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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF A PHOSPHOGLYCOLATE PHOSPHATASE FROM AQUIFEX AEOLICUS
 
Authors :  C. Ciatto, T. Min, J. Gorman, S. K. Burley, L. Shapiro, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  21 Nov 06  (Deposition) - 05 Dec 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Keywords :  Phosphatase, Structural Genomics, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Ciatto, T. Min, J. Gorman, S. K. Burley, L. Shapiro
X-Ray Crystal Structure Of A Phosphoglycolate Phosphatase From Aquifex Aeolicus
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOGLYCOLATE PHOSPHATASE
    Chains: A
    EC Number: 3.1.3.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: BC PSGX3(BC)
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: GPH
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Synonym: PGPASE, PGP

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2NYV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser A:141 -Pro A:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2NYV)

(-) 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:217
 aligned with GPH_AQUAE | O67359 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:217
                              1                                                                                                                                                                                                                 213  
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208    |  
            GPH_AQUAE     - --MRVILFDLDGTLIDSAKDIALALEKTLKELGLEEYYPDNVTKYIGGGVRALLEKVLKDKFREEYVEVFRKHYLENPVVYTKPYPEIPYTLEALKSKGFKLAVVSNKLEELSKKILDILNLSGYFDLIVGGDTFGEKKPSPTPVLKTLEILGEEPEKALIVGDTDADIEAGKRAGTKTALALWGYVKLNSQIPDFTLSRPSDLVKLMDNHIVEF--   -
               SCOP domains d2nyva_ A: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains -2nyvA01         2nyvA02 A:18-81 Putative phosphatase; domain 2                  2nyvA01 A:2-17,A:82-217  [code=3.40.50.1000, no name defined]                                                                            CATH domains
               Pfam domains ---Hydrolase-2nyvA01 A:4-176                                                                                                                                                    ----------------------------------------- Pfam domains
         Sec.struct. author .ee.eeee......eehhhhhhhhhhhhhhhh.hhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee..hhhhhhhhhhhh..eeeee...hhhhhhhhhhhh.hhhhh.eee...........hhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhh.eeeee.............eee...hhhhhhhhh...ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nyv A   1 mSLRVILFDLDGTLIDSAKDIALALEKTLKELGLEEYYPDNVTKYIGGGVRALLEKVLKDKFREEYVEVFRKHYLENPVVYTKPYPEIPYTLEALKSKGFKLAVVSNKLEELSKKILDILNLSGYFDLIVGGDTFGEKKPSPTPVLKTLEILGEEPEKALIVGDTDADIEAGKRAGTKTALALWGYVKLNSQIPDFTLSRPSDLVKLmDNHIVEFEG 217
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
                            |                                                                                                                                                                                                            208-MSE     
                            1-MSE
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: HAD (186)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (GPH_AQUAE | O67359)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008967    phosphoglycolate phosphatase activity    Catalysis of the reaction: 2-phosphoglycolate + H(2)O = glycolate + phosphate.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0046295    glycolate biosynthetic process    The chemical reactions and pathways resulting in the formation of glycolate, the anion of hydroxyethanoic acid (glycolic acid).
    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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        GPH_AQUAE | O67359: 2yy6

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