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(-) Description

Title :  CRYSTAL STRUCTURE OF CATALYTIC DOMAIN OF HUMAN BETA1, 4GALACTOSYLTRANSFERASE 7 IN CLOSED CONFORMATION IN COMPLEX WITH MANGANESE AND UDP
 
Authors :  Y. Tsutsui, B. Ramakrishnan, P. K. Qasba
Date :  15 Jan 13  (Deposition) - 25 Sep 13  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A,D  (1x)
Biol. Unit 6:  B (1x),C (1x)
Keywords :  Gt-A Fold, Closed 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, C, D
    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

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D
Biological Unit 5 (1x)A  D
Biological Unit 6 (1x) B (1x)C (1x) 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1MN4Ligand/IonMANGANESE (II) ION
2TRS4Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3UDP4Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 5 (2, 4)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 6 (2, 2)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:165 , HIS A:257 , HIS A:259 , UDP A:402 , HOH A:501BINDING SITE FOR RESIDUE MN A 401
02AC2SOFTWAREPRO 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 , TRP A:224 , HIS A:257 , HIS A:259 , ARG A:266 , MN A:401 , TRS A:403 , HOH A:501 , HOH A:531BINDING SITE FOR RESIDUE UDP A 402
03AC3SOFTWARETYR A:199 , TRP A:224 , GLY A:225 , GLU A:227 , ASP A:228 , UDP A:402 , HOH A:514BINDING SITE FOR RESIDUE TRS A 403
04AC4SOFTWAREASP B:165 , HIS B:257 , HIS B:259 , UDP B:402 , HOH B:501BINDING SITE FOR RESIDUE MN B 401
05AC5SOFTWAREPRO 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 , TRP B:224 , HIS B:257 , HIS B:259 , ARG B:266 , MN B:401 , TRS B:403 , HOH B:501 , HOH B:505 , HOH B:524BINDING SITE FOR RESIDUE UDP B 402
06AC6SOFTWARETYR B:194 , TYR B:199 , TRP B:224 , GLY B:225 , GLU B:227 , ASP B:228 , UDP B:402 , HOH B:532BINDING SITE FOR RESIDUE TRS B 403
07AC7SOFTWAREASP C:165 , HIS C:257 , HIS C:259 , UDP C:402 , HOH C:501BINDING SITE FOR RESIDUE MN C 401
08AC8SOFTWAREPRO C:100 , PHE C:101 , ARG C:102 , ARG C:104 , PHE C:139 , ASP C:163 , VAL C:164 , ASP C:165 , TYR C:194 , TRP C:224 , HIS C:257 , HIS C:259 , ARG C:266 , MN C:401 , TRS C:403 , HOH C:517 , HOH C:563BINDING SITE FOR RESIDUE UDP C 402
09AC9SOFTWAREARG C:141 , TYR C:199 , GLY C:225 , GLU C:227 , ASP C:228 , UDP C:402 , HOH C:526BINDING SITE FOR RESIDUE TRS C 403
10BC1SOFTWAREASP D:165 , HIS D:257 , HIS D:259 , UDP D:402 , HOH D:501BINDING SITE FOR RESIDUE MN D 401
11BC2SOFTWAREPRO D:100 , PHE D:101 , ARG D:102 , ARG D:104 , PHE D:139 , ASP D:163 , VAL D:164 , ASP D:165 , TYR D:194 , TRP D:224 , HIS D:257 , HIS D:259 , ARG D:266 , MN D:401 , TRS D:403 , HOH D:533 , HOH D:536 , HOH D:574BINDING SITE FOR RESIDUE UDP D 402
12BC3SOFTWAREARG D:141 , TYR D:194 , TYR D:199 , TRP D:224 , GLY D:225 , GLU D:227 , ASP D:228 , UDP D:402 , HOH D:544BINDING SITE FOR RESIDUE TRS D 403

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:316 -A:324
2B:316 -B:324
3C:316 -C:324
4D:316 -D:324

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IRQ)

