1QF4 - JenaLib

Title :   DESIGN, SYNTHESIS, AND X-RAY CRYSTAL STRUCTURE OF AN ENZYME BOUND BISUBSTRATE HYBRID INHIBITOR OF ADENYLOSUCCINATE SYNTHETASE

Authors :   S. Hanessian, P. -P. Lu, J. -Y. Sanceau, P. Chemla, K. Gohda, R. Fonne-Pf L. Prade, S. W. Cowan-Jacob

Date :   06 Apr 99 (Deposition) - 02 Dec 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Purine Biosynthesis, Synthetase, Gtp-Binding, Gtp-Hydrolysing Enzymes, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Hanessian, P. P. Lu, J. Y. Sanceau, P. Chemla, K. Gohda, R. Fonne-Pfister, L. Prade, S. W. Cowan-Jacob
An Enzyme-Bound Bisubstrate Hybrid Inhibitor Of Adenylosuccinate Synthetase
Angew. Chem. Int. Ed. Engl. V. 38 3159 1999
PubMed-ID: 10556888 | Reference-DOI: 10.1002/(SICI)1521-3773(19991102)38:21<3159::AID-AN IE3159>3.0.CO;2-2
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 4)

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:12 , ASP A:13 , LYS A:16 , ALA A:39 , GLY A:40 , HIS A:41 , ALA A:223 , GLN A:224 , MG A:433 , GDP A:434 , RPD A:435	BINDING SITE FOR RESIDUE PO4 A 432
2	AC2	SOFTWARE	ASP A:13 , GLY A:40 , PO4 A:432 , GDP A:434 , RPD A:435	BINDING SITE FOR RESIDUE MG A 433
3	AC3	SOFTWARE	ASP A:13 , GLU A:14 , GLY A:15 , LYS A:16 , GLY A:17 , GLY A:40 , HIS A:41 , THR A:42 , ARG A:305 , LYS A:331 , ASP A:333 , VAL A:334 , SER A:414 , THR A:415 , GLY A:416 , PRO A:417 , PO4 A:432 , MG A:433 , RPD A:435 , HOH A:453 , HOH A:505	BINDING SITE FOR RESIDUE GDP A 434
4	AC4	SOFTWARE	ASP A:13 , ASN A:38 , GLY A:40 , GLY A:127 , THR A:128 , THR A:129 , ARG A:143 , GLN A:224 , LEU A:228 , VAL A:238 , THR A:239 , VAL A:273 , GLY A:298 , ALA A:299 , THR A:300 , THR A:301 , ARG A:303 , ARG A:305 , PO4 A:432 , MG A:433 , GDP A:434 , HOH A:438 , HOH A:441 , HOH A:444 , HOH A:455 , HOH A:471	BINDING SITE FOR RESIDUE RPD A 435
5	ASP	AUTHOR	ARG A:305 , THR A:301 , ARG A:303	THESE RESIDUES MAKE UP THE ASPARTATE BINDING SITE ON ADENYLOSUCCINATE SYNTHETASE.
6	GNS	AUTHOR	ASP A:13 , GLU A:14 , GLY A:15 , LYS A:16 , GLY A:17 , LYS A:18 , LYS A:331 , LEU A:332 , ASP A:333 , SER A:414 , THR A:415 , GLY A:416 , PRO A:417	THESE RESIDUES MAKE UP THE GUANINE NUCLEOTIDE BINDING SITE ON ADENYLOSUCCINATE SYNTHETASE.
7	IMP	AUTHOR	ASN A:38 , THR A:129 , ARG A:143 , GLN A:224 , THR A:239 , VAL A:273	THESE RESIDUES MAKE UP THE INOSINE NUCLEOTIDE BINDING SITE ON ADENYLOSUCCINATE SYNTHETASE.

