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(-) Description

Title :  PHOSPHOPENTOMUTASE V158L VARIANT
 
Authors :  W. A. Birmingham, C. A. Starbird, T. D. Panosian, D. P. Nannemann, T. M. I B. O. Bachmann
Date :  19 Jul 13  (Deposition) - 31 Jul 13  (Release) - 30 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
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 :  W. R. Birmingham, C. A. Starbird, T. D. Panosian, D. P. Nannemann, T. M. Iverson, B. O. Bachmann
Bioretrosynthetic Construction Of A Didanosine Biosynthetic Pathway.
Nat. Chem. Biol. V. 10 392 2014
PubMed-ID: 24657930  |  Reference-DOI: 10.1038/NCHEMBIO.1494

(-) Compounds

Molecule 1 - PHOSPHOPENTOMUTASE
    Chains: A, B, C
    EC Number: 5.4.2.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BC_4087, DEOB
    Mutation: YES
    Organism Scientific: BACILLUS CEREUS
    Organism Taxid: 1396
    Synonym: PHOSPHODEOXYRIBOMUTASE

 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, 15)

Asymmetric Unit (4, 15)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL3Ligand/IonGLYCEROL
3MN8Ligand/IonMANGANESE (II) ION
4TPO3Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
3MN-1Ligand/IonMANGANESE (II) ION
4TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3MN-1Ligand/IonMANGANESE (II) ION
4TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2GOL-1Ligand/IonGLYCEROL
3MN-1Ligand/IonMANGANESE (II) ION
4TPO1Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:13 , TPO A:85 , ASP A:327 , HIS A:328BINDING SITE FOR RESIDUE MN A 401
02AC2SOFTWARETPO A:85 , ASP A:156 , ASP A:286 , HIS A:291 , HIS A:339BINDING SITE FOR RESIDUE MN A 402
03AC3SOFTWAREGLY A:27 , ASP A:28 , HIS A:334 , HOH A:582 , HOH A:677BINDING SITE FOR RESIDUE MN A 403
04AC4SOFTWARETYR A:96 , HOH A:561BINDING SITE FOR RESIDUE GOL A 404
05AC5SOFTWAREARG A:363 , GLN A:364 , ASP A:368 , HOH A:653BINDING SITE FOR RESIDUE GOL A 405
06AC6SOFTWARESER A:231 , ASP A:232 , HOH A:675BINDING SITE FOR RESIDUE ACT A 406
07AC7SOFTWAREASP B:13 , TPO B:85 , ASP B:327 , HIS B:328BINDING SITE FOR RESIDUE MN B 401
08AC8SOFTWARETPO B:85 , ASP B:156 , ASP B:286 , HIS B:291 , HIS B:339BINDING SITE FOR RESIDUE MN B 402
09AC9SOFTWARETYR B:96 , TYR B:384 , HOH B:626 , HOH B:743BINDING SITE FOR RESIDUE GOL B 403
10BC1SOFTWAREASP C:13 , TPO C:85 , ASP C:327 , HIS C:328BINDING SITE FOR RESIDUE MN C 401
11BC2SOFTWARETPO C:85 , ASP C:156 , ASP C:286 , HIS C:291 , HIS C:339BINDING SITE FOR RESIDUE MN C 402
12BC3SOFTWAREGLY C:27 , ASP C:28 , HIS C:334 , HOH C:501 , HOH C:502 , HOH C:607BINDING SITE FOR RESIDUE MN C 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LRC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4LRC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LRC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LRC)

(-) Exons   (0, 0)

(no "Exon" information available for 4LRC)

