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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PHOSPHORIBOSYL PYROPHOSPHATE (PRPP) SYNTHETASE FROM THERMOPLASMA VOLCANIUM IN COMPLEX WITH ADP.
 
Authors :  M. M. Cherney, L. T. Cherney, C. R. Garen, M. N. G. James
Date :  11 Feb 10  (Deposition) - 16 Feb 11  (Release) - 25 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.53
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phosphoribosyl Transferase, Atp Analog Binding, Atp-Binding, Kinase, Metal-Binding, Nucleotide Biosynthesis, Nucleotide-Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. M. Cherney, L. T. Cherney, C. R. Garen, M. N. James
The Structures Of Thermoplasma Volcanium Phosphoribosyl Pyrophosphate Synthetase Bound To Ribose-5-Phosphate And At Analogs.
J. Mol. Biol. V. 413 844 2011
PubMed-ID: 21963988  |  Reference-DOI: 10.1016/J.JMB.2011.09.007

(-) Compounds

Molecule 1 - RIBOSE-PHOSPHATE PYROPHOSPHOKINASE
    Chains: A, B
    EC Number: 2.7.6.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PVP16
    Expression System Strain: BL21 (DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PRS, TV0197, TVG0201915, TVN0197
    Organism Scientific: THERMOPLASMA VOLCANIUM
    Organism Taxid: 50339
    Strain: ATCC51530
    Synonym: RPPK, PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE, P-RIB-PP SYNTHETASE, PRPP SYNTHETASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

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

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:32 , ASP A:34 , GLU A:36 , HOH A:298 , HOH A:320 , HOH A:338 , HOH A:370 , HOH A:399 , HOH A:465 , HOH A:477 , ARG B:91 , GLN B:92 , HIS B:93 , TYR B:96 , HOH B:342BINDING SITE FOR RESIDUE ADP B 300
2AC2SOFTWAREARG A:91 , SER A:214 , THR A:215 , GLY A:216 , GLY A:217 , THR A:218 , HOH A:332 , HOH A:348 , HOH A:379BINDING SITE FOR RESIDUE SO4 A 287
3AC3SOFTWAREARG A:7 , SER A:58 , HOH A:310 , HOH A:419 , HOH A:450BINDING SITE FOR RESIDUE SO4 A 288
4AC4SOFTWARELYS A:11 , ARG A:15BINDING SITE FOR RESIDUE SO4 A 289
5AC5SOFTWAREARG A:91 , GLN A:92 , HIS A:93 , TYR A:96 , HIS A:124 , HOH A:386 , PHE B:32 , ASP B:34 , GLU B:36 , HOH B:322 , HOH B:325 , HOH B:326 , HOH B:346 , HOH B:349 , HOH B:368 , HOH B:496 , HOH B:499BINDING SITE FOR RESIDUE ADP A 300
6AC6SOFTWAREARG B:7 , SER B:58 , HOH B:339 , HOH B:425BINDING SITE FOR RESIDUE SO4 B 287

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LRT)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val A:196 -Pro A:197
2Val B:196 -Pro B:197

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LRT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LRT)

(-) Exons   (0, 0)

(no "Exon" information available for 3LRT)

(-) 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:284
 aligned with KPRS_THEVO | Q97CA5 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:284
                                    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    
           KPRS_THEVO     1 MKIIALRSSLKLAARIAEELKTEPVMPDERRFPDGELYLRYDEDLTGHNIFIIGNTHSDAEVMEMILTLSAIQDYRTKSVNIIAPYYGYARQHQRYKNGEPISSQILTEIYSSYSNSIATVDIHDEKTLSYSKVKFSDLHANDAIVRYYKNVDVDYVVSPDDGGLARVADISAKLGKKHFFIEKKRIDDRTVEMKVPNVDVNGKKLLIVDDIISTGGTIAKSSGLLREKGASKIYVSAVHGLFVNGSENKILQNADEIHVTDTVESKFSDISVYQEVCNYIRDI 284
               SCOP domains d3lrta1 A:1-155 automated matches                                                                                                                          d3lrta2 A:156-284 automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhhhhh...ee..eeee.....eeee........eeeee....hhhhhhhhhhhhhhhhhh...eeeeee.................hhhhhhhhhhhhh..eeeee...hhhhhhhh..eeeee.hhhhhhhhhh.....eeee....hhhhhhhhhhhhh.eeeeeeeeee..eeeeeee........eeeeeeeee..hhhhhhhhhhhhhh...eeeeeeeee....hhhhhhh....eeeee.......eee.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lrt A   1 MKIIALRSSLKLAARIAEELKTEPVMPDERRFPDGELYLRYDEDLTGHNIFIIGNTHSDAEVMEMILTLSAIQDYRTKSVNIIAPYYGYARQHQRYKNGEPISSQILTEIYSSYSNSIATVDIHDEKTLSYSKVKFSDLHANDAIVRYYKNVDVDYVVSPDDGGLARVADISAKLGKKHFFIEKKRIDDRTVEMKVPNVDVNGKKLLIVDDIISTGGTIAKSSGLLREKGASKIYVSAVHGLFVNGSENKILQNADEIHVTDTVESKFSDISVYQEVCNYIRDI 284
                                    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    