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

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
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Chain A from PDB  Type:PROTEIN  Length:431
 aligned with PURA_ECOLI | P0A7D4 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:431
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431 
           PURA_ECOLI     2 GNNVVVLGTQWGDEGKGKIVDLLTERAKYVVRYQGGHNAGHTLVINGEKTVLHLIPSGILRENVTSIIGNGVVLSPAALMKEMKELEDRGIPVRERLLLSEACPLILDYHVALDNAREKARGAKAIGTTGRGIGPAYEDKVARRGLRVGDLFDKETFAEKLKEVMEYHNFQLVNYYKAEAVDYQKVLDDTMAVADILTSMVVDVSDLLDQARQRGDFVMFEGAQGTLLDIDHGTYPYVTSSNTTAGGVATGSGLGPRYVDYVLGILKAYSTRVGAGPFPTELFDETGEFLCKQGNEFGATTGRRRRTGWLDTVAVRRAVQLNSLSGFCLTKLDVLDGLKEVKLCVAYRMPDGREVTTTPLAADDWKGVEPIYETMPGWSESTFGVKDRSGLPQAALNYIKRIEELTGVPIDIISTGPDRTETMILRDPFDA 432
               SCOP domains d1qf4a_ A: Adenylosuccinate synthetase, PurA                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1qf4A01 A:1-100,A:201-265 Adenylosuccinate Synthetase, subunit A, domain 1                          1qf4A02 A:101-200 Adenylosuccinate Synthetase, subunit A, domain 2                                  1qf4A01 A:1-100,A:201-265                                        1qf4A03 A:266-431 Adenylosuccinate Synthetase, subunit A, domain 3                                                                                                     CATH domains
               Pfam domains --Adenylsucc_synt-1qf4A01 A:3-424                                                                                                                                                                                                                                                                                                                                                                                                       ------- Pfam domains
         Sec.struct. author ..eeeeee.......hhhhhhhhhhh..eeee........eeeee..eeeee............eeee....eeehhhhhhhhhhhhhh...hhhheee....eee.hhhhhhhhhhhhhhhhh........hhhhhhhhh......hhhhh.hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhh...eeee....hhh................hhhhhhhh...hhh..eeeeeee..eee............hhhhhhhhh............eee...hhhhhhhhhhh...eeeee.hhhh....eee...eee.............hhhh...eee..eee...........hhh..hhhhhhhhhhhhhh...eeeee.......eee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------ADENYLOS------------------------------------------------------------------------------------------------------------------ADENYLOSUCCI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qf4 A   1 GNNVVVLGTQWGDEGKGKIVDLLTERAKYVVRYQGGHNAGHTLVINGEKTVLHLIPSGILRENVTSIIGNGVVLSPAALMKEMKELEDRGIPVRERLLLSEACPLILDYHVALDNAREKARGAKAIGTTGRGIGPAYEDKVARRGLRVGDLFDKETFAEKLKEVMEYHNFQLVNYYKAEAVDYQKVLDDTMAVADILTSMVVDVSDLLDQARQRGDFVMFEGAQGTLLDIDHGTYPYVTSSNTTAGGVATGSGLGPRYVDYVLGILKAYSTRVGAGPFPTELFDETGEFLCKQGNEFGATTGRRRRTGWLDTVAVRRAVQLNSLSGFCLTKLDVLDGLKEVKLCVAYRMPDGREVTTTPLAADDWKGVEPIYETMPGWSESTFGVKDRSGLPQAALNYIKRIEELTGVPIDIISTGPDRTETMILRDPFDA 431
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Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (3, 3)

Pfam Domains (1, 1)

Gene Ontology (16, 16)

Asymmetric Unit(hide GO term definitions)

Chain A (PURA_ECOLI | P0A7D4)

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: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:0046040	IMP metabolic process	The chemical reactions and pathways involving IMP, inosine monophosphate.
	GO:0046086	adenosine biosynthetic process	The chemical reactions and pathways resulting in the formation of adenosine, adenine riboside, a ribonucleoside found widely distributed in cells of every type as the free nucleoside and in combination in nucleic acids and various nucleoside coenzymes.
	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:0015949	nucleobase-containing small molecule interconversion	The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
	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: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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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