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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE WITH ADP FROM METHANOCALDOCOCCUS JANNASCHII
 
Authors :  M. Kanagawa, S. Baba, K. Fukui, S. Kuramitsu, S. Yokoyama, G. Kawai, G. Sampei, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  06 May 07  (Deposition) - 06 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  2-Layer Sandwich, Ligase, Purine Biosynthesis, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kanagawa, S. Baba, K. Fukui, S. Kuramitsu, S. Yokoyama, G. Kawai, G. Sampei
Crystal Structure Of Phosphoribosylaminoimidazole-Succinocarboxamide Synthase With Adp From Methanocaldococcus Jannaschii
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE
    Chains: A
    EC Number: 6.3.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Synonym: SAICAR SYNTHETASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2SO44Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:139 , GLU A:140 , HOH A:529 , HOH A:618BINDING SITE FOR RESIDUE SO4 A 511
2AC2SOFTWAREILE A:98 , ARG A:100 , SER A:106 , ARG A:206 , HOH A:538 , HOH A:604BINDING SITE FOR RESIDUE SO4 A 512
3AC3SOFTWARETYR A:15 , GLY A:17 , LYS A:18 , ALA A:19 , LYS A:20 , ILE A:22 , HIS A:75 , LYS A:88 , VAL A:90 , ILE A:92 , LYS A:129 , GLU A:185 , ASP A:198 , HOH A:593 , HOH A:602 , HOH A:615BINDING SITE FOR RESIDUE ADP A 500

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:81 -Pro A:82

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAICAR_SYNTHETASE_1PS01057 SAICAR synthetase signature 1.PUR7_METJA92-106  1A:92-106
2SAICAR_SYNTHETASE_2PS01058 SAICAR synthetase signature 2.PUR7_METJA179-187  1A:179-187
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAICAR_SYNTHETASE_1PS01057 SAICAR synthetase signature 1.PUR7_METJA92-106  1A:92-106
2SAICAR_SYNTHETASE_2PS01058 SAICAR synthetase signature 2.PUR7_METJA179-187  1A:179-187
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAICAR_SYNTHETASE_1PS01057 SAICAR synthetase signature 1.PUR7_METJA92-106  2A:92-106
2SAICAR_SYNTHETASE_2PS01058 SAICAR synthetase signature 2.PUR7_METJA179-187  2A:179-187

(-) Exons   (0, 0)

(no "Exon" information available for 2YZL)

(-) 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
(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:238
 aligned with PUR7_METJA | Q58987 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:239
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233         
           PUR7_METJA     4 KLEEILKKQPLYSGKAKSIYEIDDDKVLIEFRDDITAGNGAKHDVKQGKGYLNALISSKLFEALEENGVKTHYIKYIEPRYMIAKKVEIIPIEVIVRNIAAGSLCRRYPFEEGKELPFPIVQFDYKNDEYGDPMLNEDIAVALGLATREELNKIKEIALKVNEVLKKLFDEKGIILVDFKIEIGKDREGNLLVADEISPDTMRLWDKETRDVLDKDVFRKDLGDVIAKYRIVAERLGLL 242
               SCOP domains d2yzla_ A: automated matches                                                                                                                                                                                                                    SCOP domains
               CATH domains 2yzlA01 A:4-90,A:228-242 Phosphorylase  Kinase; domain 1                               2yzlA02 A:91-227 ATP-grasp fold, B domain                                                                                                2yzlA01         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh...ee...eeeee....eeeeee..eeee.-..eeee..hhhhhhhhhhhhhhhhhhhh.....eeeee...eeeee..ee..eeeeeeee..hhhhhhh......eeeeeeeeeee........eehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.eee.....eee........eeeee........hhhhhh...hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------SAICAR_SYNTHETA------------------------------------------------------------------------SAICAR_SY------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yzl A   4 KLEEILKKQPLYSGKAKSIYEIDDDKVLIEFRDDITAG-GAKHDVKQGKGYLNALISSKLFEALEENGVKTHYIKYIEPRYMIAKKVEIIPIEVIVRNIAAGSLCRRYPFEEGKELPFPIVQFDYKNDEYGDPMLNEDIAVALGLATREELNKIKEIALKVNEVLKKLFDEKGIILVDFKIEIGKDREGNLLVADEISPDTMRLWDKETRDVLDKDVFRKDLGDVIAKYRIVAERLGLL 242
                                    13        23        33       |43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233         
                                                                41 |                                                                                                                                                                                                       
                                                                  43
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (PUR7_METJA | Q58987)
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.

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        PUR7_METJA | Q58987: 2z02

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