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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN M340H-BETA-1,4-GALACTOSYLTRANSFERASE-1 (M340H-B4GAL-T1) IN COMPLEX WITH GLCNAC-BETA1,6-MAN-ALPHA-METHYL
 
Authors :  B. Ramakrishnan, P. K. Qasba
Date :  28 Mar 12  (Deposition) - 04 Jul 12  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  A,B,C  (1x)
Keywords :  Protein Carbohydrate Interactions, Gt-A Fold, Glycosyltransferase, Udp-Galactose, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Ramakrishnan, E. Boeggeman, P. K. Qasba
Binding Of N-Acetylglucosamine (Glcnac) Beta 1-6-Branched Oligosaccharide Acceptors To Beta 4-Galactosyltransferase I Reveals A New Ligand Binding Mode.
J. Biol. Chem. V. 287 28666 2012
PubMed-ID: 22740701  |  Reference-DOI: 10.1074/JBC.M112.373514

(-) Compounds

Molecule 1 - BETA-1,4-GALACTOSYLTRANSFERASE 1
    Chains: A, B, C
    EC Number: 2.4.1.-, 2.4.1.22, 2.4.1.90, 2.4.1.38
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET23A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN
    Gene: B4GALT1, GGTB2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C
Biological Unit 4 (1x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 30)

Asymmetric Unit (6, 30)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MMA3Ligand/IonO1-METHYL-MANNOSE
3MN3Ligand/IonMANGANESE (II) ION
4NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SO414Ligand/IonSULFATE ION
6UDP3Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 1 (5, 9)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MMA1Ligand/IonO1-METHYL-MANNOSE
3MN-1Ligand/IonMANGANESE (II) ION
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SO44Ligand/IonSULFATE ION
6UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 2 (5, 11)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MMA1Ligand/IonO1-METHYL-MANNOSE
3MN-1Ligand/IonMANGANESE (II) ION
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SO47Ligand/IonSULFATE ION
6UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 3 (5, 7)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MMA1Ligand/IonO1-METHYL-MANNOSE
3MN-1Ligand/IonMANGANESE (II) ION
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SO43Ligand/IonSULFATE ION
6UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 4 (5, 27)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MMA3Ligand/IonO1-METHYL-MANNOSE
3MN-1Ligand/IonMANGANESE (II) ION
4NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SO414Ligand/IonSULFATE ION
6UDP3Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (30, 30)

