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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PHOSPHATASE DOMAIN OF C. THERMOCELLUM (BACTERIAL) PNKP
 
Authors :  L. Wang, P. Smith, S. Shuman
Date :  11 Feb 13  (Deposition) - 10 Apr 13  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha/Beta Fold, Calcineurin-Like, Phosphatase, Metalloenzyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. K. Wang, P. Smith, S. Shuman
Structure And Mechanism Of The 2', 3' Phosphatase Component Of The Bacterial Pnkp-Hen1 Rna Repair System.
Nucleic Acids Res. V. 41 5864 2013
PubMed-ID: 23595150  |  Reference-DOI: 10.1093/NAR/GKT221

(-) Compounds

Molecule 1 - METALLOPHOSPHOESTERASE
    Chains: A, B
    EC Number: 3.1.3.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28-SMT
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PHOSPHATASE DOMAIN (RESIDUES 171-424)
    Gene: CTHE_2768
    Organism Scientific: CLOSTRIDIUM THERMOCELLUM
    Organism Taxid: 203119
    Strain: ATCC 27405 / DSM 1237

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 17)

Asymmetric Unit (5, 17)
No.NameCountTypeFull Name
1CIT3Ligand/IonCITRIC ACID
2GOL8Ligand/IonGLYCEROL
3MN2Ligand/IonMANGANESE (II) ION
4PG43Ligand/IonTETRAETHYLENE GLYCOL
5PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2GOL3Ligand/IonGLYCEROL
3MN-1Ligand/IonMANGANESE (II) ION
4PG42Ligand/IonTETRAETHYLENE GLYCOL
5PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 2 (3, 7)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2GOL5Ligand/IonGLYCEROL
3MN-1Ligand/IonMANGANESE (II) ION
4PG41Ligand/IonTETRAETHYLENE GLYCOL
5PGE-1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:427 , HIS A:428 , HOH A:720 , HOH A:766 , SER B:335 , GLY B:336 , LYS B:337 , TYR B:354BINDING SITE FOR RESIDUE CIT A 501
02AC2SOFTWARELYS A:176 , VAL A:313 , GLY A:317 , GLN A:331 , GLY A:332 , TYR A:366 , GLY A:368 , LYS A:369 , ALA A:370 , HOH A:719BINDING SITE FOR RESIDUE PGE A 502
03AC3SOFTWARELYS A:201 , ARG A:405 , GLU A:410 , ILE A:411 , VAL A:412 , HOH A:627 , HOH A:737BINDING SITE FOR RESIDUE PG4 A 503
04AC4SOFTWAREGLU A:328 , GLU A:329BINDING SITE FOR RESIDUE PG4 A 504
05AC5SOFTWAREGLU A:346 , THR A:347 , TYR B:344BINDING SITE FOR RESIDUE GOL A 505
06AC6SOFTWAREASN A:263 , HIS A:264 , HIS A:281 , CIT A:509 , HOH A:761 , HOH A:788 , GLY B:349 , GLU B:350 , THR B:351BINDING SITE FOR RESIDUE GOL A 506
07AC7SOFTWAREGLU A:224 , ARG B:367 , LYS B:369 , HOH B:654BINDING SITE FOR RESIDUE GOL A 507
08AC8SOFTWAREASP A:187 , HIS A:189 , ASP A:233 , CIT A:509 , HOH A:602BINDING SITE FOR RESIDUE MN A 508
09AC9SOFTWAREASP A:187 , HIS A:189 , ASP A:233 , ARG A:237 , ASN A:263 , HIS A:264 , HIS A:323 , HIS A:376 , PRO A:378 , GOL A:506 , MN A:508 , HOH A:602 , HOH A:614 , HOH A:621 , HOH A:643 , HOH A:770 , THR B:351BINDING SITE FOR RESIDUE CIT A 509
10BC1SOFTWAREASP B:187 , HIS B:189 , ASP B:233 , CIT B:502 , HOH B:603BINDING SITE FOR RESIDUE MN B 501
11BC2SOFTWAREGLU A:350 , THR A:351 , HOH A:757 , ASP B:187 , HIS B:189 , ASP B:233 , ARG B:237 , ASN B:263 , HIS B:264 , HIS B:281 , HIS B:323 , HIS B:376 , PRO B:378 , MN B:501 , HOH B:602 , HOH B:603 , HOH B:620 , HOH B:715BINDING SITE FOR RESIDUE CIT B 502
12BC3SOFTWARELYS B:175 , VAL B:252 , LYS B:253 , SER B:254 , GLY B:255 , LEU B:258 , HOH B:611 , HOH B:649 , HOH B:723 , HOH B:729BINDING SITE FOR RESIDUE PG4 B 503
13BC4SOFTWARETHR A:351 , GLY A:355 , SER B:169 , MET B:170 , THR B:377 , PRO B:378 , HOH B:715BINDING SITE FOR RESIDUE GOL B 504
14BC5SOFTWAREGLU A:340 , TYR A:344 , THR B:347 , GLY B:349BINDING SITE FOR RESIDUE GOL B 505
15BC6SOFTWARELYS B:327 , GLU B:346 , THR B:347 , TYR B:360BINDING SITE FOR RESIDUE GOL B 506
16BC7SOFTWAREGLU B:328 , GLU B:329 , HOH B:634BINDING SITE FOR RESIDUE GOL B 507
17BC8SOFTWAREASN B:273 , LYS B:302 , ALA B:303BINDING SITE FOR RESIDUE GOL B 508

