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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHORIBOSYLAMINOIMIDAZOLESUCCINOCARBOXAMIDE SYNTHASE WIT ATP FROM METHANOCALDOCOCCUS JANNASCHII
 
Authors :  M. Kanagawa, S. Baba, 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 :  2.03
Chains :  Asym./Biol. Unit :  A,B
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, S. Kuramitsu, S. Yokoyama, G. Kawai, G. Sampei
Crystal Structure Of Phosphoribosylaminoimidazolesuccinocarboxamide Synthase From Methanocaldococcus Jannaschii
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE
    Chains: A, B
    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

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CIT1Ligand/IonCITRIC ACID
3SO43Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:100 , SER A:106 , ARG A:109 , ARG A:206 , HOH A:1554BINDING SITE FOR RESIDUE SO4 A 512
2AC2SOFTWAREASN A:139 , GLU A:140 , HOH A:1530 , HOH A:1547 , HOH A:1596 , HOH A:1673 , HOH A:1676 , ASN B:139 , GLU B:140 , HOH B:2197BINDING SITE FOR RESIDUE SO4 A 513
3AC3SOFTWAREARG B:100 , GLY B:105 , SER B:106 , ARG B:206 , CIT B:2181 , HOH B:2204BINDING SITE FOR RESIDUE SO4 B 514
4AC4SOFTWARETYR 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:1595 , HOH A:1624 , HOH A:1669 , HOH A:1675BINDING SITE FOR RESIDUE ATP A 1527
5AC5SOFTWARETYR B:15 , GLY B:17 , LYS B:18 , ALA B:19 , LYS B:20 , ILE B:22 , HIS B:75 , LYS B:88 , VAL B:90 , ILE B:92 , LYS B:129 , GLU B:185 , ASP B:198 , HOH B:2243 , HOH B:2270 , HOH B:2316BINDING SITE FOR RESIDUE ATP B 1526
6AC6SOFTWAREILE B:98 , ASP B:181 , PHE B:182 , LYS B:183 , PRO B:202 , ASP B:203 , MET B:205 , ARG B:206 , ASP B:217 , LYS B:218 , ASP B:219 , ARG B:222 , SO4 B:514BINDING SITE FOR RESIDUE CIT B 2181

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z02)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:81 -Pro A:82
2Glu B:81 -Pro B:82

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z02)

(-) PROSITE Motifs  (2, 4)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2Z02)

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

    Alignment length:242
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240  
           PUR7_METJA     1 MEIKLEEILKKQPLYSGKAKSIYEIDDDKVLIEFRDDITAGNGAKHDVKQGKGYLNALISSKLFEALEENGVKTHYIKYIEPRYMIAKKVEIIPIEVIVRNIAAGSLCRRYPFEEGKELPFPIVQFDYKNDEYGDPMLNEDIAVALGLATREELNKIKEIALKVNEVLKKLFDEKGIILVDFKIEIGKDREGNLLVADEISPDTMRLWDKETRDVLDKDVFRKDLGDVIAKYRIVAERLGLL 242
               SCOP domains d2z02a_ A: automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains 2z02A01 A:1-90,A:228-242 Phosphorylase Kinase; domain 1                                   2z02A02 A:91-227 ATP-grasp fold, B domain                                                                                                2z02A01         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh.....ee...eeeee....eeeeee..eeee....eeee..hhhhhhhhhhhhhhhhhhhh.....eeeee...eeeee.eee..eeeeeeee..hhhhhhh......eeeeeeeeeee.hhhhh....hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.eeee....eee........eeeee........hhhhhh...hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------SAICAR_SYNTHETA------------------------------------------------------------------------SAICAR_SY------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z02 A   1 MEIKLEEILKKQPLYSGKAKSIYEIDDDKVLIEFRDDITAGNGAKHDVKQGKGYLNALISSKLFEALEENGVKTHYIKYIEPRYMIAKKVEIIPIEVIVRNIAAGSLCRRYPFEEGKELPFPIVQFDYKNDEYGDPMLNEDIAVALGLATREELNKIKEIALKVNEVLKKLFDEKGIILVDFKIEIGKDREGNLLVADEISPDTMRLWDKETRDVLDKDVFRKDLGDVIAKYRIVAERLGLL 242
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240  


Chain B from PDB  Type:PROTEIN  Length:242
 aligned with PUR7_METJA | Q58987 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:242
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240  
           PUR7_METJA     1 MEIKLEEILKKQPLYSGKAKSIYEIDDDKVLIEFRDDITAGNGAKHDVKQGKGYLNALISSKLFEALEENGVKTHYIKYIEPRYMIAKKVEIIPIEVIVRNIAAGSLCRRYPFEEGKELPFPIVQFDYKNDEYGDPMLNEDIAVALGLATREELNKIKEIALKVNEVLKKLFDEKGIILVDFKIEIGKDREGNLLVADEISPDTMRLWDKETRDVLDKDVFRKDLGDVIAKYRIVAERLGLL 242
               SCOP domains d2z02b_ B: automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains 2z02B01 B:1-90,B:228-242 Phosphorylase Kinase; domain 1                                   2z02B02 B:91-227 ATP-grasp fold, B domain                                                                                                2z02B01         CATH domains
           Pfam domains (1) ---------SAICAR_synt-2z02B01 B:10-241                                                                                                                                                                                                            - Pfam domains (1)
           Pfam domains (2) ---------SAICAR_synt-2z02B02 B:10-241                                                                                                                                                                                                            - Pfam domains (2)
         Sec.struct. author ...hhhhhh.....ee...eeeeeee..eeeeee..eeee....eeee..hhhhhhhhhhhhhhhhhhhh.....eeeee...eeeee..ee..eeeeeeee..hhhhhhh......eeeeeeeeeee.hhhhh....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.eee.....eee........eeeee........hhhhhh...hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------SAICAR_SYNTHETA------------------------------------------------------------------------SAICAR_SY------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z02 B   1 MEIKLEEILKKQPLYSGKAKSIYEIDDDKVLIEFRDDITAGNGAKHDVKQGKGYLNALISSKLFEALEENGVKTHYIKYIEPRYMIAKKVEIIPIEVIVRNIAAGSLCRRYPFEEGKELPFPIVQFDYKNDEYGDPMLNEDIAVALGLATREELNKIKEIALKVNEVLKKLFDEKGIILVDFKIEIGKDREGNLLVADEISPDTMRLWDKETRDVLDKDVFRKDLGDVIAKYRIVAERLGLL 242
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   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, 2)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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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  2z02
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 Related Entries

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

UniProtKB/Swiss-Prot
        PUR7_METJA | Q58987: 2yzl

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