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(-) Description

Title :  CRYSTAL STRUCTURE OF CATALYTIC DOMAIN OF HUMAN BETA1,4-GALACTOSYLTRANSFERASE-7 IN OPEN CONFORMATION WITH MANGANSES AND UDP
 
Authors :  Y. Tsutsui, B. Ramakrishnan, P. K. Qasba
Date :  15 Jan 13  (Deposition) - 25 Sep 13  (Release) - 27 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Gt-A Fold, Open Conformation, Manganese And Udp Complex, Glycosyltransferase, Golgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Tsutsui, B. Ramakrishnan, P. K. Qasba
Crystal Structures Of Beta-1, 4-Galactosyltransferase 7 Enzyme Reveal Conformational Changes And Substrate Binding.
J. Biol. Chem. V. 288 31963 2013
PubMed-ID: 24052259  |  Reference-DOI: 10.1074/JBC.M113.509984

(-) Compounds

Molecule 1 - BETA-1,4-GALACTOSYLTRANSFERASE 7
    ChainsA, B
    EC Number2.4.1.-, 2.4.1.133
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET23A
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Gene4GALACTOSYLTRANSFERASE, B4GALT7, BETA1, UNQ748/PRO1478, XGALT1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2IMD1Ligand/IonIMIDAZOLE
3MN2Ligand/IonMANGANESE (II) ION
4UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2IMD1Ligand/IonIMIDAZOLE
3MN-1Ligand/IonMANGANESE (II) ION
4UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2IMD-1Ligand/IonIMIDAZOLE
3MN-1Ligand/IonMANGANESE (II) ION
4UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 3 (3, 9)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2IMD1Ligand/IonIMIDAZOLE
3MN-1Ligand/IonMANGANESE (II) ION
4UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:100 , PHE A:101 , ARG A:102 , ARG A:104 , PHE A:139 , ASP A:163 , VAL A:164 , ASP A:165 , TYR A:194 , MN A:402 , HOH A:579 , HOH A:617BINDING SITE FOR RESIDUE UDP A 401
02AC2SOFTWAREASP A:165 , HIS A:257 , UDP A:401 , HOH A:653BINDING SITE FOR RESIDUE MN A 402
03AC3SOFTWAREARG A:138 , PHE A:139 , GLY A:223BINDING SITE FOR RESIDUE ACT A 403
04AC4SOFTWAREASP A:79 , PRO A:81 , ARG A:117 , ARG A:297BINDING SITE FOR RESIDUE ACT A 404
05AC5SOFTWAREGLY A:91 , PRO A:92 , HOH A:650 , ALA B:88 , GLY B:91 , PRO B:92 , HOH B:637BINDING SITE FOR RESIDUE ACT A 405
06AC6SOFTWAREASP A:174 , GLY A:176 , PHE A:177BINDING SITE FOR RESIDUE ACT A 406
07AC7SOFTWAREPHE A:243 , HOH A:605 , HOH A:608 , HOH B:578BINDING SITE FOR RESIDUE IMD A 407
08AC8SOFTWAREPRO B:100 , PHE B:101 , ARG B:102 , ARG B:104 , PHE B:139 , ASP B:163 , VAL B:164 , ASP B:165 , TYR B:194 , MN B:402 , HOH B:501BINDING SITE FOR RESIDUE UDP B 401
09AC9SOFTWAREASP B:165 , HIS B:257 , UDP B:401 , HOH B:636BINDING SITE FOR RESIDUE MN B 402
10BC1SOFTWAREPRO B:92 , SER B:155BINDING SITE FOR RESIDUE ACT B 403
11BC2SOFTWARETRP B:84 , GLU B:85BINDING SITE FOR RESIDUE ACT B 404

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:316 -A:324
2B:316 -B:324

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IRP)

(-) 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:232
                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.hhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhh.....eeeee...eee..............ee..................eeeeehhhhhhh...........hhhhhhhhhhhhh................eee...............eeeeeeeeeee..eeeeeeeeee......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4irp A  77 GSDIPEHWEEDASWGPHRLAVLVPFRERFEELLVFVPHMRRFLSRKKIRHHIYVLNQVDHFRFNRAALINVGFLESSNSTDYIAMHDVDLLPLNEELDYGFPEAGPFHVASPELHPLYHYKTYVGGILLLSKQHYRLCNGMSNRFWGWGREDDEFYRRIKGAGLQLFRPSGITTGYKTFRHLHFKVDREGGLNTVKYHVASRTALSVGGAPCTVLNIMLDCDKTATPWCTFS 327
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256  ||   285       295       305       315       325  
                                                                                                                                                                                                                259|                                                
                                                                                                                                                                                                                 279                                                

Chain B from PDB  Type:PROTEIN  Length:227
                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.hhhhh..eeeeeeee..hhhhhhhhhhhhhhhhhhh..eeeeeeeee......hhhhhhhhhhhhh.....eeeee...eee..............ee..................eeeeehhhhhhh...........hhhhhhhhhhhhh................eee..........eeeeeeeeeee..eeeeeeeeee......hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4irp B  77 GSDIPEHWEEDASWGPHRLAVLVPFRERFEELLVFVPHMRRFLSRKKIRHHIYVLNQVDHFRFNRAALINVGFLESSNSTDYIAMHDVDLLPLNEELDYGFPEAGPFHVASPELHPLYHYKTYVGGILLLSKQHYRLCNGMSNRFWGWGREDDEFYRRIKGAGLQLFRPSGITTGYKTFRHLREGGLNTVKYHVASRTALSVGGAPCTVLNIMLDCDKTATPWCTFS 327
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256 ||    290       300       310       320       
                                                                                                                                                                                                               258|                                            
                                                                                                                                                                                                                283                                            

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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 4IRP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)

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4irq