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J6O)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Gly A:180 -Pro A:181
2Tyr A:406 -Pro A:407
3Gly B:180 -Pro B:181
4Tyr B:406 -Pro B:407
5Leu B:425 -Glu B:426

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J6O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J6O)

(-) Exons   (0, 0)

(no "Exon" information available for 4J6O)

(-) 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:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee......eeee.....hhhhhhhhhhhh..eeee....hhhh.eeee.....eeee.........hhhhhhhhhhhhhhh..eee..hhhhhhhhhhhh........hhhhhhhhhh..hhhhhhhhhhhhhh....eee....eee.....hhhhh...hhhhhhhhhhh.eeeee.....eee...........eeee........ee...eee...hhhhh.eeeeeee...eeeeee.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j6o A 169 SMLWNNKKDEHGPFDIIGDIHGCYDELKMLLEKLGYLIEEVEGGVGSGKYRVTHPEGRKVLFLGDLVDRGPKITEVLKLVMGMVKSGIALCVPGNHDVKLLRKLNGRDVQITHGLDRTLEQLAKEPQEFIEEVKAFIDGLVSHYVLDDGKLVVAHAGMKEEFQGRGSGKVREFALYGETTGETDEYGLPVRYDWASDYRGKALVVYGHTPQAEVLKVNNTINIDTGCVFGGKLTAYRYPEREIVDVKALKTYYEPALEHHH 429
                                   178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428 


Chain B from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....ee......eeee.....hhhhhhhhhhhh..eeee....hhhh.eeee.....eeee.........hhhhhhhhhhhhhhh..eee..hhhhhhhhhhhhh.......hhhhhhhhhhh.hhhhhhhhhhhhhh....eee....eee.....hhhhh...hhhhhhhhhhh.eeeee.....eee.hhhhhh....eeee........eee..eee...hhhhh.eeeeeee...eeeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4j6o B 169 SMLWNNKKDEHGPFDIIGDIHGCYDELKMLLEKLGYLIEEVEGGVGSGKYRVTHPEGRKVLFLGDLVDRGPKITEVLKLVMGMVKSGIALCVPGNHDVKLLRKLNGRDVQITHGLDRTLEQLAKEPQEFIEEVKAFIDGLVSHYVLDDGKLVVAHAGMKEEFQGRGSGKVREFALYGETTGETDEYGLPVRYDWASDYRGKALVVYGHTPQAEVLKVNNTINIDTGCVFGGKLTAYRYPEREIVDVKALKTYYEPALE 426
                                   178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418
   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 4J6O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J6O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J6O)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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UniProtKB/TrEMBL
        A3DJ38_CLOTH | A3DJ38: 3ty5 3ty8 3ty9 4drf 4e6n 4gp6 4gp7 4jst 4jsy 4jt2 4jt4 4mde 4mdf 4qm6 4qm7

(-) Related Entries Specified in the PDB File

3ty5 CRYSTAL STRUCTURE OF C. THERMOCELLUM PNKP LIGASE DOMAIN IN COMPLEX WITH ATP
3ty8 CRYSTAL STRUCTURE OF C. THERMOCELLUM PNKP LIGASE DOMAIN APO FORM
3ty9 CRYSTAL STRUCTURE OF C. THERMOCELLUM PNKP LIGASE DOMAIN AMP -ADENYLATE
4gp6 CRYSTAL STRUCTURE OF C. THERMOCELLUM PNKP KINASE DOMAIN
4gp7 CRYSTAL STRUCTURE OF C. THERMOCELLUM PNKP KINASE DOMAIN