Asymmetric Unit (30, 30)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:282 , ASP A:315 , NAG A:402 , HOH A:593 , HOH A:659BINDING SITE FOR RESIDUE MMA A 401
02AC2SOFTWAREPHE A:276 , TYR A:282 , TYR A:285 , TRP A:310 , GLY A:311 , GLY A:312 , ASP A:314 , ASP A:315 , ARG A:355 , MMA A:401 , GOL A:409 , HOH A:593 , HOH A:629 , HOH A:653BINDING SITE FOR RESIDUE NAG A 402
03AC3SOFTWAREPRO A:183 , PHE A:184 , ARG A:185 , ARG A:187 , PHE A:222 , ASP A:248 , VAL A:249 , ASP A:250 , LYS A:275 , TRP A:310 , HIS A:340 , HIS A:343 , ASP A:346 , MN A:404 , GOL A:409 , HOH A:549 , HOH A:590 , HOH A:591 , HOH A:614 , HOH A:629 , HOH A:645BINDING SITE FOR RESIDUE UDP A 403
04AC4SOFTWAREASP A:250 , HIS A:340 , HIS A:343 , UDP A:403 , HOH A:549BINDING SITE FOR RESIDUE MN A 404
05AC5SOFTWAREGLU A:144 , PHE A:145 , ASN A:146 , ARG A:339BINDING SITE FOR RESIDUE SO4 A 405
06AC6SOFTWAREASN A:160 , TYR A:167 , PRO A:169 , ARG A:170 , HOH A:640 , HOH A:676 , HOH A:679BINDING SITE FOR RESIDUE SO4 A 406
07AC7SOFTWAREARG A:267 , HOH A:584BINDING SITE FOR RESIDUE SO4 A 407
08AC8SOFTWAREARG A:358 , ASN B:186BINDING SITE FOR RESIDUE SO4 A 408
09AC9SOFTWAREARG A:224 , TRP A:310 , GLY A:311 , GLU A:313 , ASP A:314 , NAG A:402 , UDP A:403 , HOH A:580 , HOH A:607BINDING SITE FOR RESIDUE GOL A 409
10BC1SOFTWARESER A:368 , ASP A:369 , PHE B:184 , ARG B:185 , ASN B:186 , ASN B:215 , HOH B:713BINDING SITE FOR RESIDUE GOL A 410
11BC2SOFTWARETYR B:282 , ASP B:315 , NAG B:402 , HOH B:617BINDING SITE FOR RESIDUE MMA B 401
12BC3SOFTWAREPHE B:276 , TYR B:282 , TYR B:285 , GLY B:311 , GLY B:312 , ASP B:314 , ASP B:315 , ARG B:355 , MMA B:401 , HOH B:617BINDING SITE FOR RESIDUE NAG B 402
13BC4SOFTWAREHOH A:510 , PRO B:183 , PHE B:184 , ARG B:185 , ARG B:187 , PHE B:222 , ASP B:248 , VAL B:249 , ASP B:250 , LYS B:275 , TRP B:310 , HIS B:340 , HIS B:343 , ASP B:346 , MN B:404 , GOL B:412 , HOH B:585BINDING SITE FOR RESIDUE UDP B 403
14BC5SOFTWAREASP B:250 , HIS B:340 , HIS B:343 , UDP B:403BINDING SITE FOR RESIDUE MN B 404
15BC6SOFTWAREASN B:160 , TYR B:167 , PRO B:169 , ARG B:170 , HOH B:576 , HOH B:577 , HOH B:592 , HOH B:622 , HOH B:672BINDING SITE FOR RESIDUE SO4 B 405
16BC7SOFTWAREASN B:306 , TRP B:308 , ARG B:358 , SER B:398 , HOH B:646BINDING SITE FOR RESIDUE SO4 B 406
17BC8SOFTWAREHIS B:343 , SER B:344 , HOH B:706BINDING SITE FOR RESIDUE SO4 B 407
18BC9SOFTWAREGLU B:144 , PHE B:145 , ASN B:146 , ARG B:339 , ARG B:342 , HOH B:588 , HOH B:690BINDING SITE FOR RESIDUE SO4 B 408
19CC1SOFTWAREARG B:267 , PRO B:331 , HOH B:567BINDING SITE FOR RESIDUE SO4 B 409
20CC2SOFTWAREASP B:150 , LEU B:151BINDING SITE FOR RESIDUE SO4 B 410
21CC3SOFTWAREPHE B:263 , SER B:264 , HOH B:506BINDING SITE FOR RESIDUE SO4 B 411
22CC4SOFTWAREARG B:224 , TRP B:310 , GLY B:311 , GLU B:313 , ASP B:314 , UDP B:403 , HOH B:701 , HOH B:711BINDING SITE FOR RESIDUE GOL B 412
23CC5SOFTWARETYR C:282 , NAG C:402BINDING SITE FOR RESIDUE MMA C 401
24CC6SOFTWAREPHE C:276 , TYR C:282 , TYR C:285 , TRP C:310 , GLY C:311 , GLY C:312 , ASP C:314 , ASP C:315 , ARG C:355 , MMA C:401 , GOL C:408 , HOH C:594BINDING SITE FOR RESIDUE NAG C 402
25CC7SOFTWAREPRO C:183 , PHE C:184 , ARG C:185 , ARG C:187 , PHE C:222 , ASP C:248 , VAL C:249 , ASP C:250 , LYS C:275 , TRP C:310 , HIS C:340 , HIS C:343 , ASP C:346 , MN C:404 , GOL C:408 , HOH C:544BINDING SITE FOR RESIDUE UDP C 403
26CC8SOFTWAREASP C:250 , HIS C:340 , HIS C:343 , UDP C:403 , HOH C:542BINDING SITE FOR RESIDUE MN C 404
27CC9SOFTWAREASN C:160 , TYR C:167 , PRO C:169 , ARG C:170 , HOH C:545 , HOH C:556 , HOH C:633BINDING SITE FOR RESIDUE SO4 C 405
28DC1SOFTWAREGLU C:144 , PHE C:145 , ASN C:146 , ARG C:339BINDING SITE FOR RESIDUE SO4 C 406
29DC2SOFTWAREHIS C:343 , SER C:344BINDING SITE FOR RESIDUE SO4 C 407
30DC3SOFTWAREARG C:224 , TRP C:310 , GLY C:311 , GLU C:313 , ASP C:314 , NAG C:402 , UDP C:403 , HOH C:588 , HOH C:607BINDING SITE FOR RESIDUE GOL C 408

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:130 -A:172
2A:243 -A:262
3B:130 -B:172
4B:243 -B:262
5C:130 -C:172
6C:243 -C:262

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EEM)

