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(-) Description

Title :  CRYSTAL STRUCTURE OF A NOVEL-TYPE PHOSPHOSERINE PHOSPHATASE MUTANT (H9A) FROM HYDROGENOBACTER THERMOPHILUS TK-6 IN COMPLEX WITH L-PHOSPHOSERINE
 
Authors :  Y. Chiba, S. Horita, J. Ohtsuka, H. Arai, K. Nagata, Y. Igarashi, M. Tano M. Ishii
Date :  21 Dec 12  (Deposition) - 20 Mar 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phosphatase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Chiba, S. Horita, J. Ohtsuka, H. Arai, K. Nagata, Y. Igarashi, M. Tanokura, M. Ishii
Structural Units Important For Activity Of A Novel-Type Phosphoserine Phosphatase From Hydrogenobacter Thermophilus Tk-6 Revealed By Crystal Structure Analysis
J. Biol. Chem. V. 288 11448 2013
PubMed-ID: 23479726  |  Reference-DOI: 10.1074/JBC.M112.449561

(-) Compounds

Molecule 1 - PHOSPHOSERINE PHOSPHATASE 1
    Chains: A, B
    EC Number: 3.1.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PSPA, PGMA, HTH_0103, HYDTH_0104
    Mutation: YES
    Organism Scientific: HYDROGENOBACTER THERMOPHILUS
    Organism Taxid: 608538
    Strain: DSM 6534 / IAM 12695 / TK-6
    Synonym: PSP 1, PSPASE 1, METAL-INDEPENDENT PHOSPHOSERINE PHOSPHATASE 1, IPSP1, O-PHOSPHOSERINE PHOSPHOHYDROLASE 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EDO7Ligand/Ion1,2-ETHANEDIOL
3SEP2Mod. ResiduePHOSPHOSERINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:8 , ASN A:15 , GLN A:21 , GLY A:22 , ARG A:58 , GLU A:82 , HIS A:85 , HIS A:150 , THR A:151 , CL A:302 , HOH A:406 , HOH A:419BINDING SITE FOR RESIDUE SEP A 301
02AC2SOFTWARESEP A:301BINDING SITE FOR RESIDUE CL A 302
03AC3SOFTWARESER A:29 , GLU A:30 , HOH A:416 , HOH A:423 , MET B:87 , GLY B:118BINDING SITE FOR RESIDUE EDO A 303
04AC4SOFTWAREALA A:160 , ASN A:189BINDING SITE FOR RESIDUE EDO A 304
05AC5SOFTWAREARG B:8 , ASN B:15 , TYR B:20 , GLN B:21 , GLY B:22 , ARG B:58 , GLU B:82 , HIS B:85 , HIS B:150 , THR B:151 , CL B:302 , HOH B:403 , HOH B:406BINDING SITE FOR RESIDUE SEP B 301
06AC6SOFTWARESEP B:301 , HOH B:414BINDING SITE FOR RESIDUE CL B 302
07AC7SOFTWARELYS B:130 , ASN B:189BINDING SITE FOR RESIDUE EDO B 303
08AC8SOFTWAREASP B:49 , VAL B:50 , ILE B:51 , LEU B:72 , GLU B:73BINDING SITE FOR RESIDUE EDO B 304
09AC9SOFTWARESER A:89 , MET A:91 , HOH A:446 , TRP B:14 , ARG B:19BINDING SITE FOR RESIDUE EDO B 305
10BC1SOFTWAREGLU A:13 , TRP A:14 , VAL A:17 , ARG A:19 , MET B:87 , SER B:89 , MET B:91 , HOH B:422BINDING SITE FOR RESIDUE EDO B 306
11BC2SOFTWAREASP B:103 , ARG B:106 , VAL B:114 , GLU B:115 , HOH B:426BINDING SITE FOR RESIDUE EDO B 307

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:198 -B:198

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4IJ6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IJ6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4IJ6)

(-) Exons   (0, 0)

(no "Exon" information available for 4IJ6)

(-) Sequences/Alignments

Asymmetric/Biological 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:207
                                                                                                                                                                                                                                               
               SCOP domains d4ij6a_ A: automated matches                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....................hhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhh...eee.hhhh...hhhhh..hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhh.hhhhhhhh......eeeeee....eeeeeeeehhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ij6 A   1 MVKLILVRAAESEWNPVGRYQGLLDPDLSERGKKQAKLLAQELSREHLDVIYSSPLKRTYLTALEIAEAKNLEVIKEDRIIEIDHGMWSGMLVEEVMEKYPEDFRRWVEEPHKVEFQGGESLASVYNRVKGFLEEVRKRHWNQTVVVVSHTVPMRAMYCALLGVDLSKFWSFGCDNASYSVIHMEERRNVILKLNITCHLGEFYVEA 207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       


Chain B from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                           
               SCOP domains d4ij6b_ B: automated matches                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....................hhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhh..eee.hhhh...hhhhh..hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhh.hhhhhhhh......eeeeee....eeeeeeeehhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ij6 B   1 MVKLILVRAAESEWNPVGRYQGLLDPDLSERGKKQAKLLAQELSREHLDVIYSSPLKRTYLTALEIAEAKNLEVIKEDRIIEIDHGMWSGMLVEEVMEKYPEDFRRWVEEPHKVEFQGGESLASVYNRVKGFLEEVRKRHWNQTVVVVSHTVPMRAMYCALLGVDLSKFWSFGCDNASYSVIHMEERRNVILKLNITCHLGEF 203
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4IJ6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4IJ6)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/Swiss-Prot
        PSPA_HYDTT | D3DFG8: 4ij5

(-) Related Entries Specified in the PDB File

4ij5