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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-GAL-BETA1,4-GLC-BETA
 
Authors :  B. Ramakrishnan, P. K. Qasba
Date :  28 Mar 12  (Deposition) - 04 Jul 12  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
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  (2x)
Biol. Unit 5:  A,B,C  (1x)
Keywords :  Enzyme-Carbohydrate Complex, 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 (2x): ABC
Biological Unit 5 (1x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 39)

Asymmetric Unit (7, 39)
No.NameCountTypeFull Name
1BGC3Ligand/IonBETA-D-GLUCOSE
2GAL3Ligand/IonBETA-D-GALACTOSE
3GOL4Ligand/IonGLYCEROL
4MN3Ligand/IonMANGANESE (II) ION
5NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO420Ligand/IonSULFATE ION
7UDP3Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 1 (6, 11)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2GAL1Ligand/IonBETA-D-GALACTOSE
3GOL1Ligand/IonGLYCEROL
4MN-1Ligand/IonMANGANESE (II) ION
5NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO46Ligand/IonSULFATE ION
7UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 2 (6, 14)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2GAL1Ligand/IonBETA-D-GALACTOSE
3GOL2Ligand/IonGLYCEROL
4MN-1Ligand/IonMANGANESE (II) ION
5NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO48Ligand/IonSULFATE ION
7UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 3 (6, 11)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2GAL1Ligand/IonBETA-D-GALACTOSE
3GOL1Ligand/IonGLYCEROL
4MN-1Ligand/IonMANGANESE (II) ION
5NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO46Ligand/IonSULFATE ION
7UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 4 (6, 72)
No.NameCountTypeFull Name
1BGC6Ligand/IonBETA-D-GLUCOSE
2GAL6Ligand/IonBETA-D-GALACTOSE
3GOL8Ligand/IonGLYCEROL
4MN-1Ligand/IonMANGANESE (II) ION
5NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO440Ligand/IonSULFATE ION
7UDP6Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 5 (6, 36)
No.NameCountTypeFull Name
1BGC3Ligand/IonBETA-D-GLUCOSE
2GAL3Ligand/IonBETA-D-GALACTOSE
3GOL4Ligand/IonGLYCEROL
4MN-1Ligand/IonMANGANESE (II) ION
5NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO420Ligand/IonSULFATE ION
7UDP3Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (39, 39)

