2V40 - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   HUMAN ADENYLOSUCCINATE SYNTHETASE ISOZYME 2 IN COMPLEX WITH GDP

Authors :   M. Welin, M. Moche, C. Arrowsmith, H. Berglund, R. Busam, R. Collins, L. G. Dahlgren, A. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, B. M. Hallberg, L. Holmberg-Schiavone, I. Johansson, A. Kallas, T. Karlberg, T. Kotenyova, L. Lehtio, T. Nyman, D. Ogg, C. Persson, J. Sagemark, P. Stenmark, M. Sundstrom, A. G. Thorsell, L. Tresaugues, S. Van-Den-Berg, J. Weigelt, P. Nordlund, Structural Genomics Consortium (Sgc)

Date :   27 Jun 07 (Deposition) - 10 Jul 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Ligase, Purine Biosynthesis, Adenylosuccinate Synthetase, Metal- Binding, Purine Metabolism, Nucleotide-Binding, Gdp, Adss2, Magnesium, Gtp-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Welin, M. Moche, C. Arrowsmith, H. Berglund, R. Busam, R. Collins, L. G. Dahlgren, A. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, B. M. Hallberg, L. Holmberg-Schiavone, I. Johansson, A. Kallas, T. Karlberg, T. Kotenyova, L. Lehtio, T. Nyman, D. Ogg, C. Persson, J. Sagemark, P. Stenmark, M. Sundstrom, A. G. Thorsell, S. Van-Den-Berg, J. Weigelt, P. Nordlund
Human Adenylosuccinate Synthetase Isozyme 2 In Complex With Gdp
To Be Published
PubMed: search

Molecule 1 - ADENYLOSUCCINATE SYNTHETASE ISOZYME 2
	Chains	:	A
	EC Number	:	6.3.4.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC-BSA4
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	RESIDUES 21-456
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	THE PROTEIN CHAIN CONTAINS A HEXAHISTIDINE TAIL IN THE N-TERMINUS
	Synonym	:	ADENYLOSUCCINATE SYNTHETASE ACIDIC ISOZYME, IMP-ASPARTATE LIGASE 2, ADSS 2, AMPSASE 2

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:41 , GLY A:42 , LYS A:43 , GLY A:44 , LYS A:45 , HIS A:68 , LYS A:362 , ASP A:364 , ILE A:365 , GLY A:444 , VAL A:445 , GLY A:446 , LYS A:447 , HOH A:2029 , HOH A:2513 , HOH A:2532 , HOH A:2533 , HOH A:2534 , HOH A:2535 , HOH A:2536 , HOH A:2537	BINDING SITE FOR RESIDUE GDP A1457

(no "SS Bond" information available for 2V40)

Asymmetric Unit

No.	Residues
1	Tyr A:266	-	Pro A:267

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051881	L	179	F	PURA2_HUMAN	Polymorphism	12134870	A	L	179	F

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051881	L	179	F	PURA2_HUMAN	Polymorphism	12134870	A	L	179	F

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADENYLOSUCCIN_SYN_1	PS01266	Adenylosuccinate synthetase GTP-binding site.	PURA2_HUMAN	37-44	1	A:37-44
2	ADENYLOSUCCIN_SYN_2	PS00513	Adenylosuccinate synthetase active site.	PURA2_HUMAN	165-176	1	A:165-176

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADENYLOSUCCIN_SYN_1	PS01266	Adenylosuccinate synthetase GTP-binding site.	PURA2_HUMAN	37-44	2	A:37-44
2	ADENYLOSUCCIN_SYN_2	PS00513	Adenylosuccinate synthetase active site.	PURA2_HUMAN	165-176	2	A:165-176

