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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE XYLOSIDE XYLOSYLTRANSFERASE 1 COMPLEXED WITH MANGANESE AND UDP
 
Authors :  H. Yu, H. Li
Date :  08 Oct 14  (Deposition) - 04 Nov 15  (Release) - 20 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.03
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Keywords :  Glycosyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Yu, M. Takeuchi, J. Lebarron, J. Kantharia, E. London, H. Bakker, R. S. Haltiwanger, H. Li, H. Takeuchi
Notch-Modifying Xylosyltransferase Structures Support An Sni-Like Retaining Mechanism.
Nat. Chem. Biol. V. 11 847 2015
PubMed-ID: 26414444  |  Reference-DOI: 10.1038/NCHEMBIO.1927

(-) Compounds

Molecule 1 - XYLOSIDE XYLOSYLTRANSFERASE 1
    Chains: A, B
    EC Number: 2.4.2.-
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293T
    Expression System Taxid: 9606
    Gene: XXYLT1
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION
2SO41Ligand/IonSULFATE ION
3UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2SO41Ligand/IonSULFATE ION
3UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2SO4-1Ligand/IonSULFATE ION
3UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2SO41Ligand/IonSULFATE ION
3UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:225 , ASP A:227 , HIS A:382 , UDP A:402binding site for residue MN A 401
2AC2SOFTWAREMET A:103 , PHE A:104 , THR A:105 , LEU A:113 , ASP A:225 , LEU A:226 , ASP A:227 , HIS A:382 , ASN A:384 , CYS A:385 , MN A:401 , ASP B:361 , HIS B:362binding site for residue UDP A 402
3AC3SOFTWAREARG A:261 , ARG A:268 , TYR A:364 , SER B:195binding site for residue SO4 A 403
4AC4SOFTWAREASP B:225 , ASP B:227 , HIS B:382 , UDP B:402binding site for residue MN B 401
5AC5SOFTWARETRP A:358 , ASP A:361 , HIS A:362 , MET B:103 , PHE B:104 , THR B:105 , LEU B:113 , LYS B:116 , ASP B:225 , LEU B:226 , ASP B:227 , ASN B:384 , CYS B:385 , MN B:401binding site for residue UDP B 402

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:349 -A:374
2A:356 -A:385
3B:349 -B:374
4B:356 -B:385

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:280 -Pro A:281
2Pro B:280 -Pro B:281

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WLZ)

(-) 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:286
                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee......hhhhhhhhhhhhhhhhhhh......eeeeeeeehhhhhhhhhhhhh....eeeeeeeehhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh......eeee...eee...hhhhhhhhh.......eeeee...hhhhhhhhhhhhhh...............eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh...eeeehhhhhee..hhhhhh....hhhhhhh......eee.hhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wlz A  95 PVDYHLLMMFTKAEHNAPLQAKARVALSSLLRLAKFEAHEVLNLHFVSEEASREVAKALLRELLFKCKVIFHDVAVLTDKLFPVVEAMQKYFSAYYSDSIFFLSVAMHQIMPKEIPRIIQLDLDLKYKTNIRELFEEFDNFLPGAVIGIAREMQPVYRHTFWQFRHENPKTRVGDPPPEGLPGFNSGVMLLNLEAMRQSPLYSHLLEPSWVQQLADKYHFRGHLGDQDFFTMIGMEHPELFHVLDCTWNRQLCTWWRDHGYSDVFQAYFRCEGHVKIYHGNCNTPI 389
                                   104       114       124       134       144       154   ||  169       179       189   ||  203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383      
                                                                                         158|                          193|                                                                                                                                                                                               
                                                                                          164                           198                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee......hhhhhhhhhhhhhhhhh........eeeeeee.hhhhhhhhhhhhhh.......eeehhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhhhh..hhhhhh.....eeeee...eee..hhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhh...............eeeeeeeeehhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhh...eeeehhhhhee....hhhhh...hhhhhhh......eee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wlz B  96 VDYHLLMMFTKAEHNAPLQAKARVALSSLLRLAKFEAHEVLNLHFVSEEASREVAKALLRELLFKCKVIFHDVAVLTDKLFPVVEAMQKYFSAGSGTYYSDSIFFLSVAMHQIMPKEIPRIIQLDLDLKYKTNIRELFEEFDNFLPGAVIGIAREMQPVYRHTFWQFRHENPKTRVGDPPPEGLPGFNSGVMLLNLEAMRQSPLYSHLLEPSWVQQLADKYHFRGHLGDQDFFTMIGMEHPELFHVLDCTWNRQLCTWWRDHGYSDVFQAYFRCEGHVKIYHGNCNTPIP 390
                                   105       115       125       135       145       155  ||   170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390
                                                                                        158|                                                                                                                                                                                                                                  
                                                                                         164
   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 4WLZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

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 Related Entries

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

UniProtKB/Swiss-Prot
        XXLT1_MOUSE | Q3U4G3: 4wlg 4wlm 4wm0 4wma 4wmb 4wmi 4wmk 4wn2 4wnh

(-) Related Entries Specified in the PDB File

4wlg 4wlm 4wm0 4wma 4wmb