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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SERINE PHOSPHATASE OF RNA POLYMERASE II CTD (SSU72 SUPERFAMILY) FROM DROSOPHILA MELANOGASTER. ORTHORHOMBIC CRYSTAL FORM. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET FR253.
 
Authors :  A. P. Kuzin, Y. Chen, J. Seetharaman, F. Forouhar, Y. Chinag, Y. Fang, K. Cunningham, L. -C. Ma, R. Xiao, J. Liu, M. C. Baran, T. B. Acton, B. Rost, G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (Nesg)
Date :  25 Nov 08  (Deposition) - 06 Jan 09  (Release) - 06 Jan 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Fr253 Phosphatase Ctd Serine Nesg Structure Drosofila Melanogaster, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. P. Kuzin, Y. Chen, J. Seetharaman, F. Forouhar, Y. Chinag, Y. Fang, K. Cunningham, L. -C. Ma, R. Xiao, J. Liu, M. C. Baran, T. B. Acton, B. Rost, G. T. Montelione, J. F. Hunt, L. Tong
Orthorombic Crystal Structure Of Serine Phosphatase Of Rna Polymerase Ii Ctd From Fly Drosofila Melanogaster. Northeast Structural Genomics Consortium Target Fr253.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FR253
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3) + MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CG14216, DMEL_CG14216
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: CG14216-PA (LD40846P)

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 44)

Asymmetric Unit (1, 44)
No.NameCountTypeFull Name
1MSE44Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 11)
No.NameCountTypeFull Name
1MSE11Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 11)
No.NameCountTypeFull Name
1MSE11Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 11)
No.NameCountTypeFull Name
1MSE11Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (1, 11)
No.NameCountTypeFull Name
1MSE11Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3FDF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FDF)

(-) 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:191
 aligned with Q9VWE4_DROME | Q9VWE4 from UniProtKB/TrEMBL  Length:195

    Alignment length:191
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194 
         Q9VWE4_DROME     5 SKLAVAVVCSSNMNRSMEAHNFLAKKGFNVRSYGTGERVKLPGMAFDKPNVYEFGTKYEDIYRDLESKDKEFYTQNGLLHMLDRNRRIKKCPERFQDTKEQFDIIVTVEERVYDLVVMHMESMESVDNRPVHVLNVDVVDNAEDALMGAFVITDMINMMAKSTDLDNDIDELIQEFEERRKRVILHSVLFY 195
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhh..eeeee.....eee........eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh.....eeee.hhhhhhhhhhhhhh.......eeeeeee......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..ee..eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fdf A   5 SKLAVAVVCSSNmNRSmEAHNFLAKKGFNVRSYGTGERVKLPGmAFDKPNVYEFGTKYEDIYRDLESKDKEFYTQNGLLHmLDRNRRIKKCPERFQDTKEQFDIIVTVEERVYDLVVmHmESmESVDNRPVHVLNVDVVDNAEDALmGAFVITDmINmmAKSTDLDNDIDELIQEFEERRKRVILHSVLFY 195
                                    14  |   | 24        34        44   |    54        64        74        84|       94       104       114       124  |    134       144      |154    |  164       174       184       194 
                                       17-MSE                         48-MSE                               85-MSE                              122-MSE|                     151-MSE 159-MSE                                
                                           21-MSE                                                                                                124-MSE                               162-MSE                             
                                                                                                                                                    127-MSE                             163-MSE                            


Chain B from PDB  Type:PROTEIN  Length:191
 aligned with Q9VWE4_DROME | Q9VWE4 from UniProtKB/TrEMBL  Length:195

    Alignment length:191
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194 
         Q9VWE4_DROME     5 SKLAVAVVCSSNMNRSMEAHNFLAKKGFNVRSYGTGERVKLPGMAFDKPNVYEFGTKYEDIYRDLESKDKEFYTQNGLLHMLDRNRRIKKCPERFQDTKEQFDIIVTVEERVYDLVVMHMESMESVDNRPVHVLNVDVVDNAEDALMGAFVITDMINMMAKSTDLDNDIDELIQEFEERRKRVILHSVLFY 195
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....hhhhhhhhhhhhh...eeeee....eee........eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh.....eeee.hhhhhhhhhhhhhh.......eeeeee.......hhhhhhhhhhhh.........hhhhhhhhhhhhhhhh.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fdf B   5 SKLAVAVVCSSNmNRSmEAHNFLAKKGFNVRSYGTGERVKLPGmAFDKPNVYEFGTKYEDIYRDLESKDKEFYTQNGLLHmLDRNRRIKKCPERFQDTKEQFDIIVTVEERVYDLVVmHmESmESVDNRPVHVLNVDVVDNAEDALmGAFVITDmINmmAKSTDLDNDIDELIQEFEERRKRVILHSVLFY 195
                                    14  |   | 24        34        44   |    54        64        74        84|       94       104       114       124  |    134       144      |154    |  164       174       184       194 
                                       17-MSE                         48-MSE                               85-MSE                              122-MSE|                     151-MSE 159-MSE                                
                                           21-MSE                                                                                                124-MSE                               162-MSE                             
                                                                                                                                                    127-MSE                             163-MSE                            