Asymmetric Unit (13, 13)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000366535	1a	ENSE00001441955	chr1:244615436-244614937	500	PURA2_HUMAN	1-61	61	1	A:26-61	36
1.4	ENST00000366535	4	ENSE00001009299	chr1:244601070-244600968	103	PURA2_HUMAN	62-96	35	1	A:62-96	35
1.5	ENST00000366535	5	ENSE00000961641	chr1:244600195-244600127	69	PURA2_HUMAN	96-119	24	1	A:96-119	24
1.6	ENST00000366535	6	ENSE00000961642	chr1:244595897-244595847	51	PURA2_HUMAN	119-136	18	1	A:119-136	18
1.7c	ENST00000366535	7c	ENSE00002038715	chr1:244587689-244587623	67	PURA2_HUMAN	136-158	23	1	A:136-150	15
1.8	ENST00000366535	8	ENSE00001620692	chr1:244587362-244587255	108	PURA2_HUMAN	158-194	37	1	A:163-194	32
1.9	ENST00000366535	9	ENSE00001611817	chr1:244586218-244586137	82	PURA2_HUMAN	194-221	28	1	A:194-221	28
1.10	ENST00000366535	10	ENSE00001601694	chr1:244583598-244583472	127	PURA2_HUMAN	222-264	43	1	A:222-264	43
1.11c	ENST00000366535	11c	ENSE00001800158	chr1:244582216-244582062	155	PURA2_HUMAN	264-315	52	1	A:264-315	52
1.12	ENST00000366535	12	ENSE00001636166	chr1:244581054-244580930	125	PURA2_HUMAN	316-357	42	1	A:316-357	42
1.13	ENST00000366535	13	ENSE00001592171	chr1:244579380-244579283	98	PURA2_HUMAN	357-390	34	1	A:357-390	34
1.14b	ENST00000366535	14b	ENSE00001655298	chr1:244574738-244574589	150	PURA2_HUMAN	390-440	51	1	A:390-440	51
1.15	ENST00000366535	15	ENSE00001746197	chr1:244572940-244571796	1145	PURA2_HUMAN	440-456	17	1	A:440-456	17

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:419
 aligned with PURA2_HUMAN | P30520 from UniProtKB/Swiss-Prot  Length:456

    Alignment length:431
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455 
          PURA2_HUMAN    26 GGNRVTVVLGAQWGDEGKGKVVDLLAQDADIVCRCQGGNNAGHTVVVDSVEYDFHLLPSGIINPNVTAFIGNGVVIHLPGLFEEAEKNVQKGKGLEGWEKRLIISDRAHIVFDFHQAADGIQEQQRQEQAGKNLGTTKKGIGPVYSSKAARSGLRMCDLVSDFDGFSERFKVLANQYKSIYPTLEIDIEGELQKLKGYMEKIKPMVRDGVYFLYEALHGPPKKILVEGANAALLDIDFGTYPFVTSSNCTVGGVCTGLGMPPQNVGEVYGVVKAYTTRVGIGAFPTEQDNEIGELLQTRGREFGVTTGRKRRCGWLDLVLLKYAHMINGFTALALTKLDILDMFTEIKVGVAYKLDGEIIPHIPANQEVLNKVEVQYKTLPGWNTDISNARAFKELPVNAQNYVRFIEDELQIPVKWIGVGKSRESMIQLF 456
               SCOP domains d2v40a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --2v40A01 A:28-130,A:231-296 Adenylosuccinate Synthetase, subunit A, domain 1                            2v40A02 A:131-230 Ad            enylosuccinate Synthetase, subunit A, domain 2                      2v40A01 A:28-130,A:231-296                                        2v40A03 A:297-456 Adenylosuccinate Synthetase, subunit A, domain 3                                                                                               CATH domains
               Pfam domains ----Adenylsucc_synt-2v40A01 A:30-454                                                                                                                                                                                                                                                                                                                                                                                                         -- Pfam domains
         Sec.struct. author ....eeeeee......hhhhhhhhhhh...eeee........eeeee..eeeee...hhhhhh...eeee....eeehhhhhhhhhhhhhh.hhhh.hhh.eeee...eeehhhhhhhhhhhhhh------------..hhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..eehhhhhhhhhhhh....eeee...hhhhh...............hhhhhhhhh.hhh.eeeeeeeee..eee...........hhhhhhhhhhh...........eee.eehhhhhhhhhhhh..eeeeehhhhhhhh.eeeeeeeeee..eee.....hhhhhh..eeeeeeee..........hhhhhhhhhhhhhhhhhhhhh..eeeee.......eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------ADENYLOS------------------------------------------------------------------------------------------------------------------------ADENYLOSUCCI---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:26-61 [INCOMPLETE]Exon 1.4  PDB: A:62-96             ----------------------Exon 1.6          ---------------------Exon 1.8  PDB: A:163-194 [INCOMPLETE]---------------------------Exon 1.10  PDB: A:222-264 UniProt: 222-264 ---------------------------------------------------Exon 1.12  PDB: A:316-357 UniProt: 316-357--------------------------------Exon 1.14b  PDB: A:390-440 UniProt: 390-440        ---------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------Exon 1.5  PDB: A:96-119 ----------------Exon 1.7c [INCOMPLETE] -----------------------------------Exon 1.9  PDB: A:194-221    ------------------------------------------Exon 1.11c  PDB: A:264-315 UniProt: 264-315         -----------------------------------------Exon 1.13  PDB: A:357-390         -------------------------------------------------Exon 1.15         Transcript 1 (2)
                 2v40 A  26 GGNRVTVVLGAQWGDEGKGKVVDLLAQDADIVCRCQGGNNAGHTVVVDSVEYDFHLLPSGIINPNVTAFIGNGVVIHLPGLFEEAEKNVQKGKGLEGWEKRLIISDRAHIVFDFHQAADGIQEQQ------------KKGIGPVYSSKAARSGLRMCDLVSDFDGFSERFKVLANQYKSIYPTLEIDIEGELQKLKGYMEKIKPMVRDGVYFLYEALHGPPKKILVEGANAALLDIDFGTYPFVTSSNCTVGGVCTGLGMPPQNVGEVYGVVKAYTTRVGIGAFPTEQDNEIGELLQTRGREFGVTTGRKRRCGWLDLVLLKYAHMINGFTALALTKLDILDMFTEIKVGVAYKLDGEIIPHIPANQEVLNKVEVQYKTLPGWNTDISNARAFKELPVNAQNYVRFIEDELQIPVKWIGVGKSRESMIQLF 456
                                    35        45        55        65        75        85        95       105       115       125       135       145    |    -       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455 
                                                                                                                                                      150          163