(-) 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
                                                                                                                                                                                                                                                                                                                                                                                                                                       
               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....eeeeeeehhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeee..................eeeeee................hhhhhhhhhhhhh.........hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lrc A   2 NKYKRIFLVVMDSVGIGEAPDAEQFGDLGSDTIGHIAEHMNGLQMPNMVKLGLGNIREMKGISKVEKPLGYYTKMQEKSTGKDtMTGHWEIMGLYIDTPFQVFPEGFPKELLDELEEKTGRKIIGNKPASGTEILDELGQEQMETGSLIVYTSADSLLQIAAHEEVVPLDELYKICKIARELTLDEKYMVGRVIARPFVGEPGNFTRTPNRHDYALKPFGRTVMNELKDSDYDVIAIGKISDIYDGEGVTESLRTKSNMDGMDKLVDTLNMDFTGLSFLNLVDFDALFGHRRDPQGYGEALQEYDARLPEVFAKLKEDDLLLITADHGNDPIHPGTDHTREYVPLLAYSPSMKEGGQELPLRQTFADIGATVAENFGVKMPEYGTSFLNEL 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
                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee..........hhhhh....hhhhhhhhhh....hhhhhhhhhhhhh.............eeeee.......hhhhhhhhhh...............hhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh.eeeee....eeeeeee....hhhhhhhhhhhhhhhh.hhhhh..eeeeeeeeee..eeee.....eee......hhhhhhhhh..eeeee.hhhhhh......eee...hhhhhhhhhhhhhh....eeeeeeehhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeee..................eeeeee................hhhhhhhhhhhhh.........hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lrc B   3 KYKRIFLVVMDSVGIGEAPDAEQFGDLGSDTIGHIAEHMNGLQMPNMVKLGLGNIREMKGISKVEKPLGYYTKMQEKSTGKDtMTGHWEIMGLYIDTPFQVFPEGFPKELLDELEEKTGRKIIGNKPASGTEILDELGQEQMETGSLIVYTSADSLLQIAAHEEVVPLDELYKICKIARELTLDEKYMVGRVIARPFVGEPGNFTRTPNRHDYALKPFGRTVMNELKDSDYDVIAIGKISDIYDGEGVTESLRTKSNMDGMDKLVDTLNMDFTGLSFLNLVDFDALFGHRRDPQGYGEALQEYDARLPEVFAKLKEDDLLLITADHGNDPIHPGTDHTREYVPLLAYSPSMKEGGQELPLRQTFADIGATVAENFGVKMPEYGTSFLNEL 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
                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee...................hhhhhhhhhhh...hhhhhhhhhhhhh.............eeeee.......hhhhhhhhhh...............hhhhhhhhhhhhh..eee....hhhhhhhhhhhhhhhhh.eeeee....eeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee..eeee.....eee......hhhhhhhhh..eeeee.hhhhhh......eee...hhhhhhhhhhhhhh....eeeeeeehhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeee..................eeeeee.................hhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lrc C   3 KYKRIFLVVMDSVGIGEAPDAEQFGDLGSDTIGHIAEHMNGLQMPNMVKLGLGNIREMKGISKVEKPLGYYTKMQEKSTGKDtMTGHWEIMGLYIDTPFQVFPEGFPKELLDELEEKTGRKIIGNKPASGTEILDELGQEQMETGSLIVYTSADSLLQIAAHEEVVPLDELYKICKIARELTLDEKYMVGRVIARPFVGEPGNFTRTPNRHDYALKPFGRTVMNELKDSDYDVIAIGKISDIYDGEGVTESLRTKSNMDGMDKLVDTLNMDFTGLSFLNLVDFDALFGHRRDPQGYGEALQEYDARLPEVFAKLKEDDLLLITADHGNDPIHPGTDHTREYVPLLAYSPSMKEGGQELPLRQTFADIGATVAENFGVKMPEYGTSFLNEL 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)
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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 4LRC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LRC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LRC)

(-) Gene Ontology  (14, 14)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DEOB_BACCR | Q818Z9: 3m8w 3m8y 3m8z 3ot9 3twz 3tx0 3un2 3un3 3un5 3uny 3uo0 4lr7 4lr8 4lr9 4lra 4lrb 4lrd 4lre 4lrf

(-) Related Entries Specified in the PDB File

3m8z 3twz 3tx0 3un3 4lr7 4lr8 4lr9 4lra 4lrb 4lrd 4lre 4lrf