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(-) Description

Title :  CRYSTAL STRUCTURE OF A PHOSPHOSERINE PHOSPHATASE (SERB) FROM HELICOBACTER PYLORI
 
Authors :  B. Syed Ibrahim, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  05 Mar 10  (Deposition) - 23 Mar 10  (Release) - 23 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Nysgxrc, Psi Ii, Phophoserine Phosphatase, Protein Structure Initiative, Structural Genomics, New York Sgx Research Center For Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Syed Ibrahim, S. K. Burley, S. Swaminathan
Crystal Structure Of A Phosphoserine Phosphatase (Serb) From Helicobacter Pylori
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHOSERINE PHOSPHATASE (SERB)
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3) RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HP_0652
    Organism Common: CAMPYLOBACTER PYLORI
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 33)

Asymmetric Unit (3, 33)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION
2MG5Ligand/IonMAGNESIUM ION
3MSE23Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 11)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION
3MSE11Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION
3MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:8 , ASP A:10 , ASP A:164 , HOH A:319 , HOH A:321 , HOH A:323BINDING SITE FOR RESIDUE MG A 300
02AC2SOFTWAREASP A:8 , GLY A:97 , LYS A:141 , ASN A:167 , HOH A:323BINDING SITE FOR RESIDUE CL A 302
03AC3SOFTWAREPHE A:46 , HIS A:47 , SER A:138BINDING SITE FOR RESIDUE CL A 303
04AC4SOFTWAREASP B:8 , ASP B:10 , ASP B:164 , HOH B:315 , HOH B:316 , HOH B:324BINDING SITE FOR RESIDUE MG B 300
05AC5SOFTWAREGLY B:97 , LYS B:141 , ASN B:167BINDING SITE FOR RESIDUE CL B 302
06AC6SOFTWAREASP C:8 , ASP C:10 , ASP C:164 , HOH C:313 , HOH C:317 , HOH C:326BINDING SITE FOR RESIDUE MG C 300
07AC7SOFTWAREGLY C:97 , LYS C:141BINDING SITE FOR RESIDUE CL C 302
08AC8SOFTWAREASP C:199 , HOH C:312BINDING SITE FOR RESIDUE MG C 301
09AC9SOFTWAREASP D:8 , ASP D:10 , ASP D:164 , HOH D:328BINDING SITE FOR RESIDUE MG D 300
10BC1SOFTWAREASP D:8 , GLY D:97 , LYS D:141 , ASN D:167 , HOH D:327BINDING SITE FOR RESIDUE CL D 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M1Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3M1Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M1Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3M1Y)

(-) Exons   (0, 0)

(no "Exon" information available for 3M1Y)

(-) 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:203
 aligned with O25367_HELPY | O25367 from UniProtKB/TrEMBL  Length:207

    Alignment length:207
                             1                                                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       
         O25367_HELPY     - -MQKLAVFDFDSTLVNAETIESLARAWGVFDEVKTITLKAMNGETDFHKSLILRVSKLKNMPLKLAKEVCESLPLFEGALELVSALKEKNYKVVCFSGGFDLATNHYRDLLHLDAAFSNTLIVENDALNGLVTGHMMFSHSKGEMLLVLQRLLNISKTNTLVVGDGANDLSMFKHAHIKIAFNAKEVLKQHATHCINEPDLALIKPL 206
               SCOP domains d3m1ya_ A: automated matches                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee........hhhhhhhhhh.hhhhhh.....----..hhhhhhhhhhhh....hhhhhhhhhh......hhhhhhhhhhh..eeeeeeeeeehhhhhhhhhhhh..eeeeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhh.....eeeee.hhhhhhhhh...eeeee..hhhhhh...eee...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m1y A   0 SLQKLAVFDFDSTLVNAETIESLARAWGVFDEVKTITLK----ETDFHKSLILRVSKLKNmPLKLAKEVCESLPLFEGALELVSALKEKNYKVVCFSGGFDLATNHYRDLLHLDAAFSNTLIVENDALNGLVTGHmmFSHSKGEmLLVLQRLLNISKTNTLVVGDGANDLSmFKHAHIKIAFNAKEVLKQHATHCINEPDLALIKPL 206
                                     9        19        29        |-   |    49        59|       69        79        89        99       109       119       129     ||139    |  149       159       169 |     179       189       199       
                                                                 38   43               60-MSE                                                                    135-MSE  144-MSE                    171-MSE                               
                                                                                                                                                                  136-MSE                                                                  


Chain B from PDB  Type:PROTEIN  Length:206
 aligned with O25367_HELPY | O25367 from UniProtKB/TrEMBL  Length:207

    Alignment length:206
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201      
         O25367_HELPY     2 QKLAVFDFDSTLVNAETIESLARAWGVFDEVKTITLKAMNGETDFHKSLILRVSKLKNMPLKLAKEVCESLPLFEGALELVSALKEKNYKVVCFSGGFDLATNHYRDLLHLDAAFSNTLIVENDALNGLVTGHMMFSHSKGEMLLVLQRLLNISKTNTLVVGDGANDLSMFKHAHIKIAFNAKEVLKQHATHCINEPDLALIKPLI 207
               SCOP domains d3m1yb_ B: automated matches                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee........hhhhhhhhhh.hhhhhhhhhhhhh....hhhhhhhhhhhh....hhhhhhhhhh......hhhhhhhhhhhh.eeeeeeeeeehhhhhhhhhhh...eeeeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhh...eeeee..hhhhhhhh.eee...hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m1y B   2 QKLAVFDFDSTLVNAETIESLARAWGVFDEVKTITLKAmNGETDFHKSLILRVSKLKNmPLKLAKEVCESLPLFEGALELVSALKEKNYKVVCFSGGFDLATNHYRDLLHLDAAFSNTLIVENDALNGLVTGHmmFSHSKGEmLLVLQRLLNISKTNTLVVGDGANDLSmFKHAHIKIAFNAKEVLKQHATHCINEPDLALIKPLI 207
                                    11        21        31        41        51        61        71        81        91       101       111       121       131   ||  141  |    151       161       171       181       191       201      
                                                                 40-MSE              60-MSE                                                                    135-MSE  144-MSE                    171-MSE                                
                                                                                                                                                                136-MSE                                                                   


