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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C. ELEGANS PROTEIN O-FUCOSYLTRANSFERASE 2 (CEPOFUT2) DOUBLE MUTANT (R298K-R299K) IN COMPLEX WITH GDP AND THE HUMAN TSR1 FROM THROMBOSPONDIN 1
 
Authors :  J. Valero-Gonzalez, C. Leonhard-Melief, E. Lira-Navarrete, G. Jimen C. Hernandez-Ruiz, M. C. Pallares, I. Yruela, D. Vasudevan, A. Lostao F. Corzana, H. Takeuchi, R. S. Haltiwanger, R. Hurtado-Guerrero
Date :  19 Nov 15  (Deposition) - 27 Jan 16  (Release) - 15 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, Pofut2, Waters, Fusion Protein, Afm, Itc, Glycosyltransferase, Site-Directed Mutagenesis, Molecular Dynamics, Tsr1 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Valero-Gonzalez, C. Leonhard-Melief, E. Lira-Navarrete, G. Jimenez-Oses, C. Hernandez-Ruiz, M. C. Pallares, I. Yruela, D. Vasudevan, A. Lostao, F. Corzana, H. Takeuchi, R. S. Haltiwanger, R. Hurtado-Guerrero
A Proactive Role Of Water Molecules In Acceptor Recognition Of Thrombospondin Type 1 Repeats By Protein-O-Fucosyltransferase 2
Nat. Chem. Biol. V. 12 240 2016
PubMed-ID: 26854667  |  Reference-DOI: 10.1038/NCHEMBIO.2019

(-) Compounds

Molecule 1 - GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 2,THROMBOSPONDIN-1
    Chains: A, B
    EC Number: 2.4.1.221
    Engineered: YES
    Expression System: KOMAGATAELLA PASTORIS
    Expression System Plasmid: PPICZALPHAA
    Expression System Strain: X33
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Gene: PAD-2, K10G9.3, THBS1, TSP, TSP1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: CAENORHABDITIS ELEGANS, HOMO SAPIENS
    Organism Taxid: 6239, 9606
    Synonym: PATTERNING DEFECTIVE PROTEIN 2,PEPTIDE-O-FUCOSYLTRANSFERASE 2,O-FUCT-2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1EDO10Ligand/Ion1,2-ETHANEDIOL
2GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (3, 7)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY B:53 , PHE B:54 , ASN B:55 , LEU B:56 , HIS B:89 , HIS B:90 , HIS B:288 , ARG B:290 , ALA B:327 , THR B:328 , ASP B:329 , ALA B:363 , ASP B:366 , SER B:382 , THR B:383 , PHE B:384 , HOH B:2011 , HOH B:2012 , HOH B:2031 , HOH B:2180 , HOH B:2186 , HOH B:2206 , HOH B:2207BINDING SITE FOR RESIDUE GDP B 1426
02AC2SOFTWAREGLY A:53 , PHE A:54 , ASN A:55 , LEU A:56 , HIS A:288 , ARG A:290 , ALA A:327 , THR A:328 , ASP A:329 , ALA A:363 , ASP A:366 , SER A:382 , THR A:383 , PHE A:384 , HOH A:2012 , HOH A:2218 , HOH A:2227 , HOH A:2256 , HOH A:2257BINDING SITE FOR RESIDUE GDP A 1428
03AC3SOFTWARESER A:176BINDING SITE FOR RESIDUE EDO A 1430
04AC4SOFTWARELYS A:419 , LYS A:421 , HOH A:2258BINDING SITE FOR RESIDUE EDO A 1431
05AC5SOFTWAREARG B:72BINDING SITE FOR RESIDUE EDO B 1428
06AC6SOFTWARELYS B:41 , HOH B:2050BINDING SITE FOR RESIDUE EDO B 1429
07AC7SOFTWAREHIS B:136 , TRP B:141 , GLY B:1021 , ILE B:1022 , THR B:1045 , HOH B:2078 , HOH B:3033BINDING SITE FOR RESIDUE EDO B 1431
08AC8SOFTWARETRP B:141 , GLY B:142 , GLU B:144 , VAL B:146 , LYS B:148 , GLN B:191BINDING SITE FOR RESIDUE EDO B 1430
09AC9SOFTWAREGLY B:142 , THR B:143 , GLN B:1042 , THR B:1043 , HOH B:3023 , HOH B:3024BINDING SITE FOR RESIDUE EDO B 1432
10BC1SOFTWAREARG A:101BINDING SITE FOR RESIDUE EDO A 1432
11BC2SOFTWAREGLN A:1024 , ARG A:1025 , GLY A:1026 , HOH A:2150BINDING SITE FOR RESIDUE EDO A 1433
12BC3SOFTWARELYS A:151 , HIS A:203 , ASN A:205 , HOH A:2093 , HOH A:2128 , HOH A:2129Binding site for Mono-Saccharide NAG A1427 bound to ASN A 205
13BC4SOFTWARELYS B:151 , GLN B:186 , ASN B:205Binding site for Mono-Saccharide NAG B1427 bound to ASN B 205

