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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ISOFORM OF DL-GLYCEROL-3-PHOSPHATASE, RHR2P, FROM SACCHAROMYCES CEREVISIAE
 
Authors :  K. Tan, E. Evdokimova, M. Kudritska, A. Savchenko, A. Edwards, A. Joach Midwest Center For Structural Genomics (Mcsg)
Date :  13 Jul 07  (Deposition) - 07 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Apc7326, Dl-Glycerol-3-Phosphatase Isoform, Rhr2P, Saccharomyces Cerevisiae, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, E. Evdokimova, M. Kudritska, A. Savchenko, A. Edwards, A. Joachimiak
The Crystal Structure Of An Isoform Of Dl-Glycerol-3-Phosphatase, Rhr2P From Saccharomyces Cerevisiae.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - (DL)-GLYCEROL-3-PHOSPHATASE 1
    Chains: A
    EC Number: 3.1.3.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: P15TV LIC
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: GPP1, RHR2, YIL053W
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric/Biological Unit (5, 12)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3EDO2Ligand/Ion1,2-ETHANEDIOL
4HG4Ligand/IonMERCURY (II) ION
5SO44Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:227 , LYS A:228 , LYS A:230 , CYS A:232 , ILE A:235 , CL A:279BINDING SITE FOR RESIDUE HG A 274
02AC2SOFTWAREPHE A:38 , ALA A:117 , CYS A:121 , HIS A:239BINDING SITE FOR RESIDUE HG A 275
03AC3SOFTWAREARG A:178 , ALA A:211 , GLY A:212 , CYS A:213BINDING SITE FOR RESIDUE HG A 276
04AC4SOFTWAREHIS A:72 , HIS A:75 , HOH A:449BINDING SITE FOR RESIDUE HG A 277
05AC5SOFTWAREASP A:39 , ASP A:41 , ASP A:200 , SO4 A:280 , HOH A:500 , HOH A:501BINDING SITE FOR RESIDUE CA A 278
06AC6SOFTWARECYS A:232 , ASP A:233 , ILE A:234 , ILE A:235 , TYR A:263 , HG A:274BINDING SITE FOR RESIDUE CL A 279
07AC7SOFTWAREASP A:39 , VAL A:40 , ASP A:41 , GLY A:76 , THR A:136 , SER A:137 , GLY A:138 , LYS A:168 , CA A:278 , HOH A:438 , HOH A:442BINDING SITE FOR RESIDUE SO4 A 280
08AC8SOFTWAREARG A:56 , PHE A:65 , ALA A:67 , GLU A:68 , HOH A:301 , HOH A:352 , HOH A:432 , HOH A:447BINDING SITE FOR RESIDUE SO4 A 281
09AC9SOFTWARELYS A:60 , LYS A:209 , HOH A:460 , HOH A:512BINDING SITE FOR RESIDUE SO4 A 282
10BC1SOFTWAREALA A:52 , ARG A:56 , HIS A:72 , GLN A:166 , HIS A:170 , HOH A:476BINDING SITE FOR RESIDUE SO4 A 283
11BC2SOFTWAREARG A:140 , LYS A:144 , ARG A:154BINDING SITE FOR RESIDUE EDO A 284
12BC3SOFTWARELYS A:237 , ASN A:238 , HOH A:387 , HOH A:444 , HOH A:487BINDING SITE FOR RESIDUE EDO A 285

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QLT)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:27 -Pro A:28
2Lys A:168 -Pro A:169

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QLT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QLT)

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YIL053W1YIL053W.1IX:255113-255865753GPP1_YEAST1-2502501A:22-271250

(-) 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:251
 aligned with GPP1_YEAST | P41277 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:251
                             1                                                                                                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249 
           GPP1_YEAST     - -MPLTTKPLSLKINAALFDVDGTIIISQPAIAAFWRDFGKDKPYFDAEHVIHISHGWRTYDAIAKFAPDFADEEYVNKLEGEIPEKYGEHSIEVPGAVKLCNALNALPKEKWAVATSGTRDMAKKWFDILKIKRPEYFITANDVKQGKPHPEPYLKGRNGLGFPINEQDPSKSKVVVFEDAPAGIAAGKAAGCKIVGIATTFDLDFLKEKGCDIIVKNHESIRVGEYNAETDEVELIFDDYLYAKDDLLKW 250
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------2qltA01              2qltA02 A:48-109 Putative phosphatase; domain 2               2qltA01 A:27-47,A:110-265  [code=3.40.50.1000, no name defined]                                                                                             ------ CATH domains
               Pfam domains ------------Hydrolase-2qltA01 A:33-212                                                                                                                                                          ----------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee.eeee......eehhhhhhhhhhhhhh.....hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhh.hhh.eeee...hhhhhhhhhhhhh......eehhhhh......hhhhhhhhhhh.......hhhhh.eeeee.hhhhhhhhhhh..eeeee....hhhhhh.....eee.hhh.eee.........eeeee....ee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 -Exon 1.1  PDB: A:22-271 UniProt: 1-250                                                                                                                                                                                                                     Transcript 1
                 2qlt A  21 AMPLTTKPLSLKINAALFDVDGTIIISQPAIAAFWRDFGKDKPYFDAEHVIHISHGWRTYDAIAKFAPDFADEEYVNKLEGEIPEKYGEHSIEVPGAVKLCNALNALPKEKWAVATSGTRDMAKKWFDILKIKRPEYFITANDVKQGKPHPEPYLKGRNGLGFPINEQDPSKSKVVVFEDAPAGIAAGKAAGCKIVGIATTFDLDFLKEKGCDIIVKNHESIRVGEYNAETDEVELIFDDYLYAKDDLLKW 271
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270
   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 2QLT)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: HAD (186)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GPP1_YEAST | P41277)
molecular function
    GO:0000121    glycerol-1-phosphatase activity    Catalysis of the reaction: glycerol-1-phosphate + H2O = glycerol + 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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0006114    glycerol biosynthetic process    The chemical reactions and pathways resulting in the formation of glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
    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.
    GO:0006970    response to osmotic stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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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