2CNQ - JenaLib

Title :   ATOMIC RESOLUTION STRUCTURE OF SAICAR-SYNTHASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH ADP, AICAR, SUCCINATE

Authors :   D. V. Urusova, S. V. Antonyuk, A. I. Grebenko, V. M. Levdikov, V. V. Barynin, A. N. Popov, V. S. Lamzin, W. R. Melik-Adamyan

Date :   23 May 06 (Deposition) - 08 Jun 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.00

Chains :   Asym./Biol. Unit : A

Keywords :   Ligase, Phosphoribosylaminoimidazolesuccinocarboxamide (Saicar) Syn Ligase, Synthetase, Acetylation, Atp-Binding Protein, Purine Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. V. Urusova, S. V. Antonyuk, A. I. Grebenko, V. M. Levdikov, V. V. Barynin, A. N. Popov, V. S. Lamzin, W. R. Melik-Adamyan
Saicar Synthase: Substrate Recognition, Conformational Flexibility And Catalysis.
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 13)

Sites (12, 12)

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ADP A:1307 , HOH A:2518 , HOH A:2538 , HOH A:2670 , HOH A:2684	BINDING SITE FOR RESIDUE MG A1314
02	AC2	SOFTWARE	GLU A:52 , ARG A:289 , TRP A:304 , SER A:305 , HOH A:2716 , HOH A:2717 , HOH A:2718 , HOH A:2719 , HOH A:2720	BINDING SITE FOR RESIDUE SO4 A1315
03	AC3	SOFTWARE	LYS A:225 , HOH A:2721 , HOH A:2722 , HOH A:2723 , HOH A:2726	BINDING SITE FOR RESIDUE SO4 A1316
04	AC4	SOFTWARE	ARG A:73 , ASN A:74 , LEU A:76 , ASP A:78 , HIS A:110 , HOH A:2255 , HOH A:2348 , HOH A:2721 , HOH A:2724 , HOH A:2726 , HOH A:2727 , HOH A:2728	BINDING SITE FOR RESIDUE SO4 A1317
05	AC5	SOFTWARE	PHE A:262 , ARG A:287 , LYS A:291 , HOH A:2640 , HOH A:2641 , HOH A:2729 , HOH A:2730 , HOH A:2731 , HOH A:2733	BINDING SITE FOR RESIDUE SO4 A1318
06	AC6	SOFTWARE	LYS A:5 , GLU A:185 , ASP A:186 , HOH A:2703 , HOH A:2704 , HOH A:2705 , HOH A:2706 , HOH A:2707 , HOH A:2708	BINDING SITE FOR RESIDUE SIN A1312
07	AC7	SOFTWARE	TYR A:42 , LYS A:131 , ARG A:242 , GLN A:261 , ARG A:264 , HOH A:2584 , HOH A:2681 , HOH A:2709 , HOH A:2710 , HOH A:2711 , HOH A:2712 , HOH A:2713	BINDING SITE FOR RESIDUE SIN A1313
08	AC8	SOFTWARE	GLY A:18 , LYS A:19 , VAL A:20 , ARG A:21 , ILE A:23 , LEU A:31 , PHE A:33 , HIS A:75 , HIS A:110 , HIS A:112 , LEU A:114 , LYS A:143 , GLU A:219 , VAL A:232 , ASP A:233 , MG A:1314 , HOH A:2078 , HOH A:2079 , HOH A:2518 , HOH A:2538 , HOH A:2670 , HOH A:2671 , HOH A:2672 , HOH A:2673 , HOH A:2674 , HOH A:2676 , HOH A:2677 , HOH A:2678 , HOH A:2684	BINDING SITE FOR RESIDUE ADP A1307
09	AC9	SOFTWARE	GLU A:118 , ILE A:120 , ARG A:122 , GLY A:127 , SER A:128 , ASP A:171 , ASP A:215 , LYS A:217 , ASP A:239 , SER A:240 , SER A:241 , ARG A:242 , ARG A:264 , ADP A:1311 , HOH A:2078 , HOH A:2539 , HOH A:2679 , HOH A:2680 , HOH A:2681 , HOH A:2682 , HOH A:2683 , HOH A:2684 , HOH A:2685 , HOH A:2686 , HOH A:2696 , HOH A:2698	BINDING SITE FOR RESIDUE AMZ A1308
10	BC1	SOFTWARE	GLU A:62 , LYS A:66 , VAL A:77 , ILE A:79 , ILE A:85 , LEU A:107 , LEU A:108 , ASP A:186 , HOH A:2270 , HOH A:2460 , HOH A:2687 , HOH A:2688 , HOH A:2689 , HOH A:2690 , HOH A:2691 , HOH A:2692 , HOH A:2693 , HOH A:2694 , HOH A:2695	BINDING SITE FOR RESIDUE AMZ A1309
11	BC2	SOFTWARE	GLU A:62 , LYS A:66 , VAL A:77 , ILE A:79 , ILE A:85 , SER A:106 , LEU A:107 , LEU A:108 , ASP A:186 , HOH A:2194 , HOH A:2270 , HOH A:2460 , HOH A:2689 , HOH A:2690 , HOH A:2691 , HOH A:2692 , HOH A:2693 , HOH A:2694 , HOH A:2695	BINDING SITE FOR RESIDUE AMP A1310
12	BC3	SOFTWARE	LYS A:19 , SER A:40 , ALA A:41 , TYR A:42 , ASP A:43 , HIS A:170 , ASP A:171 , LYS A:260 , ARG A:264 , AMZ A:1308 , HOH A:2131 , HOH A:2136 , HOH A:2429 , HOH A:2682 , HOH A:2683 , HOH A:2686 , HOH A:2696 , HOH A:2698 , HOH A:2699 , HOH A:2700 , HOH A:2701 , HOH A:2710	BINDING SITE FOR RESIDUE ADP A1311