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:154 -A:187
2A:407 -A:414
3A:1014 -A:1046
4A:1018 -A:1051
5A:1029 -A:1036
6B:154 -B:187
7B:407 -B:414
8B:1014 -B:1046
9B:1018 -B:1051
10B:1029 -B:1036

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro A:156 -Pro A:157

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FOE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FOE)

(-) Exons   (0, 0)

(no "Exon" information available for 5FOE)

(-) 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:429
                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......hhhhhhhhhhhhhhhhhhhhhh..eeeeee.........hhhhh.hhhhhhhhh.eeehhhhhhh.....eee...............eeee.....hhhhhheeee..eee.hhhhh.......ee.eeee.hhhhhhhhhhhhhhh...eeee.hhhhh......hhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhh.....hhhhh........eeeeeeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhh.....eee........hhhhhhhhhhhhhhheeeee....hhhhhhhhhhhhhhh.hhhhh.........................................eeeeeee..............eeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5foe A   40 EKKFLLYDVNFGEGFNLRRDVYMRVANTVRSLRDSGENYILVLPPWGREVALSWRLFFDLESLNRFIPVIEFEDFLDENRPIDQVIYLQHYAEGWGTEYVRKFEKRSCLPPAESHYKQVEEFKWKGWFYSYEDVYSRNFQCVSIQGDSGTLKDLLKHSNFSESTSIMVDRAETILHEHYGEVDYWKARRSMRYSNDLVDVADAFRKKYLDSDDKRDKTKLVDDWTKEKPRRTAIGGPYLGIHWRRRDFLYAKKAQLPTIPGTAKILQDLCKKLDLQKIYLATDAPDQEVDELKALLNGELEVYRFTDTQKLNDGQIAIIDQYLCAHAAYFIGSYESTFTFRIQEDREIIGFPISTTFNRLCPDTEPTCEQPAKWKIVYSSDGWSPWSEWTSCSTSCGNGIQQRGRSCDSLNNRCEGSSVQTRTCHIQEC 1051
                                    49        59        69        79       |96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426|     1012      1022      1032      1042         
                                                                          87|                                                                                                                                                                                                                                                                                                                                        426|                                                
                                                                           95                                                                                                                                                                                                                                                                                                                                        1003                                                


Chain B from PDB  Type:PROTEIN  Length:435
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......hhhhhhhhhhhhhhhhhhhhhh...eeeee................hhhhh.hhhhhhh...eeehhhhhh......eeeeee............eeee.....hhhhhheeee..eee.hhhhh.......eeeeeee.hhhhhhhhhhhhhhh...eeeeehhhhh......hhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhh.....hhhhh........eeeeeeee..hhhhhhhhhhh.hhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhh......eee........hhhhhhhhhhhhhhheeeee....hhhhhhhhhhhhhhh.hhhhh........................................eeeeeee..............eeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5foe B   40 EKKFLLYDVNFGEGFNLRRDVYMRVANTVRSLRDSGENYILVLPPWGRLHHWKRMEVALSWRLFFDLESLNRFIPVIEFEDFLDENRPIDQVIYLQHYAEGWGTEYVRKFEKRSCLPPAESHYKQVEEFKWKGWFYSYEDVYSRNFQCVSIQGDSGTLKDLLKHSNFSESTSIMVDRAETILHEHYGEVDYWKARRSMRYSNDLVDVADAFRKKYLDSDDKRDKTKLVDDWTKEKPRRTAIGGPYLGIHWRRRDFLYAKKAQLPTIPGTAKILQDLCKKLDLQKIYLATDAPDQEVDELKALLNGELEVYRFTDTQKLNDGQIAIIDQYLCAHAAYFIGSYESTFTFRIQEDREIIGFPISTTFNRLCPDTEPTCEQPAKWKIVYSDGWSPWSEWTSCSTSCGNGIQQRGRSCDSLNNRCEGSSVQTRTCHIQEC 1051
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419     |1006      1016      1026      1036      1046     
                                                                                                                                                                                                                                                                                                                                                                                                                           425|                                                
                                                                                                                                                                                                                                                                                                                                                                                                                           1003
   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  (0, 0)

(no "SCOP Domain" information available for 5FOE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FOE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FOE)

(-) Gene Ontology  (98, 100)

Asymmetric Unit(hide GO term definitions)

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  5foe
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  TSP1_HUMAN | P07996
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  2.4.1.221
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 Related Entries

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        TSP1_HUMAN | P07996: 1lsl 1ux6 1z78 1za4 2erf 2es3 2ouh 2ouj 3r6b

(-) Related Entries Specified in the PDB File

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