Chain C from PDB  Type:PROTEIN  Length:191
 aligned with Q9VWE4_DROME | Q9VWE4 from UniProtKB/TrEMBL  Length:195

    Alignment length:191
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194 
         Q9VWE4_DROME     5 SKLAVAVVCSSNMNRSMEAHNFLAKKGFNVRSYGTGERVKLPGMAFDKPNVYEFGTKYEDIYRDLESKDKEFYTQNGLLHMLDRNRRIKKCPERFQDTKEQFDIIVTVEERVYDLVVMHMESMESVDNRPVHVLNVDVVDNAEDALMGAFVITDMINMMAKSTDLDNDIDELIQEFEERRKRVILHSVLFY 195
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....hhhhhhhhhhhhh...eeeee....eeeeeee..eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.....eeee.hhhhhhhhhhhhh........eeeeeee....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..ee..eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fdf C   5 SKLAVAVVCSSNmNRSmEAHNFLAKKGFNVRSYGTGERVKLPGmAFDKPNVYEFGTKYEDIYRDLESKDKEFYTQNGLLHmLDRNRRIKKCPERFQDTKEQFDIIVTVEERVYDLVVmHmESmESVDNRPVHVLNVDVVDNAEDALmGAFVITDmINmmAKSTDLDNDIDELIQEFEERRKRVILHSVLFY 195
                                    14  |   | 24        34        44   |    54        64        74        84|       94       104       114       124  |    134       144      |154    |  164       174       184       194 
                                       17-MSE                         48-MSE                               85-MSE                              122-MSE|                     151-MSE 159-MSE                                
                                           21-MSE                                                                                                124-MSE                               162-MSE                             
                                                                                                                                                    127-MSE                             163-MSE                            


Chain D from PDB  Type:PROTEIN  Length:191
 aligned with Q9VWE4_DROME | Q9VWE4 from UniProtKB/TrEMBL  Length:195

    Alignment length:191
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194 
         Q9VWE4_DROME     5 SKLAVAVVCSSNMNRSMEAHNFLAKKGFNVRSYGTGERVKLPGMAFDKPNVYEFGTKYEDIYRDLESKDKEFYTQNGLLHMLDRNRRIKKCPERFQDTKEQFDIIVTVEERVYDLVVMHMESMESVDNRPVHVLNVDVVDNAEDALMGAFVITDMINMMAKSTDLDNDIDELIQEFEERRKRVILHSVLFY 195
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.........hhhhhhh....eeeee....eee........eee....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.................eeee.hhhhhhhhhhhhhh.......eeeeee.....hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh........eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fdf D   5 SKLAVAVVCSSNmNRSmEAHNFLAKKGFNVRSYGTGERVKLPGmAFDKPNVYEFGTKYEDIYRDLESKDKEFYTQNGLLHmLDRNRRIKKCPERFQDTKEQFDIIVTVEERVYDLVVmHmESmESVDNRPVHVLNVDVVDNAEDALmGAFVITDmINmmAKSTDLDNDIDELIQEFEERRKRVILHSVLFY 195
                                    14  |   | 24        34        44   |    54        64        74        84|       94       104       114       124  |    134       144      |154    |  164       174       184       194 
                                       17-MSE                         48-MSE                               85-MSE                              122-MSE|                     151-MSE 159-MSE                                
                                           21-MSE                                                                                                124-MSE                               162-MSE                             
                                                                                                                                                    127-MSE                             163-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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q9VWE4_DROME | Q9VWE4)
molecular function
    GO:0008420    CTD phosphatase activity    Catalysis of the reaction: phospho-(DNA-directed RNA polymerase) + H2O = (DNA-directed RNA polymerase) + phosphate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
biological process
    GO:0070940    dephosphorylation of RNA polymerase II C-terminal domain    The process of removing a phosphate group from an amino acid residue in the C-terminal domain of RNA polymerase II. Some dephosphorylation occurs during transcription while some may occur after the enzyme is released from the template in order to prepare it for the beginning of the transcription cycle again. RNA polymerase II with little or no phosphorylation is referred to as the hypophosphorylated or II(A) form.
    GO:0031124    mRNA 3'-end processing    Any process involved in forming the mature 3' end of an mRNA molecule.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
cellular component
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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        Q9VWE4_DROME | Q9VWE4: 3fmv 3omw 3omx 3p9y 4imi 4imj 4ygx

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