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(-) Description

Title :  CRYSTAL STRUCTURE OF A N-ACETYLNEURAMINIC ACID PHOSPHATASE (NANP) FROM MUS MUSCULUS AT 1.90 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  21 Mar 06  (Deposition) - 18 Apr 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Protein C20Orf147 Homolog (17391249) From Mus Musculus At 1. 90 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HALOACID DEHALOGENASE-LIKE HYDROLASE DOMAIN CONTAINING 4
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: 17391249
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3NA1Ligand/IonSODIUM ION
4PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3NA-1Ligand/IonSODIUM ION
4PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3NA-1Ligand/IonSODIUM ION
4PO42Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:12 , ASP A:14 , ASP A:189 , PO4 A:251 , HOH A:312 , HOH A:350BINDING SITE FOR RESIDUE NA A 249
2AC2SOFTWAREARG A:72 , ARG A:104 , LYS A:141BINDING SITE FOR RESIDUE CL A 250
3AC3SOFTWAREASP A:12 , LEU A:13 , ASP A:14 , THR A:131 , ASN A:132 , LYS A:164 , NA A:249 , HOH A:288 , HOH A:350BINDING SITE FOR RESIDUE PO4 A 251
4AC4SOFTWAREASN A:15 , THR A:16 , LEU A:17 , ILE A:18 , HOH A:347BINDING SITE FOR RESIDUE EDO A 252

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:164 -Pro A:165

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2GFH)

(-) 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:246
 aligned with NANP_MOUSE | Q9CPT3 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:250
                               1                                                                                                                                                                                                                                                      
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247
           NANP_MOUSE     - ---MGLSRVRAVFFDLDNTLIDTAGASRRGMLEVIKLLQSKYHYKEEAEIICDKVQVKLSKECFHPYSTCITDVRTSHWEEAIQETKGGADNRKLAEECYFLWKSTRLQHMILADDVKAMLTELRKEVRLLLLTNGDRQTQREKIEACACQSYFDAIVIGGEQKEEKPAPSIFYHCCDLLGVQPGDCVMVGDTLETDIQGGLNAGLKATVWINKSGRVPLTSSPMPHYMVSSVLELPALLQSIDCKVSMS 247
               SCOP domains ---d2gfha1 A:1-247 N-acylneuraminate-9-phosphatase NANP                                                                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.....eeee.......hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh....----hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhhhh.eeee.hhh.....hhhhhhhhhhhhh.hhh.eeeee....hhhhhhhhh...eeeee...............eee.hhhhhhhhhhhhh...ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gfh A  -2 HHHMGLSRVRAVFFDLDNTLIDTAGASRRGMLEVIKLLQSKYHYKEEAEIICDKVQVKLSKECFH----CITDVRTSHWEEAIQETKGGADNRKLAEECYFLWKSTRLQHMILADDVKAMLTELRKEVRLLLLTNGDRQTQREKIEACACQSYFDAIVIGGEQKEEKPAPSIFYHCCDLLGVQPGDCVMVGDTLETDIQGGLNAGLKATVWINKSGRVPLTSSPMPHYMVSSVLELPALLQSIDCKVSMS 247
                                     7        17        27        37        47        57    |   67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247
                                                                                           62   67
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2GFH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GFH)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (NANP_MOUSE | Q9CPT3)
molecular function
    GO:0050124    N-acylneuraminate-9-phosphatase activity    Catalysis of the reaction: N-acylneuraminate 9-phosphate + H2O = N-acylneuraminate + 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.
biological process
    GO:0006045    N-acetylglucosamine biosynthetic process    The chemical reactions and pathways resulting in the formation of N-acetylglucosamine. The D isomer is a common structural unit of glycoproteins in plants, bacteria and animals; it is often the terminal sugar of an oligosaccharide group of a glycoprotein.
    GO:0046380    N-acetylneuraminate biosynthetic process    The chemical reactions and pathways resulting in the formation of N-acetylneuraminate, the anion of 5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-3-ulosonic acid.
    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: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.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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