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(-) Description

Title :  CRYSTAL STRUCTURE OF PFKB PROTEIN FROM POLAROMONAS SP. JS666
 
Authors :  R. Agarwal, S. Chamala, B. Evans, R. Foti, A. Gizzi, B. Hellerich, A. Kar J. Lafleur, R. Siedel, G. Villigas, W. Zencheck, S. C. Almo, S. Swamina York Structural Genomics Research Consortium (Nysgrc)
Date :  21 Feb 12  (Deposition) - 21 Mar 12  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Structural Genomics, Psi-Biology, New York Structural Genomics Research Consortium, Nysgrc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Agarwal, S. C. Almo, S. Swaminathan
Crystal Structure Of Pfkb Protein From Polaromonas Sp. Js66
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PFKB
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)RIPL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BPRO_1737
    Organism Scientific: POLAROMONAS SP. JS666
    Organism Taxid: 296591

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 38)

Asymmetric Unit (2, 38)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2MSE36Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 18)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE18Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 18)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE18Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMSE A:36 , ARG A:132 , ARG A:194 , HOH A:522BINDING SITE FOR RESIDUE CL A 401
2AC2SOFTWAREMSE C:36 , ARG C:132BINDING SITE FOR RESIDUE CL C 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DU5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4DU5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DU5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DU5)

(-) Exons   (0, 0)

(no "Exon" information available for 4DU5)

(-) 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:294
 aligned with Q12CR9_POLSJ | Q12CR9 from UniProtKB/TrEMBL  Length:314

    Alignment length:309
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303         
         Q12CR9_POLSJ     4 ALDVITFGEAMMLLVADRPGPLEHAEAFHKRTAGAETNVAIGLARLGLKVGWASRLGTDSMGRYLLAAMAAEGIDCSHVVCDATQKTGFQFKGKVTDGSDPPVEYHRKGSAASHMGVADIDEAWLLSARHLHATGVFPAISATTLPAARKTMDLMRAAGRSVSFDPNLRPTLWATPELMRDAINDLATRADWVLPGMEEGRFLTGETTPEGVARFYRQLGAKLVVVKLGAEGAYFDGEAGSGRVAGFPVAEVVDTVGAGDGFAVGVISALLDGLGVPEAVKRGAWIGARAVQVLGDSEGLPTRAELNAA 312
               SCOP domains d4du5a_ A: automated matches                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...eeeeee....hhhhh.eeeeeeehhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhh...eeeeeee.......eeee......--..eeee....hhhhhhhhhhhhhhhh.eeeeeee.hhhhh..hhhhhhhhhhhhhhhh..eeeee...hhhhh.hhhhhhhhhhhhhh...ee..hhhhhhhhhh..hhhhhhhhhhhh...eeeee.hhh.eeeee..eeeee.....-------.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh------...hhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4du5 A  26 ALDVITFGEAmmLLVADRPGPLEHAEAFHKRTAGAETNVAIGLARLGLKVGWASRLGTDSmGRYLLAAmAAEGIDCSHVVCDATQKTGFQFKGKVTDG--PPVEYHRKGSAASHmGVADIDEAWLLSARHLHATGVFPAISATTLPAARKTmDLmRAAGRSVSFDPNLRPTLWATPELmRDAINDLATRADWVLPGmEEGRFLTGETTPEGVARFYRQLGAKLVVVKLGAEGAYFDGEAGSGRVAGFPV-------GAGDGFAVGVISALLDGLGVPEAVKRGAWIGARAVQ------GLPTRAELNAA 334
                                    35||      45        55        65        75        85|       95       105       115       | -|      135    |  145       155       165       175 |  |  185       195       205       215      |225       235       245       255       265        |-      |285       295       305       315 |     325         
                                     36-MSE                                            86-MSE  94-MSE                      123  |           140-MSE                              177-MSE                    204-MSE           222-MSE                                             274     282                                317    324          
                                      37-MSE                                                                                  126                                                   180-MSE                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:295
 aligned with Q12CR9_POLSJ | Q12CR9 from UniProtKB/TrEMBL  Length:314

