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(-) Description

Title :  PHOSPHORYLATED BACILLUS CEREUS PHOSPHOPENTOMUTASE SOAKED WITH GLUCOSE 1,6-BISPHOSPHATE
 
Authors :  T. M. Iverson, W. R. Birmingham, T. D. Panosian, D. P. Nannemann, B. O. Ba
Date :  16 Nov 11  (Deposition) - 29 Feb 12  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Alkaline Phosphatase Family, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. M. Iverson, T. D. Panosian, W. R. Birmingham, D. P. Nannemann, B. O. Bachmann
Molecular Differences Between A Mutase And A Phosphatase: Investigations Of The Activation Step In Bacillus Cereus Phosphopentomutase.
Biochemistry V. 51 1964 2012
PubMed-ID: 22329805  |  Reference-DOI: 10.1021/BI201761H

(-) Compounds

Molecule 1 - PHOSPHOPENTOMUTASE
    ChainsA, B, C
    EC Number5.4.2.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GeneDEOB, BC_4087
    Organism ScientificBACILLUS CEREUS
    Organism Taxid1396
    SynonymPHOSPHODEOXYRIBOMUTASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric Unit (4, 13)
No.NameCountTypeFull Name
1G161Ligand/IonALPHA-D-GLUCOSE 1,6-BISPHOSPHATE
2MN8Ligand/IonMANGANESE (II) ION
3TPO3Mod. Amino AcidPHOSPHOTHREONINE
4TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1G161Ligand/IonALPHA-D-GLUCOSE 1,6-BISPHOSPHATE
2MN-1Ligand/IonMANGANESE (II) ION
3TPO1Mod. Amino AcidPHOSPHOTHREONINE
4TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1G16-1Ligand/IonALPHA-D-GLUCOSE 1,6-BISPHOSPHATE
2MN-1Ligand/IonMANGANESE (II) ION
3TPO1Mod. Amino AcidPHOSPHOTHREONINE
4TRS-1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1G16-1Ligand/IonALPHA-D-GLUCOSE 1,6-BISPHOSPHATE
2MN-1Ligand/IonMANGANESE (II) ION
3TPO1Mod. Amino AcidPHOSPHOTHREONINE
4TRS-1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETPO A:85 , ASP A:156 , ASP A:286 , HIS A:291 , HIS A:339BINDING SITE FOR RESIDUE MN A 395
02AC2SOFTWAREASP A:13 , TPO A:85 , ASP A:327 , HIS A:328BINDING SITE FOR RESIDUE MN A 396
03AC3SOFTWAREGLY A:27 , ASP A:28 , HIS A:334 , HOH A:432 , HOH A:465 , HOH A:466BINDING SITE FOR RESIDUE MN A 397
04AC4SOFTWARESER A:131 , GLY A:132 , SER A:154 , VAL A:158 , ARG A:197 , ARG A:208 , ARG A:212 , HOH A:403 , HOH A:404BINDING SITE FOR RESIDUE G16 A 398
05AC5SOFTWARETYR A:96 , HOH A:490BINDING SITE FOR RESIDUE TRS A 399
06AC6SOFTWARETPO B:85 , ASP B:156 , ASP B:286 , HIS B:291 , HIS B:339BINDING SITE FOR RESIDUE MN B 395
07AC7SOFTWAREASP B:13 , TPO B:85 , ASP B:327 , HIS B:328BINDING SITE FOR RESIDUE MN B 396
08AC8SOFTWARETPO C:85 , ASP C:156 , ASP C:286 , HIS C:291 , HIS C:339BINDING SITE FOR RESIDUE MN C 395
09AC9SOFTWAREASP C:13 , TPO C:85 , ASP C:327 , HIS C:328BINDING SITE FOR RESIDUE MN C 396
10BC1SOFTWAREGLY C:27 , ASP C:28 , HIS C:334 , HOH C:470 , HOH C:471 , HOH C:472BINDING SITE FOR RESIDUE MN C 397

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3UO0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3UO0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3UO0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3UO0)

(-) Exons   (0, 0)

(no "Exon" information available for 3UO0)

