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(-) Description

Title :  THE CRYSTAL STRUCTURE OF HUMAN N-ACETYLNEURAMINIC ACID PHOSPHATASE, NANP
 
Authors :  E. Ugochukwu, R. Cocking, W. W. Yue, A. C. W. Pike, A. Roos, J. R. C. Muniz, F. Von Delft, C. Bountra, C. H. Arrowsmith, J. Weigelt, A. Edwards, U. Oppermann
Date :  28 Nov 08  (Deposition) - 23 Dec 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  N-Acetylneuraminate, Neu5Ac-9- Phosphate, Carbohydrate Metabolism, N-Acetylneuraminic Acid Phosphatase, Nanp, Hdhd4, Hydrolase, Magnesium, Sialic Acid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Ugochukwu, R. Cocking, W. W. Yue, A. C. W. Pike, A. Roos, J. R. C. Muniz F. Von Delft, C. Bountra, C. H. Arrowsmith, J. Weigelt, A. Edwards, U. Oppermann
The Crystal Structure Of Human N-Acetylneuraminic Acid Phosphatase, Nanp
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - N-ACYLNEURAMINATE-9-PHOSPHATASE
    Chains: A
    EC Number: 3.1.3.29
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28-BSA4
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: R3-PRARE2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NEU5AC-9-PASE, HALOACID DEHALOGENASE-LIKE HYDROLASE DOMAIN-CONTAINING PROTEIN 4, NANP

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2NA1Ligand/IonSODIUM ION
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:12 , ASP A:14 , ASP A:189 , CL A:1246 , PO4 A:1249 , HOH A:2075BINDING SITE FOR RESIDUE NA A1245
2AC2SOFTWAREASN A:15 , THR A:190 , NA A:1245 , HOH A:2088BINDING SITE FOR RESIDUE CL A1246
3AC3SOFTWARELYS A:55 , LYS A:58BINDING SITE FOR RESIDUE CL A1247
4AC4SOFTWAREARG A:72 , ARG A:104 , LYS A:141 , HOH A:2085 , HOH A:2086BINDING SITE FOR RESIDUE PO4 A1248
5AC5SOFTWAREASP A:12 , LEU A:13 , ASP A:14 , THR A:131 , ASN A:132 , LYS A:164 , NA A:1245 , HOH A:2075 , HOH A:2087 , HOH A:2088BINDING SITE FOR RESIDUE PO4 A1249

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W4M)

(-) 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 2W4M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W4M)

(-) Exons   (0, 0)

(no "Exon" information available for 2W4M)

(-) 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:250
 aligned with NANP_HUMAN | Q8TBE9 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:250
                                  1                                                                                                                                                                                                                                                   
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244
           NANP_HUMAN     - ------MGLSRVRAVFFDLDNTLIDTAGASRRGMLEVIKLLQSKYHYKEEAEIICDKVQVKLSKECFHPYNTCITDLRTSHWEEAIQETKGGAANRKLAEECYFLWKSTRLQHMTLAEDVKAMLTELRKEVRLLLLTNGDRQTQREKIEACACQSYFDAVVVGGEQREEKPAPSIFYYCCNLLGVQPGDCVMVGDTLETDIQGGLNAGLKATVWINKNGIVPLKSSPVPHYMVSSVLELPALLQSIDCKV 244
               SCOP domains d2w4ma_ A: automated matches                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------HAD_2-2w4mA01 A:9-209                                                                                                                                                                                    ----------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh.....eeee.......hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhheeeeee..hhhhhhhhhhhh.hhhhh.eeee.hhh.....hhhhhhhhhhhhh.hhh.eeeee....hhhhhhhhhh..eeeee...............eee.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w4m A  -5 NLYFQSMGLSRVRAVFFDLDNTLIDTAGASRRGMLEVIKLLQSKYHYKEEAEIICDKVQVKLSKECFHPYNTCITDLRTSHWEEAIQETKGGAANRKLAEECYFLWKSTRLQHMTLAEDVKAMLTELRKEVRLLLLTNGDRQTQREKIEACACQSYFDAVVVGGEQREEKPAPSIFYYCCNLLGVQPGDCVMVGDTLETDIQGGLNAGLKATVWINKNGIVPLKSSPVPHYMVSSVLELPALLQSIDCKV 244
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2W4M)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: HAD (186)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (NANP_HUMAN | Q8TBE9)
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.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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        NANP_HUMAN | Q8TBE9: 4knv 4knw

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