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(-) Description

Title :  SAICAR-SYNTHASE COMPLEXED WITH ATP
 
Authors :  S. V. Antonyuk, A. I. Grebenko, V. M. Levdikov, D. V. Urusova, W. R. Melik-Adamyan, V. S. Lamzin, K. Wilson
Date :  30 Jan 03  (Deposition) - 06 Mar 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Synthetase, Atp Binding Protein, Phosphoribosylaminoimidazolesuccinocarboxamide (Saicar) Synthase, Purine Biosynthesis, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. V. Antonyuk, A. I. Grebenko, V. M. Levdikov, D. V. Urusova, W. R. Melik-Adamyan, V. S. Lamzin, K. Wilson
X-Ray Structure Of Saicar-Synthase Complexed With Atp
Kristallografiya V. 46 620 2001
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHORIBOSYLAMIDOIMIDAZOLE- SUCCINOCARBOXAMIDE SYNTHASE
    Chains: A
    EC Number: 6.3.2.6
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: SAICAR SYNTHETASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric/Biological Unit (5, 7)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2AMP1Ligand/IonADENOSINE MONOPHOSPHATE
3ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
4MG2Ligand/IonMAGNESIUM ION
5SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:122 , GLY A:127 , SER A:128 , ARG A:242 , HOH A:2323 , HOH A:2519BINDING SITE FOR RESIDUE SO4 A 308
2AC2SOFTWAREARG A:73 , ASN A:74 , ASP A:78 , HIS A:110 , HOH A:2183 , HOH A:2520 , HOH A:2521 , HOH A:2522 , HOH A:2523BINDING SITE FOR RESIDUE SO4 A 309
3AC3SOFTWAREATP A:307 , HOH A:2397BINDING SITE FOR RESIDUE MG A 310
4AC4SOFTWARESER A:61 , GLU A:234 , VAL A:235 , HOH A:2150BINDING SITE FOR RESIDUE MG A 311
5AC5SOFTWAREGLY A:18 , LYS A:19 , ARG A:21 , ILE A:23 , LEU A:31 , PHE A:33 , HIS A:75 , HIS A:110 , HIS A:112 , LYS A:143 , GLU A:219 , VAL A:232 , ASP A:233 , MG A:310 , HOH A:2397 , HOH A:2508 , HOH A:2509 , HOH A:2510 , HOH A:2511 , HOH A:2512 , HOH A:2513 , HOH A:2514 , HOH A:2515 , HOH A:2516 , HOH A:2517BINDING SITE FOR RESIDUE ATP A 307
6AC6SOFTWAREGLU A:62 , VAL A:77 , ILE A:79 , ILE A:85 , SER A:106 , LEU A:107 , LEU A:108 , HOH A:2524 , HOH A:2525 , HOH A:2526BINDING SITE FOR RESIDUE AMP A 315

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OBD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OBD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OBD)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAICAR_SYNTHETASE_1PS01057 SAICAR synthetase signature 1.PUR7_YEAST114-128  1A:114-128
2SAICAR_SYNTHETASE_2PS01058 SAICAR synthetase signature 2.PUR7_YEAST213-221  1A:213-221

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YAR015W1YAR015W.1I:169370-170290921PUR7_YEAST1-3063061A:1-304 (gaps)304

(-) 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:299
 aligned with PUR7_YEAST | P27616 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:304
                                    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 MSITKTELDGILPLVARGKVRDIYEVDAGTLLFVATDRISAYDVIMENSIPEKGILLTKLSEFWFKFLSNDVRNHLVDIAPGKTIFDYLPAKLSEPKYKTQLEDRSLLVHKHKLIPLEVIVRGYITGSAWKEYVKTGTVHGLKQPQGLKESQEFPEPIFTPSTKAEQGEHDENISPAQAAELVGEDLSRRVAELAVKLYSKCKDYAKEKGIIIADTKFEFGIDEKTNEIILVDEVLTPDSSRFWNGASYKVGESQDSYDKQFLRDWLTANKLNGVNGVKMPQDIVDRTRAKYIEAYETLTGSKW 304
               SCOP domains d1obda_ A: SAICAR synthase                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -1obdA01 A:2-112 Phosphorylase Kinase; domain 1                                                                 1obdA02 A:113-258 ATP-grasp fold, B domain                                                                                                        ---------------------------------------------- CATH domains
               Pfam domains ----------SAICAR_synt-1obdA01 A:11-284                                                                                                                                                                                                                                                      -------------------- Pfam domains
         Sec.struct. author .............eeee...eeeeeee..eeeeee....ee..ee......hhhhhhhhhhhhhhhhh....ee.........hhhhhhhhhhhhhhhhhhhh..eeeee..ee....eeeeee.hhhhhhhhhhhhee..ee.........eeeeeee..ee..-----.ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeee....eeeee...........................hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------SAICAR_SYNTHETA------------------------------------------------------------------------------------SAICAR_SY----------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-304 (gaps) UniProt: 1-306 [INCOMPLETE]                                                                                                                                                                                                                                                        Transcript 1
                 1obd A   1 xSITKTELDGILPLVARGKVRDIYEVDAGTLLFVATDRISAYDVIMENSIPEKGILLTKLSEFWFKFLSNDVRNHLVDIAPGKTIFDYLPAKLSEPKYKTQLEDRSLLVHKHKLIPLEVIVRGYITGSAWKEYVKTGTVHGLKQPQGLKESQEFPEPIFTPSTKA-----DENISPAQAAELVGEDLSRRVAELAVKLYSKCKDYAKEKGIIIADTKFEFGIDEKTNEIILVDEVLTPDSSRFWNGASYKVGESQDSYDKQFLRDWLTANKLNGVNGVKMPQDIVDRTRAKYIEAYETLTGSKW 304
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    |    -|      180       190       200       210       220       230       240       250       260       270       280       290       300    
                            |                                                                                                                                                                 165   171                                                                                                                                     
                            1-ACE
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 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: SAICAR_synt] (7)

(-) 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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PUR7_YEAST | P27616: 1a48 1obg 2cnq 2cnu 2cnv

(-) Related Entries Specified in the PDB File

1a48 SAICAR SYNTHASE