Chain B from PDB  Type:PROTEIN  Length:286
 aligned with KPRS_THEVO | Q97CA5 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:286
                                    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      
           KPRS_THEVO     1 MKIIALRSSLKLAARIAEELKTEPVMPDERRFPDGELYLRYDEDLTGHNIFIIGNTHSDAEVMEMILTLSAIQDYRTKSVNIIAPYYGYARQHQRYKNGEPISSQILTEIYSSYSNSIATVDIHDEKTLSYSKVKFSDLHANDAIVRYYKNVDVDYVVSPDDGGLARVADISAKLGKKHFFIEKKRIDDRTVEMKVPNVDVNGKKLLIVDDIISTGGTIAKSSGLLREKGASKIYVSAVHGLFVNGSENKILQNADEIHVTDTVESKFSDISVYQEVCNYIRDIDA 286
               SCOP domains d3lrtb1 B:1-155 automated matches                                                                                                                          d3lrtb2 B:156-286 automated matches                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Pribosyltran_N-3lrtB03 B:1-114                                                                                    --------------------Pribosyltran-3lrtB01 B:135-240                                                                            ---------------------------------------------- Pfam domains (1)
           Pfam domains (2) Pribosyltran_N-3lrtB04 B:1-114                                                                                    --------------------Pribosyltran-3lrtB02 B:135-240                                                                            ---------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeee...hhhhhhhhhhhh...ee..eeee.....eeee........eeeee....hhhhhhhhhhhhhhhhhh...eeeeee.................hhhhhhhhhhhhh..eeeee...hhhhhhhh..eeeee.hhhhhhhhhh.....eeee....hhhhhhhhhhhhh.eeeeeeeeee..eeeeeee........eeeeeeeee..hhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhh...eeeee.......eee.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lrt B   1 MKIIALRSSLKLAARIAEELKTEPVMPDERRFPDGELYLRYDEDLTGHNIFIIGNTHSDAEVMEMILTLSAIQDYRTKSVNIIAPYYGYARQHQRYKNGEPISSQILTEIYSSYSNSIATVDIHDEKTLSYSKVKFSDLHANDAIVRYYKNVDVDYVVSPDDGGLARVADISAKLGKKHFFIEKKRIDDRTVEMKVPNVDVNGKKLLIVDDIISTGGTIAKSSGLLREKGASKIYVSAVHGLFVNGSENKILQNADEIHVTDTVESKFSDISVYQEVCNYIRDIDA 286
                                    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
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LRT)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: PRTase-like (59)
(-)
Clan: no clan defined [family: Pribosyltran_N] (7)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (KPRS_THEVO | Q97CA5)
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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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:0004749    ribose phosphate diphosphokinase activity    Catalysis of the reaction: D-ribose 5-phosphate + ATP = 5-phospho-alpha-D-ribose 1-diphosphate + AMP + 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:0006015    5-phosphoribose 1-diphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of 5-phosphoribose 1-diphosphate, also known as 5-phosphoribosyl-1-pyrophosphate.
    GO:0009116    nucleoside metabolic process    The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
    GO:0009165    nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
    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:0009156    ribonucleoside monophosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of a ribonucleoside monophosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with phosphate on the sugar.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KPRS_THEVO | Q97CA5: 3lpn 3mbi 3nag

(-) Related Entries Specified in the PDB File

1ibs 1u9y 1u9z 2h06 2h07 2hcr 3lpn