    Alignment length:310
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313
         Q12CR9_POLSJ     4 ALDVITFGEAMMLLVADRPGPLEHAEAFHKRTAGAETNVAIGLARLGLKVGWASRLGTDSMGRYLLAAMAAEGIDCSHVVCDATQKTGFQFKGKVTDGSDPPVEYHRKGSAASHMGVADIDEAWLLSARHLHATGVFPAISATTLPAARKTMDLMRAAGRSVSFDPNLRPTLWATPELMRDAINDLATRADWVLPGMEEGRFLTGETTPEGVARFYRQLGAKLVVVKLGAEGAYFDGEAGSGRVAGFPVAEVVDTVGAGDGFAVGVISALLDGLGVPEAVKRGAWIGARAVQVLGDSEGLPTRAELNAAK 313
               SCOP domains d4du5b_ B: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...eeeeee....hhhhh.eeeeeeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhh.......eeee......eeee......--..eeee....hhhhh.....hhhhhhheeeeeee.hhhhh..hhhhhhhhhhhhhhh...eeeee...hhhhh.hhhhhhhhhhhhhh...ee..hhhhhhhhhh..hhhhhhhhhhhhh..eeeeeee..eeeeee..eeeee.....-------.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.------...hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4du5 B  26 ALDVITFGEAmmLLVADRPGPLEHAEAFHKRTAGAETNVAIGLARLGLKVGWASRLGTDSmGRYLLAAmAAEGIDCSHVVCDATQKTGFQFKGKVTDG--PPVEYHRKGSAASHmGVADIDEAWLLSARHLHATGVFPAISATTLPAARKTmDLmRAAGRSVSFDPNLRPTLWATPELmRDAINDLATRADWVLPGmEEGRFLTGETTPEGVARFYRQLGAKLVVVKLGAEGAYFDGEAGSGRVAGFPV-------GAGDGFAVGVISALLDGLGVPEAVKRGAWIGARAVQ------GLPTRAELNAAK 335
                                    35||      45        55        65        75        85|       95       105       115       | -|      135    |  145       155       165       175 |  |  185       195       205       215      |225       235       245       255       265        |-      |285       295       305       315 |     325       335
                                     36-MSE                                            86-MSE  94-MSE                      123  |           140-MSE                              177-MSE                    204-MSE           222-MSE                                             274     282                                317    324           
                                      37-MSE                                                                                  126                                                   180-MSE                                                                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:294
 aligned with Q12CR9_POLSJ | Q12CR9 from UniProtKB/TrEMBL  Length:314

