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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PARALOGUE OF THE HUMAN FORMYLGLYCINE GENERATING ENZYME
 
Authors :  A. Dickmanns, M. G. Rudolph, R. Ficner
Date :  01 Dec 04  (Deposition) - 08 Feb 05  (Release) - 26 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Formylglycine, Sulfatases, Multiple Sulfatase Deficiency, Homodimer, Duf323, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Dickmanns, B. Schmidt, M. G. Rudolph, M. Mariappan, T. Dierks, K. Von Figura, R. Ficner
Crystal Structure Of Human Pfge, The Paralog Of The C{Alpha}-Formylglycine-Generating Enzyme
J. Biol. Chem. V. 280 15180 2005
PubMed-ID: 15687489  |  Reference-DOI: 10.1074/JBC.M414317200

(-) Compounds

Molecule 1 - SULFATASE MODIFYING FACTOR 2
    Chains: A, B
    Engineered: YES
    Gene: SUMF2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: HT1080 CELLS
    Synonym: C-ALPHA-FORMYGLYCINE- GENERATING ENZYME 2, UNQ1968/PRO4500

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2FUC1Ligand/IonALPHA-L-FUCOSE
3MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARENAG A:2 , HOH A:1226 , HOH A:1241 , HOH A:1262BINDING SITE FOR RESIDUE NAG A 1
02AC2SOFTWARENAG A:1 , FUC A:3 , GLU A:80 , PRO A:190 , ASN A:191BINDING SITE FOR RESIDUE NAG A 2
03AC3SOFTWARENAG A:2 , HOH A:1226BINDING SITE FOR RESIDUE FUC A 3
04AC4SOFTWARENAG B:2 , ASN B:191 , GLU B:207 , GLY B:209 , HOH B:2253BINDING SITE FOR RESIDUE NAG B 1
05AC5SOFTWARENAG B:1BINDING SITE FOR RESIDUE NAG B 2
06AC6SOFTWAREASN A:194 , LEU A:195 , ASP A:208 , PHE A:210 , HOH A:1006 , HOH A:1018BINDING SITE FOR RESIDUE CA A 1001
07AC7SOFTWAREASN B:194 , LEU B:195 , ASP B:208 , PHE B:210 , HOH B:2021 , HOH B:2025BINDING SITE FOR RESIDUE CA B 1002
08AC8SOFTWAREASP B:229 , LEU B:230 , GLY B:232 , VAL B:234 , GLU B:236 , HOH B:2059BINDING SITE FOR RESIDUE CA B 1003
09AC9SOFTWAREASP A:229 , LEU A:230 , GLY A:232 , VAL A:234 , GLU A:236 , HOH A:1047BINDING SITE FOR RESIDUE CA A 1004
10BC1SOFTWAREPHE B:94 , TRP B:118 , SER B:283 , HOH B:2212 , HOH B:2274BINDING SITE FOR RESIDUE MPD B 2001

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:156 -A:290
2B:156 -B:290

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:52 -Pro A:53
2Phe A:200 -Pro A:201
3Gly B:52 -Pro B:53
4Phe B:200 -Pro B:201

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_046951D51ESUMF2_HUMANPolymorphism4245575A/BE51E
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Y4J)

(-) Exons   (0, 0)

(no "Exon" information available for 1Y4J)

