhhh.....eeee....eeeee..ee..eeeeeeee.hhhhhhhhh.....eeeeeeeeeee.hhhhh..eehhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeee..eeeee.......eeeee........hhhhhh...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------SAICAR_SYNTHETA------------------------------------------------------------------------SAICAR_SY-------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gqr A   1 mQKQAELYRGKAKTVYSTENPDLLVLEFRNDTSAGDGARIEQFDRKGmVNNKFNYFImSKLAEAGIPTQmERLLSDTECLVKKLDmVPVECVVRNRAAGSLVKRLGIEEGIELNPPLFDLFLKNDAmHDPmVNESYCETFGWVSKENLARmKELTYKANDVLKKLFDDAGLILVDFKLEFGLYKGEVVLGDEFSPDGSRLWDKETLEKmDKDRFRQSLGGLIEAYEAVARRLGVQLD 237
                            |       10        20        30        40       |50       |60        70        80     |  90       100       110       120      |130|      140       150|      160       170       180       190       200       210       220       230       
                            |                                             48-MSE    58-MSE      70-MSE          86-MSE                                  127-MSE                 151-MSE                                                   209-MSE                        
                            1-MSE                                                                                                                           131-MSE

Chain B from PDB  Type:PROTEIN  Length:237
 aligned with PUR7_ECOLI | P0A7D7 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
           PUR7_ECOLI     1 MQKQAELYRGKAKTVYSTENPDLLVLEFRNDTSAGDGARIEQFDRKGMVNNKFNYFIMSKLAEAGIPTQMERLLSDTECLVKKLDMVPVECVVRNRAAGSLVKRLGIEEGIELNPPLFDLFLKNDAMHDPMVNESYCETFGWVSKENLARMKELTYKANDVLKKLFDDAGLILVDFKLEFGLYKGEVVLGDEFSPDGSRLWDKETLEKMDKDRFRQSLGGLIEAYEAVARRLGVQLD 237
               SCOP domains d2gqrb_ B: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------2gqrB02 B:85-220 ATP-grasp fold, B domain                                                                                               ----------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee...eeee......eeeeee..ee........ee..hhhhhhhhhhhhhhhhhhhh.....eeee....eeeee..ee..eeeeeeee.hhhhhhhhh.....eeeeeeeeeee........eehhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeee..eeeee.......eeeee........hhhhhh...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------SAICAR_SYNTHETA------------------------------------------------------------------------SAICAR_SY-------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gqr B   1 mQKQAELYRGKAKTVYSTENPDLLVLEFRNDTSAGDGARIEQFDRKGmVNNKFNYFImSKLAEAGIPTQmERLLSDTECLVKKLDmVPVECVVRNRAAGSLVKRLGIEEGIELNPPLFDLFLKNDAmHDPmVNESYCETFGWVSKENLARmKELTYKANDVLKKLFDDAGLILVDFKLEFGLYKGEVVLGDEFSPDGSRLWDKETLEKmDKDRFRQSLGGLIEAYEAVARRLGVQLD 237
                            |       10        20        30        40       |50       |60        70        80     |  90       100       110       120      |130|      140       150|      160       170       180       190       200       210       220       230       
                            1-MSE                                         48-MSE    58-MSE      70-MSE          86-MSE                                  127-MSE                 151-MSE                                                   209-MSE                        
                                                                                                                                                            131-MSE

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: SAICAR synthase-like (28)

Superfamily: SAICAR synthase-like (28)

Family: automated matches (12)

Protein domain: automated matches (12)

Escherichia coli [TaxId: 562] (2)

1a	d2gqra_	A:
1b	d2gqrb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: D-amino Acid Aminotransferase; Chain A, domain 1 (175)

Homologous Superfamily: ATP-grasp fold, B domain (118)

Escherichia coli. Organism_taxid: 562. (17)

1a	2gqrA02	A:85-220
1b	2gqrB02	B:85-220

(no "Pfam Domain" information available for 2GQR)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PUR7_ECOLI | P0A7D7)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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: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:0004638	phosphoribosylaminoimidazole carboxylase activity	Catalysis of the reaction: 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + 2 H(+) = 5-amino-1-(5-phospho-D-ribosyl)imidazole + CO(2).
	GO:0004639	phosphoribosylaminoimidazolesuccinocarboxamide synthase activity	Catalysis of the reaction: 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate + ATP = (2S)-2-[5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinate + 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:0046084	adenine biosynthetic process	The chemical reactions and pathways resulting in the formation of adenine, 6-aminopurine, one of the five main bases found in nucleic acids and a component of numerous important derivatives of its corresponding ribonucleoside, adenosine.
	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.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asn A:114 - Pro A:115	[ RasMol ]
		Asn B:114 - Pro B:115	[ RasMol ]

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	2gqr
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 22)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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