(-) 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:391
 aligned with DEOB_BACCR | Q818Z9 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:391
                                    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       361       371       381       391 
           DEOB_BACCR     2 NKYKRIFLVVMDSVGIGEAPDAEQFGDLGSDTIGHIAEHMNGLQMPNMVKLGLGNIREMKGISKVEKPLGYYTKMQEKSTGKDTMTGHWEIMGLYIDTPFQVFPEGFPKELLDELEEKTGRKIIGNKPASGTEILDELGQEQMETGSLIVYTSADSVLQIAAHEEVVPLDELYKICKIARELTLDEKYMVGRVIARPFVGEPGNFTRTPNRHDYALKPFGRTVMNELKDSDYDVIAIGKISDIYDGEGVTESLRTKSNMDGMDKLVDTLNMDFTGLSFLNLVDFDALFGHRRDPQGYGEALQEYDARLPEVFAKLKEDDLLLITADHGNDPIHPGTDHTREYVPLLAYSPSMKEGGQELPLRQTFADIGATVAENFGVKMPEYGTSFLNEL 392
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.........hhhhhh....hhhhhhhhhh....hhhhhhhhhhhhh.............eeeee.......hhhhhhhhhh...............hhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh.eeeee....eeeeeee....hhhhhhhhhhhhhhhh.hhhhh..eeeeeeeeee..eeee....eeee......hhhhhhhhh..eeeee.hhhhhh......eee...hhhhhhhhhhhhhh....eeeeeeehhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeee..................eeeeee................hhhhhhhhhhhh..........hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uo0 A   2 NKYKRIFLVVMDSVGIGEAPDAEQFGDLGSDTIGHIAEHMNGLQMPNMVKLGLGNIREMKGISKVEKPLGYYTKMQEKSTGKDtMTGHWEIMGLYIDTPFQVFPEGFPKELLDELEEKTGRKIIGNKPASGTEILDELGQEQMETGSLIVYTSADSVLQIAAHEEVVPLDELYKICKIARELTLDEKYMVGRVIARPFVGEPGNFTRTPNRHDYALKPFGRTVMNELKDSDYDVIAIGKISDIYDGEGVTESLRTKSNMDGMDKLVDTLNMDFTGLSFLNLVDFDALFGHRRDPQGYGEALQEYDARLPEVFAKLKEDDLLLITADHGNDPIHPGTDHTREYVPLLAYSPSMKEGGQELPLRQTFADIGATVAENFGVKMPEYGTSFLNEL 392
                                    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       361       371       381       391 
                                                                                                              85-TPO                                                                                                                                                                                                                                                                                                               

Chain B from PDB  Type:PROTEIN  Length:390
 aligned with DEOB_BACCR | Q818Z9 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:390
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392
           DEOB_BACCR     3 KYKRIFLVVMDSVGIGEAPDAEQFGDLGSDTIGHIAEHMNGLQMPNMVKLGLGNIREMKGISKVEKPLGYYTKMQEKSTGKDTMTGHWEIMGLYIDTPFQVFPEGFPKELLDELEEKTGRKIIGNKPASGTEILDELGQEQMETGSLIVYTSADSVLQIAAHEEVVPLDELYKICKIARELTLDEKYMVGRVIARPFVGEPGNFTRTPNRHDYALKPFGRTVMNELKDSDYDVIAIGKISDIYDGEGVTESLRTKSNMDGMDKLVDTLNMDFTGLSFLNLVDFDALFGHRRDPQGYGEALQEYDARLPEVFAKLKEDDLLLITADHGNDPIHPGTDHTREYVPLLAYSPSMKEGGQELPLRQTFADIGATVAENFGVKMPEYGTSFLNEL 392
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee.........hhhhhh....hhhhhhhhhh....hhhhhhhhhhhhh.............eeeee.......hhhhhhhhhh...............hhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh.eeeee....eeeeeee....hhhhhhhhhhhhhhhh.hhhhh..eeeeeeeeee..eeee.....eee......hhhhhhhhh..eeeee.hhhhhh......eee...hhhhhhhhhhhhhhh...eeeeeeehhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeee..................eeeeee................hhhhhhhhhhhh..........hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3uo0 B   3 KYKRIFLVVMDSVGIGEAPDAEQFGDLGSDTIGHIAEHMNGLQMPNMVKLGLGNIREMKGISKVEKPLGYYTKMQEKSTGKDtMTGHWEIMGLYIDTPFQVFPEGFPKELLDELEEKTGRKIIGNKPASGTEILDELGQEQMETGSLIVYTSADSVLQIAAHEEVVPLDELYKICKIARELTLDEKYMVGRVIARPFVGEPGNFTRTPNRHDYALKPFGRTVMNELKDSDYDVIAIGKISDIYDGEGVTESLRTKSNMDGMDKLVDTLNMDFTGLSFLNLVDFDALFGHRRDPQGYGEALQEYDARLPEVFAKLKEDDLLLITADHGNDPIHPGTDHTREYVPLLAYSPSMKEGGQELPLRQTFADIGATVAENFGVKMPEYGTSFLNEL 392
                                    12        22        32        42        52        62        72        82  |     92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392
                                                                                                             85-TPO                                                                                                                                                                                                                                                                                                               

