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(-) Description

Title :  CRYSTAL STRUCTURE OF YEDP, PHOSPHATASE-LIKE DOMAIN PROTEIN FROM ESCHERICHIA COLI K12
 
Authors :  Y. Kim, A. Joachimiak, M. Cymborowski, T. Skarina, A. Savchenko, A. Edwards, Midwest Center For Structural Genomics (Mcsg)
Date :  28 Oct 04  (Deposition) - 14 Dec 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.26
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hypothetical Protein, Conserved Protein, Phophatase-Like Domain, Predicted Hydrolase, Sucrose-6F-Phosphate Phosphohydrolase (S6Pp), Structural Genomics, Protein Structure Initiative, Psi, Mcsg, Midwest Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, A. Joachimiak, M. Cymborowski, T. Skarina, A. Savchenko, A. Edwards
Crystal Structure Of Yedp, Phosphatase-Like Domain Protein From Escherichia Coli K12
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE MANNOSYL-3-PHOSPHOGLYCERATE PHOSPHATASE
    Chains: A, B
    EC Number: 3.1.3.70
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Gene: YEDP
    Organism Scientific: ESCHERICHIA COLI K12
    Organism Taxid: 83333
    Strain: K12
    Synonym: MPGP, YEDP

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2PG41Ligand/IonTETRAETHYLENE GLYCOL
3PGE1Ligand/IonTRIETHYLENE GLYCOL
4SO43Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:175 , ALA A:176 , ARG A:177 , PHE A:178 , HIS A:180BINDING SITE FOR RESIDUE SO4 A 501
2AC2SOFTWAREILE A:76 , GLN A:190 , TRP A:194 , HOH A:787BINDING SITE FOR RESIDUE SO4 A 502
3AC3SOFTWARESER B:48 , GLY B:175 , ALA B:176 , ARG B:177 , PHE B:178 , HIS B:180BINDING SITE FOR RESIDUE SO4 B 503
4AC4SOFTWARELEU A:36 , LEU A:212 , TYR A:227 , PG4 A:602 , HOH A:668 , HOH A:740 , HOH A:762BINDING SITE FOR RESIDUE 1PE A 601
5AC5SOFTWAREALA A:29 , TRP A:32 , 1PE A:601 , PGE A:603 , HOH A:761BINDING SITE FOR RESIDUE PG4 A 602
6AC6SOFTWAREPG4 A:602BINDING SITE FOR RESIDUE PGE A 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XVI)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:88 -Pro A:89
2Phe B:88 -Pro B:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XVI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XVI)

(-) Exons   (0, 0)

(no "Exon" information available for 1XVI)

(-) 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:232
 aligned with MPGP_ECOLI | P76329 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:232
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233  
           MPGP_ECOLI     4 IQQPLLVFSDLDGTLLDSHSYDWQPAAPWLTRLREANVPVILCSSKTSAEMLYLQKTLGLQGLPLIAENGAVIQLAEQWQEIDGFPRIISGISHGEISLVLNTLREKEHFKFTTFDDVDDATIAEWTGLSRSQAALTQLHEASVTLIWRDSDERMAQFTARLNELGLQFMQGARFWHVLDASAGKDQAANWIIATYQQLSGKRPTTLGLGDGPNDAPLLEVMDYAVIVKGLN 235
               SCOP domains d1xvia_ A: Putative mannosyl-3-phosphoglycerate phosphatase MPGP (YedP)                                                                                                                                                                  SCOP domains
               CATH domains 1xviA01 A:4-92,A:187-235  [code=3.40.50.1000, no name defined]                           1xviA02 A:93-186 Putative mannosyl-3-phosphoglycerate phosphatase; domain 2                   1xviA01 A:4-92,A:187-235                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee...............hhhhhhhhhhh...eeee...hhhhhhhhhhhh......eeehhh.eee............eee...hhhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhh.hhhhhhhhhh....eeeee..hhhhhhhhhhhhhhh.eeeee....eeeee...hhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhh..eeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xvi A   4 IQQPLLVFSDLDGTLLDSHSYDWQPAAPWLTRLREANVPVILCSSKTSAEMLYLQKTLGLQGLPLIAENGAVIQLAEQWQEIDGFPRIISGISHGEISLVLNTLREKEHFKFTTFDDVDDATIAEWTGLSRSQAALTQLHEASVTLIWRDSDERMAQFTARLNELGLQFMQGARFWHVLDASAGKDQAANWIIATYQQLSGKRPTTLGLGDGPNDAPLLEVMDYAVIVKGLN 235
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233  


Chain B from PDB  Type:PROTEIN  Length:234
 aligned with MPGP_ECOLI | P76329 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:234
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    
           MPGP_ECOLI     1 MFSIQQPLLVFSDLDGTLLDSHSYDWQPAAPWLTRLREANVPVILCSSKTSAEMLYLQKTLGLQGLPLIAENGAVIQLAEQWQEIDGFPRIISGISHGEISLVLNTLREKEHFKFTTFDDVDDATIAEWTGLSRSQAALTQLHEASVTLIWRDSDERMAQFTARLNELGLQFMQGARFWHVLDASAGKDQAANWIIATYQQLSGKRPTTLGLGDGPNDAPLLEVMDYAVIVKGL 234
               SCOP domains d1xvib_ B: Putative mannosyl-3-phosphoglycerate phosphatase MPGP (YedP)                                                                                                                                                                    SCOP domains
               CATH domains 1xviB01 B:1-92,B:187-234  [code=3.40.50.1000, no name defined]                              1xviB02 B:93-186 Putative mannosyl-3-phosphoglycerate phosphatase; domain 2                   1xviB01 B:1-92,B:187-234                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeee...............hhhhhhhhhhh...eeee...hhhhhhhhhhhh......eeehhh.eee............eee...hhhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhh.hhhhhhhhh....eeeeee..hhhhhhhhhhhhhhh.eeeee....eeeee...hhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhh..eeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xvi B   1 MFSIQQPLLVFSDLDGTLLDSHSYDWQPAAPWLTRLREANVPVILCSSKTSAEMLYLQKTLGLQGLPLIAENGAVIQLAEQWQEIDGFPRIISGISHGEISLVLNTLREKEHFKFTTFDDVDDATIAEWTGLSRSQAALTQLHEASVTLIWRDSDERMAQFTARLNELGLQFMQGARFWHVLDASAGKDQAANWIIATYQQLSGKRPTTLGLGDGPNDAPLLEVMDYAVIVKGL 234
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1XVI)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MPGP_ECOLI | P76329)
molecular function
    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:0050531    mannosyl-3-phosphoglycerate phosphatase activity    Catalysis of the reaction: 2-(alpha-D-mannosyl)-3-phosphoglycerate + H(2)O = 2-(alpha-D-mannosyl)-D-glycerate + phosphate.
    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.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0051479    mannosylglycerate biosynthetic process    The chemical reactions and pathways resulting in the formation of mannosylglycerate, a very common compatible solute in thermophilic and hyperthermophilic organisms.
    GO:0044283    small molecule biosynthetic process    The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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