(-) 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:273
                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4eema_ A: automated matches                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................hhhhhhhhh.......ee.........eeeeeeee..hhhhhhhhhhhhhhhhhhh..eeeeeeeee......hhhhhhhhhhhhhh......eeeee...eee.............ee...ee.hhh...........eeeeehhhhhhh...........hhhhhhhhhhhhh............eeee.............hhhhhhhhhhhhh...hhhhh..eeeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eem A 126 SLPACPEESPLLVGPMLIEFNMPVDLELVAKQNPNVKMGGRYAPRDCVSPHKVAIIIPFRNRQEHLKYWLYYLHPVLQRQQLDYGIYVINQAGDTIFNRAKLLNVGFQEALKDYDYTCFVFSDVDLIPMNDHNAYRCFSQPRHISVAMDKFGFSLPYVQYFGGVSALSKQQFLTINGFPNNYWGWGGEDDDIFNRLVFRGMSISRPNAVVGTTRHIRHSRDKKNEPNPQRFDRIAHTKETMLSDGLNSLTYQVLDVQRYPLYTQITVDIGTPS 398
                                   135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395   


Chain B from PDB  Type:PROTEIN  Length:273
                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4eemb_ B: automated matches                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................hhhhhhhhh.......ee.........eeeeeeee..hhhhhhhhhhhhhhhhhhh..eeeeeeeee......hhhhhhhhhhhhhh......eeeee...eee.............ee...ee.hhh...........eeeeehhhhhhh...........hhhhhhhhhhhhh............eeee.............hhhhhhhhhhhhh...hhhhh..eeeeeeee..eeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eem B 126 SLPACPEESPLLVGPMLIEFNMPVDLELVAKQNPNVKMGGRYAPRDCVSPHKVAIIIPFRNRQEHLKYWLYYLHPVLQRQQLDYGIYVINQAGDTIFNRAKLLNVGFQEALKDYDYTCFVFSDVDLIPMNDHNAYRCFSQPRHISVAMDKFGFSLPYVQYFGGVSALSKQQFLTINGFPNNYWGWGGEDDDIFNRLVFRGMSISRPNAVVGTTRHIRHSRDKKNEPNPQRFDRIAHTKETMLSDGLNSLTYQVLDVQRYPLYTQITVDIGTPS 398
                                   135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395   


Chain C from PDB  Type:PROTEIN  Length:273
                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4eemc_ C: automated matches                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................hhhhhhhhh.......ee.........eeeeeeee..hhhhhhhhhhhhhhhhhhh..eeeeeeeee......hhhhhhhhhhhhhhhhh...eeeee...eee.............ee...ee.hhh...........eeeeehhhhhhh...........hhhhhhhhhhhhh............eeee.............hhhhhhhhhhhhh...hhhhh..eeeeeeee..eeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eem C 126 SLPACPEESPLLVGPMLIEFNMPVDLELVAKQNPNVKMGGRYAPRDCVSPHKVAIIIPFRNRQEHLKYWLYYLHPVLQRQQLDYGIYVINQAGDTIFNRAKLLNVGFQEALKDYDYTCFVFSDVDLIPMNDHNAYRCFSQPRHISVAMDKFGFSLPYVQYFGGVSALSKQQFLTINGFPNNYWGWGGEDDDIFNRLVFRGMSISRPNAVVGTTRHIRHSRDKKNEPNPQRFDRIAHTKETMLSDGLNSLTYQVLDVQRYPLYTQITVDIGTPS 398
                                   135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395
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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  (1, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (60, 60)

Asymmetric Unit(hide GO term definitions)

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  B4GT1_HUMAN | P15291
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 Related Entries

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

UniProtKB/Swiss-Prot
        B4GT1_HUMAN | P15291: 2ae7 2aec 2aes 2agd 2ah9 2fy7 2fya 2fyb 3ee5 4ee3 4ee4 4ee5 4eea 4eeg 4eeo 4l41

(-) Related Entries Specified in the PDB File

4ee3 M340H-B4GAL-T1 COMPLEX WITH A PENTASACCHARIDE
4ee4 M340H-B4GAL-T1 COMPLEX WITH A TETRASACCHARIDE
4ee5 M340H-B4GAL-T1 COMPLEX WITH TRISACCHARIDE
4eea M340H-B4GAL-T1 COMPLEX WITH GLCNAC-BETA1,6-GAL-BETA1,4-GLC- BETA
4eeg M340H-B4GAL-T1 COMPLEX WITH GLCNAC-BETA1,6-GAL-BETA
4eeo M340H-B4GAL-T1 COMPLEX WITH GLCNAC-BETA1,6-GLCNAC-ALPHA- BENZYL