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: Nitrogenase iron protein-like (152)

Protein domain: automated matches (19)

Human (Homo sapiens) [TaxId: 9606] (2)

d2v40a_

Asymmetric Unit

Clans(

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Families(

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Organisms( (-)

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Clan: P-loop_NTPase (1112)

Family: Adenylsucc_synt (18)

Homo sapiens (Human) (1)

Adenylsucc_synt-2v40A01

A:30-454

Asymmetric Unit(hide GO term definitions)

Chain A (PURA2_HUMAN | P30520)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0004019	adenylosuccinate synthase activity	Catalysis of the reaction: L-aspartate + GTP + IMP = N(6)-(1,2-dicarboxyethyl)-AMP + GDP + 3 H(+) + phosphate.
	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: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:0042301	phosphate ion binding	Interacting selectively and non-covalently with 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:0044208	'de novo' AMP biosynthetic process	The chemical reactions and pathways resulting in the formation of adenosine monophosphate (AMP) from inosine 5'-monophosphate (IMP).
	GO:0006167	AMP biosynthetic process	The chemical reactions and pathways resulting in the formation of AMP, adenosine monophosphate.
	GO:0046040	IMP metabolic process	The chemical reactions and pathways involving IMP, inosine monophosphate.
	GO:0006531	aspartate metabolic process	The chemical reactions and pathways involving aspartate, the anion derived from aspartic acid, 2-aminobutanedioic acid.
	GO:0071257	cellular response to electrical 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 an electrical stimulus.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	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.
	GO:0009168	purine ribonucleoside monophosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of purine ribonucleoside monophosphate, a compound consisting of a purine base linked to a ribose sugar esterified with phosphate on the sugar.
	GO:0060359	response to ammonium ion	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ammonium ion stimulus.
	GO:0014074	response to purine-containing compound	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a purine-containing compound stimulus.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric Unit
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	2v40
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Description

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Ligands, Modified Residues, Ions (1, 1)

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SS Bonds (0, 0)

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