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(-) Description

Title :  PHOSPHORIBULOKINASE FROM RHODOBACTER SPHEROIDES
 
Authors :  D. H. T. Harrison, J. Runquist, A. Holub, H. Miziorko
Date :  16 Mar 98  (Deposition) - 17 Jun 98  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (8x)
Biol. Unit 3:  A  (2x)
Keywords :  Transferase, Kinase, Calvin Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. H. Harrison, J. A. Runquist, A. Holub, H. M. Miziorko
The Crystal Structure Of Phosphoribulokinase From Rhodobacter Sphaeroides Reveals A Fold Similar To That Of Adenylate Kinase.
Biochemistry V. 37 5074 1998
PubMed-ID: 9548738  |  Reference-DOI: 10.1021/BI972805Y
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHORIBULOKINASE
    Cell LineBL21
    ChainsA
    EC Number2.7.1.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPETBPRKWT
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    GenePRKA
    Organism ScientificRHODOBACTER SPHAEROIDES
    Organism Taxid1063

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (8x)A
Biological Unit 3 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:69 , LYS A:165 , ARG A:186 , ARG A:187BINDING SITE FOR RESIDUE SO4 A 401
2CICUNKNOWNASP A:42 , ASP A:169 , LYS A:165 , ARG A:187 , SO4 A:401CATALYTIC SITE

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1A7J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1A7J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1A7J)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PHOSPHORIBULOKINASEPS00567 Phosphoribulokinase signature.KPPR1_RHOSH165-178  1A:165-178
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PHOSPHORIBULOKINASEPS00567 Phosphoribulokinase signature.KPPR1_RHOSH165-178  1A:165-178
Biological Unit 2 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PHOSPHORIBULOKINASEPS00567 Phosphoribulokinase signature.KPPR1_RHOSH165-178  8A:165-178
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PHOSPHORIBULOKINASEPS00567 Phosphoribulokinase signature.KPPR1_RHOSH165-178  2A:165-178

(-) Exons   (0, 0)

(no "Exon" information available for 1A7J)

(-) 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:279
 aligned with KPPR1_RHOSH | P12033 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:288
                                    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        
          KPPR1_RHOSH     2 SKKHPIISVTGSSGAGTSTVKHTFDQIFRREGVKAVSIEGDAFHRFNRADMKAELDRRYAAGDATFSHFSYEANELKELERVFREYGETGQGRTRTYVHDDAEAARTGVAPGNFTDWRDFDSDSHLLFYEGLHGAVVNSEVNIAGLADLKIGVVPVINLEWIQKIHRDRATRGYTTEAVTDVILRRMHAYVHCIVPQFSQTDINFQRVPVVDTSNPFIARWIPTADESVVVIRFRNPRGIDFPYLTSMIHGSWMSRANSIVVPGNKLDLAMQLILTPLIDRVVRESKV 289
               SCOP domains d1a7ja_ A: Ph   osphoribulokinase                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1a7jA00 A:2-2   89 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee...---..hhhhhhhhhhhh....eeeeehhhh....hhhhhhhhhhhhhh.........hhh..hhhhhhhhhhhhhh.........------.....................eeeeee............hhh..eeeeeee.hhhhhhhhhhhh..........hhhhhhhhhhhhhhh.hhhhh...eeeeeee......hhh......hhheeeeeee.......hhhhhhh....eeee..eeeeehhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------PHOSPHORIBULOK--------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1a7j A   2 SKKHPIISVTGSS---TSTVKHTFDQIFRREGVKAVSIEGDAFHRFNRADMKAELDRRYAAGDATFSHFSYEANELKELERVFREYGETGQGRTRTYV------ARTGVAPGNFTDWRDFDSDSHLLFYEGLHGAVVNSEVNIAGLADLKIGVVPVINLEWIQKIHRDRATRGYTTEAVTDVILRRMHAYVHCIVPQFSQTDINFQRVPVVDTSNPFIARWIPTADESVVVIRFRNPRGIDFPYLTSMIHGSWMSRANSIVVPGNKLDLAMQLILTPLIDRVVRESKV 289
                                    11  |   | 21        31        41        51        61        71        81        91       | -    |  111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281        
                                       14  18                                                                               99    106                                                                                                                                                                                       

   Legend:   → Mismatch (orange background)
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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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1A7J)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (KPPR1_RHOSH | P12033)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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:0008974    phosphoribulokinase activity    Catalysis of the reaction: D-ribulose 5-phosphate + ATP = D-ribulose 1,5-bisphosphate + ADP + 2 H(+).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0015979    photosynthesis    The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
    GO:0019253    reductive pentose-phosphate cycle    The fixation of carbon dioxide (CO2) as glucose in the chloroplasts of C3 plants; uses ATP and NADPH formed in the light reactions of photosynthesis; carbon dioxide reacts with ribulose 1,5-bisphosphate (catalyzed by the function of ribulose-bisphosphate carboxylase) to yield two molecules of 3-phosphoglycerate; these are then phosphorylated by ATP to 1,3-bisphosphateglyceraldehyde which, in turn, is then reduced by NADPH to glyceraldehyde 3-phosphate. The glyceraldehyde 3-phosphate is converted to fructose 5-phosphate and ribulose 5-phosphate by aldolase and other enzymes; the ribulose 5-phosphate is phosphorylated by ATP to ribulose 1,5-bisphosphate.

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