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(-) Description

Title :  STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM VII - SOS COMPLEX - 2.2A
 
Authors :  M. Zebisch, E. Y. Jones
Date :  04 Sep 14  (Deposition) - 25 Feb 15  (Release) - 18 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Wnt, Esterase, Extracellular, Alpha/Beta Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Kakugawa, P. F. Langton, M. Zebisch, S. A. Howell, T. Chang, Y. Liu, T. Feizi, G. Bineva, N. O'Reilly, A. P. Snijders, E. Y. Jones, J. Vincen
Notum Deacylates Wnt Proteins To Suppress Signalling Activity.
Nature V. 519 187 2015
PubMed-ID: 25731175  |  Reference-DOI: 10.1038/NATURE14259

(-) Compounds

Molecule 1 - PROTEIN NOTUM HOMOLOG
    Chains: A
    EC Number: 3.1.1.1
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293T
    Expression System Common: HUMAN
    Expression System Plasmid: PHLSEC
    Expression System Taxid: 9606
    Fragment: RESIDUES 81-451
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: GLYCOSYLATED AT N96

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SCR1Ligand/IonSUCROSE OCTASULFATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:117 , ARG A:118 , ARG A:119 , ASN A:174 , LYS A:224 , LYS A:272 , HIS A:276 , GLU A:289 , ARG A:292 , HIS A:412 , ARG A:416 , HIS A:419 , HOH A:2088 , HOH A:2114 , HOH A:2115BINDING SITE FOR RESIDUE SCR A1453
2AC2SOFTWAREARG A:90BINDING SITE FOR RESIDUE CL A1454
3AC3SOFTWAREASN A:96 , VAL A:99 , SER A:193 , PRO A:447BINDING SITE FOR MONO-SACCHARIDE NAG A1452 BOUND TO ASN A 96

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:101 -A:183
2A:130 -A:136
3A:279 -A:285
4A:306 -A:318
5A:386 -A:449
6A:413 -A:432
7A:440 -A:445

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4UZ9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4UZ9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UZ9)

(-) Exons   (0, 0)

(no "Exon" information available for 4UZ9)

(-) 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:356
                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..............eeeee......eeeeee.......hhhhhhhhhhhhhhhh.......ee..hhhhh............eeeee......................hhhhhhhhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....................hhhhhhhhhhhhhh...hhhhhh.....hhhhhhhhhhhhhhh...eeee...eehhhhhhh.........hhhhhhhhhhhhhhhhhhhh....eee...ee.....hhhhhh.ee..eehhhhhhhhhhhhhh....eee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uz9 A  86 NEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSCPVHLVDSCPWPHCNPSCPT 451
                                    95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415     ||435       445      
                                                                                                                                                                                                                                                                                                                                                                         421|                   
                                                                                                                                                                                                                                                                                                                                                                          432
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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  (0, 0)

(no "SCOP Domain" information available for 4UZ9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UZ9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UZ9)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4uz9)
 

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  3.1.1.1
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NOTUM_HUMAN | Q6P988: 4uyu 4uyw 4uyz 4uz1 4uz5 4uz6 4uz7 4uza 4uzl 4uzq 4wbh

(-) Related Entries Specified in the PDB File

4uyu STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM I IODIDE COMPLEX - 2.3A
4uyw STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM I HEPARIN FRAGMENT COMPLEX - 1.7A
4uyz STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM II - 2.8A
4uz1 STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM III - 1.4A
4uz5 STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM IV - 2.1A
4uz6 STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM V - SOS COMPLEX - 1.9A
4uz7 STRUCTURE OF THE WNT DEACETYLASE NOTUM - CRYSTAL FORM VII - SOS COMPLEX - 2.2A
4uza STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM VIII - PHOSPHATE COMPLEX - 2.4A
4uzj STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM III - 1.4A
4uzk STRUCTURE OF THE WNT DEACYLASE NOTUM FROM DROSOPHILA - CRYSTAL FORM II - 1.9A
4uzl STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM I MYRISTOLEATE COMPLEX - 2.1A
4uzq STRUCTURE OF THE WNT DEACYLASE NOTUM IN COMPLEX WITH O-PALMITOLEOYL SERINE - CRYSTAL FORM IX - 1.5A
4wbh