Chain C from PDB  Type:PROTEIN  Length:208
 aligned with O25367_HELPY | O25367 from UniProtKB/TrEMBL  Length:207

    Alignment length:209
                             1                                                                                                                                                                                                           207 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       | 
         O25367_HELPY     - -MQKLAVFDFDSTLVNAETIESLARAWGVFDEVKTITLKAMNGETDFHKSLILRVSKLKNMPLKLAKEVCESLPLFEGALELVSALKEKNYKVVCFSGGFDLATNHYRDLLHLDAAFSNTLIVENDALNGLVTGHMMFSHSKGEMLLVLQRLLNISKTNTLVVGDGANDLSMFKHAHIKIAFNAKEVLKQHATHCINEPDLALIKPLI-   -
               SCOP domains d3m1yc_ C: automated matches                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee........hhhhhhhhhhhhhhhhhhhhhhh...-.hhhhhhhhhhhhhh...hhhhhhhhh......hhhhhhhhhhhh.eeeeeeeeeehhhhhhhhhhhh..eeeeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhh.....eeeee....hhhhhh...eeeee..hhhhhhhh.eee...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m1y C   0 SLQKLAVFDFDSTLVNAETIESLARAWGVFDEVKTITLKAmNG-TDFHKSLILRVSKLKNmPLKLAKEVCESLPLFEGALELVSALKEKNYKVVCFSGGFDLATNHYRDLLHLDAAFSNTLIVENDALNGLVTGHmmFSHSKGEmLLVLQRLLNISKTNTLVVGDGANDLSmFKHAHIKIAFNAKEVLKQHATHCINEPDLALIKPLIE 208
                                     9        19        29        39| | |   49        59|       69        79        89        99       109       119       129     ||139    |  149       159       169 |     179       189       199         
                                                                   40-MSE              60-MSE                                                                    135-MSE  144-MSE                    171-MSE                                 
                                                                     42 |                                                                                         136-MSE                                                                    
                                                                       44                                                                                                                                                                    


Chain D from PDB  Type:PROTEIN  Length:206
 aligned with O25367_HELPY | O25367 from UniProtKB/TrEMBL  Length:207

    Alignment length:207
                             1                                                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       
         O25367_HELPY     - -MQKLAVFDFDSTLVNAETIESLARAWGVFDEVKTITLKAMNGETDFHKSLILRVSKLKNMPLKLAKEVCESLPLFEGALELVSALKEKNYKVVCFSGGFDLATNHYRDLLHLDAAFSNTLIVENDALNGLVTGHMMFSHSKGEMLLVLQRLLNISKTNTLVVGDGANDLSMFKHAHIKIAFNAKEVLKQHATHCINEPDLALIKPL 206
               SCOP domains d3m1yd_ D: automated matches                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------Hydrolase-3m1yD01 D:17-17 6                                                                                                                                     ------------------------------ Pfam domains (1)
           Pfam domains (2) -----------------Hydrolase-3m1yD02 D:17-17 6                                                                                                                                     ------------------------------ Pfam domains (2)
           Pfam domains (3) -----------------Hydrolase-3m1yD03 D:17-17 6                                                                                                                                     ------------------------------ Pfam domains (3)
           Pfam domains (4) -----------------Hydrolase-3m1yD04 D:17-17 6                                                                                                                                     ------------------------------ Pfam domains (4)
         Sec.struct. author ...eeeeee........hhhhhhhhhh.hhhhhhhhhhhhhh-..hhhhhhhhhhhh....hhhhhhhhhh.......hhhhhhhhhhh.eeeeeeeeeehhhhhhhhhhh...eeeeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhh...eeeee..hhhhhh...eee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m1y D   0 SLQKLAVFDFDSTLVNAETIESLARAWGVFDEVKTITLKAmN-ETDFHKSLILRVSKLKNmPLKLAKEVCESLPLFEGALELVSALKEKNYKVVCFSGGFDLATNHYRDLLHLDAAFSNTLIVENDALNGLVTGHmmFSHSKGEmLLVLQRLLNISKTNTLVVGDGANDLSmFKHAHIKIAFNAKEVLKQHATHCINEPDLALIKPL 206
                                     9        19        29        39|| |    49        59|       69        79        89        99       109       119       129     ||139    |  149       159       169 |     179       189       199       
                                                                   40-MSE              60-MSE                                                                    135-MSE  144-MSE                    171-MSE                               
                                                                    41 |                                                                                          136-MSE                                                                  
                                                                      43
   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 3M1Y)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: HAD (186)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (O25367_HELPY | O25367)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0004647    phosphoserine phosphatase activity    Catalysis of the reaction: L(or D)-O-phosphoserine + H2O = L(or D)-serine + phosphate.
biological process
    GO:0006564    L-serine biosynthetic process    The chemical reactions and pathways resulting in the formation of L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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  3m1y
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  O25367_HELPY | O25367
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