(-) 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:266
 aligned with SUMF2_HUMAN | Q8NBJ7 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:267
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       
          SUMF2_HUMAN    28 TSMVQLQGGRFLMGTNSPDSRDGDGPVREATVKPFAIDIFPVTNKDFRDFVREKKYRTEAEMFGWSFVFEDFVSDELRNKATQPMKSVLWWLPVEKAFWRQPAGPGSGIRERLEHPVLHVSWNDARAYCAWRGKRLPTEEEWEFAARGGLKGQVYPWGNWFQPNRTNLWQGKFPKGDKAEDGFHGVSPVNAFPAQNNYGLYDLLGNVWEWTASPYQAAEQDMRVLRGASWIDTADGSANHRARVTTRMGNTPDSASDNLGFRCAADA 294
               SCOP domains d1y4ja1 A:28-294 Sulfatase modifying factor 2                                                                                                                                                                                                                               SCOP domains
               CATH domains 1y4jA00 A:28-294 paralog of FGE (formylglycine-generating enzyme)                                                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee..............eeeee..eeee....hhhhhhhhhhhhh..hhhhhhheeeee.hhhhhhhhhh.-........eeeee.........................hhhhhhhhhhhh.....hhhhhhhhhhh...........................................................eeeeeee..hhhhh.eeee....................eeee........ee...eee. Sec.struct. author
                 SAPs(SNPs) -----------------------E--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y4j A  28 TSMVQLQGGRFLMGTNSPDSRDGEGPVREATVKPFAIDIFPVTNKDFRDFVREKKYRTEAEMFGWSFVFEDFVSDELRNKA-QPMKSVLWWLPVEKAFWRQPAGPGSGIRERLEHPVLHVSWNDARAYCAWRGKRLPTEEEWEFAARGGLKGQVYPWGNWFQPNRTNLWQGKFPKGDKAEDGFHGVSPVNAFPAQNNYGLYDLLGNVWEWTASPYQAAEQDMRVLRGASWIDTADGSANHRARVTTRMGNTPDSASDNLGFRCAADA 294
                                    37        47        57        67        77        87        97       107| |    117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       
                                                                                                          108 |                                                                                                                                                                                        
                                                                                                            110                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:268
 aligned with SUMF2_HUMAN | Q8NBJ7 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:268
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286        
          SUMF2_HUMAN    27 ATSMVQLQGGRFLMGTNSPDSRDGDGPVREATVKPFAIDIFPVTNKDFRDFVREKKYRTEAEMFGWSFVFEDFVSDELRNKATQPMKSVLWWLPVEKAFWRQPAGPGSGIRERLEHPVLHVSWNDARAYCAWRGKRLPTEEEWEFAARGGLKGQVYPWGNWFQPNRTNLWQGKFPKGDKAEDGFHGVSPVNAFPAQNNYGLYDLLGNVWEWTASPYQAAEQDMRVLRGASWIDTADGSANHRARVTTRMGNTPDSASDNLGFRCAADA 294
               SCOP domains d1y4jb_ B: Sulfatase modifying factor 2                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1y4jB00 B:27-294 paralog of FGE (formylglycine-generating enzyme)                                                                                                                                                                                                            CATH domains
           Pfam domains (1) FGE-sulfatase-1y4jB01 B:27-292                                                                                                                                                                                                                                            -- Pfam domains (1)
           Pfam domains (2) FGE-sulfatase-1y4jB02 B:27-292                                                                                                                                                                                                                                            -- Pfam domains (2)
         Sec.struct. author ...eeee..eeeee..............eeeee..eeee....hhhhhhhhhhhhh..hhhhhhheeeee.hhhhhhhhhhh.........eeeee.............hhhhh.......hhhhhhhhhhhh.....hhhhhhhhhhh...........................................................eeeeeee..hhhhh.eeee....................eeee........ee...eee. Sec.struct. author
                 SAPs(SNPs) ------------------------E--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y4j B  27 ATSMVQLQGGRFLMGTNSPDSRDGEGPVREATVKPFAIDIFPVTNKDFRDFVREKKYRTEAEMFGWSFVFEDFVSDELRNKATQPMKSVLWWLPVEKAFWRQPAGPGSGIRERLEHPVLHVSWNDARAYCAWRGKRLPTEEEWEFAARGGLKGQVYPWGNWFQPNRTNLWQGKFPKGDKAEDGFHGVSPVNAFPAQNNYGLYDLLGNVWEWTASPYQAAEQDMRVLRGASWIDTADGSANHRARVTTRMGNTPDSASDNLGFRCAADA 294
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: FGE-sulfatase] (9)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SUMF2_HUMAN | Q8NBJ7)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0043687    post-translational protein modification    The process of covalently altering one or more amino acids in a protein after the protein has been completely translated and released from the ribosome.
cellular component
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1y1e 1y1f 1y1g 1y1h 1y1i 1y1j