(-) 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:246
                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............eeeeeeee..hhhhhhhhhhhhhhhhhhh..eeeeeeeee......hhhhhhhhhhhhh.....eeeee...eee..............ee..................eeeeehhhhhhh...........hhhhhhhhhhhhh...........hhhh.eee...............hhhhhh.............eeeeeeeeeee..eeeeeeeeee......hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4irq A  82 EHWEEDASWGPHRLAVLVPFRERFEELLVFVPHMRRFLSRKKIRHHIYVLNQVDHFRFNRAALINVGFLESSNSTDYIAMHDVDLLPLNEELDYGFPEAGPFHVASPELHPLYHYKTYVGGILLLSKQHYRLCNGMSNRFWGWGREDDEFYRRIKGAGLQLFRPSGITTGYKTFRHLHDPAWRKRDQKRIAAQKQEQFKVDREGGLNTVKYHVASRTALSVGGAPCTVLNIMLDCDKTATPWCTFS 327
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321      

Chain B from PDB  Type:PROTEIN  Length:240
                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeee..hhhhhhhhhhhhhhhhhhh..eeeeeeeee......hhhhhhhhhhhhh.....eeeee....ee..............ee..................eeeeehhhhhhh...........hhhhhhhhhhhhh................ee................hhhhhh.............eeeeeeeeeee..eeeeeeeeee......hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4irq B  88 ASWGPHRLAVLVPFRERFEELLVFVPHMRRFLSRKKIRHHIYVLNQVDHFRFNRAALINVGFLESSNSTDYIAMHDVDLLPLNEELDYGFPEAGPFHVASPELHPLYHYKTYVGGILLLSKQHYRLCNGMSNRFWGWGREDDEFYRRIKGAGLQLFRPSGITTGYKTFRHLHDPAWRKRDQKRIAAQKQEQFKVDREGGLNTVKYHVASRTALSVGGAPCTVLNIMLDCDKTATPWCTFS 327
                                    97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327

Chain C from PDB  Type:PROTEIN  Length:249
                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeeeee..hhhhhhhhhhhhhhhhhhh..eeeeeeeee......hhhhhhhhhhhhh.....eeeee...eee..............ee..................eeeeehhhhhhh...........hhhhhhhhhhhh............hhhh.eee.............hhhhhh...............eeeeeeeeeee..eeeeeeeeee......hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4irq C  79 DIPEHWEEDASWGPHRLAVLVPFRERFEELLVFVPHMRRFLSRKKIRHHIYVLNQVDHFRFNRAALINVGFLESSNSTDYIAMHDVDLLPLNEELDYGFPEAGPFHVASPELHPLYHYKTYVGGILLLSKQHYRLCNGMSNRFWGWGREDDEFYRRIKGAGLQLFRPSGITTGYKTFRHLHDPAWRKRDQKRIAAQKQEQFKVDREGGLNTVKYHVASRTALSVGGAPCTVLNIMLDCDKTATPWCTFS 327
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318         

Chain D from PDB  Type:PROTEIN  Length:243
                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeee..hhhhhhhhhhhhhhhhhhh..eeeeeeeee......hhhhhhhhhhhhh.....eeeee...eee..............ee..................eeeeehhhhhhh...........hhhhhhhhhhhhh...........hhhh.eee...............hhhhhh.............eeeeeeeeeee..eeeeeeeeee......hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4irq D  85 EEDASWGPHRLAVLVPFRERFEELLVFVPHMRRFLSRKKIRHHIYVLNQVDHFRFNRAALINVGFLESSNSTDYIAMHDVDLLPLNEELDYGFPEAGPFHVASPELHPLYHYKTYVGGILLLSKQHYRLCNGMSNRFWGWGREDDEFYRRIKGAGLQLFRPSGITTGYKTFRHLHDPAWRKRDQKRIAAQKQEQFKVDREGGLNTVKYHVASRTALSVGGAPCTVLNIMLDCDKTATPWCTFS 327
                                    94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324   

   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)

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        B4GT7_HUMAN | Q9UBV74irp

(-) Related Entries Specified in the PDB File

3lw6 DROSOPHILA BETA1,4GALACTOSYLTRANSFERASE
4irp CATALYTIC DOMAIN OF HUMAN BETA1,4GALACTOSYLTRANSFERASE 7 IN OPEN CONFORMATION