    Alignment length:309
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303         
         Q12CR9_POLSJ     4 ALDVITFGEAMMLLVADRPGPLEHAEAFHKRTAGAETNVAIGLARLGLKVGWASRLGTDSMGRYLLAAMAAEGIDCSHVVCDATQKTGFQFKGKVTDGSDPPVEYHRKGSAASHMGVADIDEAWLLSARHLHATGVFPAISATTLPAARKTMDLMRAAGRSVSFDPNLRPTLWATPELMRDAINDLATRADWVLPGMEEGRFLTGETTPEGVARFYRQLGAKLVVVKLGAEGAYFDGEAGSGRVAGFPVAEVVDTVGAGDGFAVGVISALLDGLGVPEAVKRGAWIGARAVQVLGDSEGLPTRAELNAA 312
               SCOP domains d4du5c_ C: automated matches                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...eeeeee..........eeeeeeehhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhh...eeeeeee.......eeee.....--...eeee...hhhhhhhhhhhhhhhhh.eeeeeee.hhhhh..hhhhhhhhhhhhhhhh..eeeee...hhhhh.hhhhhhhhhhhhhhhh.ee..hhhhhhhhhh..hhhhhhhhhhhh...eeeee.hhh.eeeee..eeeee.....-------.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.------...hhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4du5 C  26 ALDVITFGEAmmLLVADRPGPLEHAEAFHKRTAGAETNVAIGLARLGLKVGWASRLGTDSmGRYLLAAmAAEGIDCSHVVCDATQKTGFQFKGKVTD--DPPVEYHRKGSAASHmGVADIDEAWLLSARHLHATGVFPAISATTLPAARKTmDLmRAAGRSVSFDPNLRPTLWATPELmRDAINDLATRADWVLPGmEEGRFLTGETTPEGVARFYRQLGAKLVVVKLGAEGAYFDGEAGSGRVAGFPV-------GAGDGFAVGVISALLDGLGVPEAVKRGAWIGARAVQ------GLPTRAELNAA 334
                                    35||      45        55        65        75        85|       95       105       115      |125       135    |  145       155       165       175 |  |  185       195       205       215      |225       235       245       255       265        |-      |285       295       305       315 |     325         
                                     36-MSE                                            86-MSE  94-MSE                     122  |            140-MSE                              177-MSE                    204-MSE           222-MSE                                             274     282                                317    324          
                                      37-MSE                                                                                 125                                                    180-MSE                                                                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:294
 aligned with Q12CR9_POLSJ | Q12CR9 from UniProtKB/TrEMBL  Length:314

    Alignment length:310
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313
         Q12CR9_POLSJ     4 ALDVITFGEAMMLLVADRPGPLEHAEAFHKRTAGAETNVAIGLARLGLKVGWASRLGTDSMGRYLLAAMAAEGIDCSHVVCDATQKTGFQFKGKVTDGSDPPVEYHRKGSAASHMGVADIDEAWLLSARHLHATGVFPAISATTLPAARKTMDLMRAAGRSVSFDPNLRPTLWATPELMRDAINDLATRADWVLPGMEEGRFLTGETTPEGVARFYRQLGAKLVVVKLGAEGAYFDGEAGSGRVAGFPVAEVVDTVGAGDGFAVGVISALLDGLGVPEAVKRGAWIGARAVQVLGDSEGLPTRAELNAAK 313
               SCOP domains d4du5d_ D: autom ated matches                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...eeeee.-...hhhhh.eeeeeeehhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhh..eeeeeeee......eeeee.....--...eeee...hhhhhhhhhhhhhhhhhheeeeeee.hhhhh..hhhhhhhhhhhhhhhh..eeeee...hhhhh.hhhhhhhhhhhhhhhh.ee..hhhhhhhhhh..hhhhhhhhhhhh...eeeeeee..eeeeee..eeeee.....-------.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.------...hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4du5 D  26 ALDVITFGEAmmLLVA-RPGPLEHAEAFHKRTAGAETNVAIGLARLGLKVGWASRLGTDSmGRYLLAAmAAEGIDCSHVVCDATQKTGFQFKGKVTD--DPPVEYHRKGSAASHmGVADIDEAWLLSARHLHATGVFPAISATTLPAARKTmDLmRAAGRSVSFDPNLRPTLWATPELmRDAINDLATRADWVLPGmEEGRFLTGETTPEGVARFYRQLGAKLVVVKLGAEGAYFDGEAGSGRVAGFPV-------GAGDGFAVGVISALLDGLGVPEAVKRGAWIGARAVQ------GLPTRAELNAAK 335
                                    35||   | |45        55        65        75        85|       95       105       115      |125       135    |  145       155       165       175 |  |  185       195       205       215      |225       235       245       255       265        |-      |285       295       305       315 |     325       335
                                     36-MSE1 |                                         86-MSE  94-MSE                     122  |            140-MSE                              177-MSE                    204-MSE           222-MSE                                             274     282                                317    324           
                                      37-MSE43                                                                               125                                                    180-MSE
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DU5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DU5)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q12CR9_POLSJ | Q12CR9)
molecular function
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0016773    phosphotransferase activity, alcohol group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
    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: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.

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