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (1, 1)

Sequences/Alignments

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:302
 aligned with PUR7_YEAST | P27616 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:305
                                    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     
           PUR7_YEAST     1 MSITKTELDGILPLVARGKVRDIYEVDAGTLLFVATDRISAYDVIMENSIPEKGILLTKLSEFWFKFLSNDVRNHLVDIAPGKTIFDYLPAKLSEPKYKTQLEDRSLLVHKHKLIPLEVIVRGYITGSAWKEYVKTGTVHGLKQPQGLKESQEFPEPIFTPSTKAEQGEHDENISPAQAAELVGEDLSRRVAELAVKLYSKCKDYAKEKGIIIADTKFEFGIDEKTNEIILVDEVLTPDSSRFWNGASYKVGESQDSYDKQFLRDWLTANKLNGVNGVKMPQDIVDRTRAKYIEAYETLTGSKWS 305
               SCOP domains d2cnqa_ A: SAICAR synthase                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -2cnqA01 A:2-112 Phosphorylase Kinase; domain 1                                                                 2cnqA02 A:113-258 ATP-grasp fold, B domain                                                                                                        ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeee...eeeeeee..eeeeee....ee..ee......hhhhhhhhhhhhhhhhh....ee.........hhhhhhhhhhhhhhhhhhhh..eeeee..ee....eeeeee.hhhhhhhhhhhhee..ee.........eeeeeee......---......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeeee....eeeee........eeeee..............hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------SAICAR_SYNTHETA------------------------------------------------------------------------------------SAICAR_SY------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-305 (gaps) UniProt: 1-306 [INCOMPLETE]                                                                                                                                                                                                                                                         Transcript 1
                 2cnq A   1 xSITKTELDGILPLVARGKVRDIYEVDAGTLLFVATDRISAYDVIMENSIPEKGILLTKLSEFWFKFLSNDVRNHLVDIAPGKTIFDYLPAKLSEPKYKTQLEDRSLLVHKHKLIPLEVIVRGYITGSAWKEYVKTGTVHGLKQPQGLKESQEFPEPIFTPSTKA---EHDENISPAQAAELVGEDLSRRVAELAVKLYSKCKDYAKEKGIIIADTKFEFGIDEKTNEIILVDEVLTPDSSRFWNGASYKVGESQDSYDKQFLRDWLTANKLNGVNGVKMPQDIVDRTRAKYIEAYETLTGSKWS 305
                            |       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     
                            |                                                                                                                                                                 165 169                                                                                                                                        
                            1-ACE

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (2, 2)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PUR7_YEAST | P27616)

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.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ACE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ADP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		AMP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		AMZ	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SIN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2cnq)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2cnq
		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)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	PUR7_YEAST \| P27616
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	6.3.2.6
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description