Chain C from PDB  Type:PROTEIN  Length:390
 aligned with DEOB_BACCR | Q818Z9 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:390
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392
           DEOB_BACCR     3 KYKRIFLVVMDSVGIGEAPDAEQFGDLGSDTIGHIAEHMNGLQMPNMVKLGLGNIREMKGISKVEKPLGYYTKMQEKSTGKDTMTGHWEIMGLYIDTPFQVFPEGFPKELLDELEEKTGRKIIGNKPASGTEILDELGQEQMETGSLIVYTSADSVLQIAAHEEVVPLDELYKICKIARELTLDEKYMVGRVIARPFVGEPGNFTRTPNRHDYALKPFGRTVMNELKDSDYDVIAIGKISDIYDGEGVTESLRTKSNMDGMDKLVDTLNMDFTGLSFLNLVDFDALFGHRRDPQGYGEALQEYDARLPEVFAKLKEDDLLLITADHGNDPIHPGTDHTREYVPLLAYSPSMKEGGQELPLRQTFADIGATVAENFGVKMPEYGTSFLNEL 392
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee...................hhhhhhhhhh....hhhhhhhhhhhhh.............eeeee.......hhhhhhhhhh...............hhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh.eeeee....eeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee..eeee.....eee......hhhhhhhhh..eeeee.hhhhhh......eee...hhhhhhhhhhhhhhh...eeeeeeehhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeee..................eeeeee................hhhhhhhhhhhh..........hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3uo0 C   3 KYKRIFLVVMDSVGIGEAPDAEQFGDLGSDTIGHIAEHMNGLQMPNMVKLGLGNIREMKGISKVEKPLGYYTKMQEKSTGKDtMTGHWEIMGLYIDTPFQVFPEGFPKELLDELEEKTGRKIIGNKPASGTEILDELGQEQMETGSLIVYTSADSVLQIAAHEEVVPLDELYKICKIARELTLDEKYMVGRVIARPFVGEPGNFTRTPNRHDYALKPFGRTVMNELKDSDYDVIAIGKISDIYDGEGVTESLRTKSNMDGMDKLVDTLNMDFTGLSFLNLVDFDALFGHRRDPQGYGEALQEYDARLPEVFAKLKEDDLLLITADHGNDPIHPGTDHTREYVPLLAYSPSMKEGGQELPLRQTFADIGATVAENFGVKMPEYGTSFLNEL 392
                                    12        22        32        42        52        62        72        82  |     92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392
                                                                                                             85-TPO                                                                                                                                                                                                                                                                                                               

   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  (0, 0)

(no "SCOP Domain" information available for 3UO0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UO0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UO0)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (DEOB_BACCR | Q818Z9)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008973    phosphopentomutase activity    Catalysis of the reaction: D-ribose 1-phosphate = D-ribose 5-phosphate.
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:0043094    cellular metabolic compound salvage    Any process which produces a useful metabolic compound from derivatives of it without de novo synthesis, as carried out by individual cells.
    GO:0009264    deoxyribonucleotide catabolic process    The chemical reactions and pathways resulting in the breakdown of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    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:0009166    nucleotide catabolic process    The chemical reactions and pathways resulting in the breakdown 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:0009117    nucleotide metabolic process    The chemical reactions and pathways involving a nucleotide, a 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).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        DEOB_BACCR | Q818Z93m8w 3m8y 3m8z 3ot9 3twz 3tx0 3un2 3un3 3un5 3uny 4lr7 4lr8 4lr9 4lra 4lrb 4lrc 4lrd 4lre 4lrf

(-) Related Entries Specified in the PDB File

3twz PHOSPHORYLATED PHOSPHOPENTOMUTASE IN SPACE GROUP P212121
3tx0 UNPHOSPHORYLATED PHOSPHOPENTOMUTASE IN SPACE GROUP P212121
3un2 PHOSPHOPENTOMUTASE T85Q VARIANT
3un3 PHOSPHOPENTOMUTASE T85Q VARIANT SOAKED WITH GLUCOSE 1,6- BISPHOSPHATE
3un5 PHOSPHOPENTOMUTASE T85E VARIANT
3uny PHOSPHOPENTOMUTASE T85E VARIANT SOAKED WITH GLUCOSE 1,6- BISPHOSPHATE