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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE ATPASE SUBUNIT FROM AQUIFEX AEOLICUS
 
Authors :  K. Okada, S. Tamura, S. Baba, M. Kanagawa, 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 :  2.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Purine Nucleotide Biosynthetic Pathway, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Metabolic Systems, Atp-Binding, Decarboxylase, Lyase, Nucleotide-Binding, Purine Biosynthesis, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Okada, S. Tamura, S. Baba, M. Kanagawa, G. Kawai, G. Sampei
Crystal Structure Of Phosphoribosylaminoimidazole Carboxylase Atpase Subunit From Aquifex Aeolicus
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE ATPASE SUBUNIT
    Chains: A, B
    EC Number: 4.1.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PURK
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Synonym: AIR CARBOXYLASE, AIRC

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:323 , ARG A:329BINDING SITE FOR RESIDUE SO4 A 1
2AC2SOFTWARELYS B:33 , LYS B:323 , ARG B:329BINDING SITE FOR RESIDUE SO4 B 357

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:39 -A:45

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Val A:209 -Pro A:210
2Ile B:81 -Pro B:82
3Val B:209 -Pro B:210

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z04)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z04)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z04)

(-) 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:309
 aligned with PURK_AQUAE | O66608 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:353
                                    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   
           PURK_AQUAE     2 LTVGILGGGQLGWMTILEGRKLGFKFHVLEDKENAPACRVADRCFRTGQISEFVDSCDIITYEFEHIKDEVLEKCESKLIPNPQALYVKKSRIREKLFLKKHGFPVPEFLVIKRDEIIDALKSFKLPVVIKAEKLGYDGKGQYRIKKLEDANQVVKNHDKEESFIIEEFVKFEAEISCIGVRDREGKTYFYPQPFNKHEEGILIYNYVPYAKLKEAEEITKRLMELLDIVGVFTVEFFLLKDGRVLINEFAPRVHNTGHWTLDGAYTSQFENLLRAITEMPLGSTELKLPSGMVNILGKSYEEIPLKEILSVEGAKLYWYGKEKKPRRKVGHVNVVGRSKEEVVEKVERVFTL 354
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh.eeeee.....hhhhhhh.eeehhhhhhhhhhhh.eeee.....hhhhhhhhh......hhhhhhhhhhhhhhhhhhh.......eee.--------------.eeee..------------------------------.eeee.....eeeeeeeee.....eee..eeeeeee..eeeeeeeeee.hhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeee...hhhhhhhhhhh..hhhhhhhhhhh............eeeeeee..hhhhhhhhhhh....eeeee.........eeeeeeee..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z04 A   2 LTVGILGGGQLGWmTILEGRKLGFKFHVLEDKENAPACRVADRCFRTGQISEFVDSCDIITYEFEHIKDEVLEKCESKLIPNPQALYVKKSRIREKLFLKKHGFPVPEFLVI--------------PVVIKAE------------------------------FIIEEFVKFEAEISCIGVRDREGKTYFYPQPFNKHEEGILIYNYVPYAKLKEAEEITKRLmELLDIVGVFTVEFFLLKDGRVLINEFAPRVHNTGHWTLDGAYTSQFENLLRAITEmPLGSTELKLPSGmVNILGKSYEEIPLKEILSVEGAKLYWYGKEKKPRRKVGHVNVVGRSKEEVVEKVERVFTL 354
                                    11   |    21        31        41        51        61        71        81        91       101       111 |       -      |131  |      -         -         -   |   171       181       191       201       211       221   |   231       241       251       261       271       281       291  |    301       311       321       331       341       351   
                                        15-MSE                                                                                           113            128   134                            165                                                         225-MSE                                                 281-MSE      294-MSE                                                        


Chain B from PDB  Type:PROTEIN  Length:325
 aligned with PURK_AQUAE | O66608 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:355
                                    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     
           PURK_AQUAE     2 LTVGILGGGQLGWMTILEGRKLGFKFHVLEDKENAPACRVADRCFRTGQISEFVDSCDIITYEFEHIKDEVLEKCESKLIPNPQALYVKKSRIREKLFLKKHGFPVPEFLVIKRDEIIDALKSFKLPVVIKAEKLGYDGKGQYRIKKLEDANQVVKNHDKEESFIIEEFVKFEAEISCIGVRDREGKTYFYPQPFNKHEEGILIYNYVPYAKLKEAEEITKRLMELLDIVGVFTVEFFLLKDGRVLINEFAPRVHNTGHWTLDGAYTSQFENLLRAITEMPLGSTELKLPSGMVNILGKSYEEIPLKEILSVEGAKLYWYGKEKKPRRKVGHVNVVGRSKEEVVEKVERVFTLLK 356
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------ATP-grasp-2z04B01 B:1        00-266                                                                                                                                    ------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------ATP-grasp-2z04B02 B:1        00-266                                                                                                                                    ------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh.eeeee.....hhhhhhh.eeehhhhhhhhhhh..eeee.....hhhhhhh........hhhhhhh.hhhhhhhhhhh.......eeeeehhhhh.--------.eeee.....----------------------...eeeee......eeeeeeeee.....eee..eeeeee....eeeeeeeee.hhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeee...hhhhhhhhhhh..hhhhhhhhhhh............eeeeeee..hhhhhhhhhhh....eeeee.........eeeeeeee..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z04 B   2 LTVGILGGGQLGWmTILEGRKLGFKFHVLEDKENAPACRVADRCFRTGQISEFVDSCDIITYEFEHIKDEVLEKCESKLIPNPQALYVKKSRIREKLFLKKHGFPVPEFLVIKRDEIID--------VVIKAEKLGY----------------------KEESFIIEEFVKFEAEISCIGVRDREGKTYFYPQPFNKHEEGILIYNYVPYAKLKEAEEITKRLmELLDIVGVFTVEFFLLKDGRVLINEFAPRVHNTGHWTLDGAYTSQFENLLRAITEmPLGSTELKLPSGmVNILGKSYEEIPLKEILSVEGAKLYWYGKEKKPRRKVGHVNVVGRSKEEVVEKVERVFTLLK 356
                                    11   |    21        31        41        51        61        71        81        91       101       111        |-       131      |  -         -       161       171       181       191       201       211       221   |   231       241       251       261       271       281       291  |    301       311       321       331       341       351     
                                        15-MSE                                                                                                  120      129      138                    161                                                             225-MSE                                                 281-MSE      294-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "SCOP Domain" information available for 2Z04)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Z04)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: ATP-grasp (83)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PURK_AQUAE | O66608)
molecular function
    GO:0034028    5-(carboxyamino)imidazole ribonucleotide synthase activity    Catalysis of the reaction: 5-amino-1-(5-phospho-D-ribosyl)imidazole + ATP + bicarbonate = 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole + ADP + 3 H(+) + phosphate.
    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: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: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.

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