Asymmetric Unit (39, 39)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:275 , TRP A:310 , GAL A:402 , NAG A:403 , HOH A:702BINDING SITE FOR RESIDUE BGC A 401
02AC2SOFTWARETRP A:310 , ARG A:355 , PHE A:356 , BGC A:401 , NAG A:403BINDING SITE FOR RESIDUE GAL A 402
03AC3SOFTWAREPHE A:276 , TYR A:282 , TYR A:285 , GLY A:311 , GLY A:312 , ASP A:314 , ASP A:315 , ARG A:355 , BGC A:401 , GAL A:402 , GOL A:406 , HOH A:650BINDING SITE FOR RESIDUE NAG A 403
04AC4SOFTWAREPRO 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 , HIS A:340 , HIS A:343 , ASP A:346 , MN A:405 , GOL A:406 , HOH A:565 , HOH A:625 , HOH A:673 , HOH A:691BINDING SITE FOR RESIDUE UDP A 404
05AC5SOFTWAREASP A:250 , HIS A:340 , HIS A:343 , UDP A:404BINDING SITE FOR RESIDUE MN A 405
06AC6SOFTWARETRP A:310 , GLY A:311 , GLU A:313 , ASP A:314 , NAG A:403 , UDP A:404 , HOH A:584 , HOH A:758BINDING SITE FOR RESIDUE GOL A 406
07AC7SOFTWAREGLU A:144 , PHE A:145 , ASN A:146 , ARG A:339BINDING SITE FOR RESIDUE SO4 A 407
08AC8SOFTWAREASN A:160 , TYR A:167 , PRO A:169 , ARG A:170 , HOH A:605 , HOH A:692 , HOH A:753BINDING SITE FOR RESIDUE SO4 A 408
09AC9SOFTWAREARG A:267 , HOH A:566 , HOH A:581BINDING SITE FOR RESIDUE SO4 A 409
10BC1SOFTWAREHIS A:343 , SER A:344BINDING SITE FOR RESIDUE SO4 A 410
11BC2SOFTWARELYS A:162 , MET A:163BINDING SITE FOR RESIDUE SO4 A 411
12BC3SOFTWAREPHE A:318 , SER A:327 , ILE A:328 , PHE B:318 , ILE B:328BINDING SITE FOR RESIDUE SO4 A 412
13BC4SOFTWAREGAL B:402 , NAG B:403BINDING SITE FOR RESIDUE BGC B 401
14BC5SOFTWARETRP B:310 , ARG B:355 , BGC B:401 , NAG B:403BINDING SITE FOR RESIDUE GAL B 402
15BC6SOFTWAREPHE B:276 , TYR B:282 , TYR B:285 , GLY B:311 , GLY B:312 , ASP B:314 , ASP B:315 , ARG B:355 , BGC B:401 , GAL B:402 , GOL B:406 , HOH B:504BINDING SITE FOR RESIDUE NAG B 403
16BC7SOFTWAREPRO 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:405 , GOL B:406 , HOH B:528 , HOH B:596 , HOH B:614BINDING SITE FOR RESIDUE UDP B 404
17BC8SOFTWAREASP B:250 , HIS B:340 , HIS B:343 , UDP B:404BINDING SITE FOR RESIDUE MN B 405
18BC9SOFTWARETRP B:310 , GLY B:311 , GLU B:313 , NAG B:403 , UDP B:404 , HOH B:504 , HOH B:770 , HOH B:775BINDING SITE FOR RESIDUE GOL B 406
19CC1SOFTWARESER A:368 , ASP A:369 , ARG B:185 , ASN B:186 , ASN B:215 , HOH B:767BINDING SITE FOR RESIDUE GOL B 407
20CC2SOFTWAREGLU B:144 , PHE B:145 , ASN B:146 , ARG B:339 , ARG B:342BINDING SITE FOR RESIDUE SO4 B 408
21CC3SOFTWAREASN B:160 , TYR B:167 , PRO B:169 , ARG B:170 , HOH B:562 , HOH B:579 , HOH B:628 , HOH B:708BINDING SITE FOR RESIDUE SO4 B 409
22CC4SOFTWAREARG B:267 , PRO B:331 , HOH B:577BINDING SITE FOR RESIDUE SO4 B 410
23CC5SOFTWAREHIS B:343 , SER B:344BINDING SITE FOR RESIDUE SO4 B 411
24CC6SOFTWAREGLN B:233 , TYR B:376 , HOH B:575BINDING SITE FOR RESIDUE SO4 B 412
25CC7SOFTWAREPRO B:148 , VAL B:149 , ASP B:150 , TYR B:196BINDING SITE FOR RESIDUE SO4 B 413
26CC8SOFTWAREASN B:306 , TRP B:308 , ARG B:358 , PRO B:397 , SER B:398 , HOH B:627BINDING SITE FOR RESIDUE SO4 B 414
27CC9SOFTWAREASP B:150 , LEU B:151 , GLU B:152 , LYS B:192 , HOH B:685BINDING SITE FOR RESIDUE SO4 B 415
28DC1SOFTWARETRP C:310 , GAL C:402 , NAG C:403 , HOH C:645BINDING SITE FOR RESIDUE BGC C 401
29DC2SOFTWAREARG C:355 , BGC C:401 , NAG C:403BINDING SITE FOR RESIDUE GAL C 402
30DC3SOFTWAREPHE C:276 , TYR C:282 , TYR C:285 , GLY C:311 , GLY C:312 , ASP C:314 , ASP C:315 , ARG C:355 , BGC C:401 , GAL C:402 , GOL C:406BINDING SITE FOR RESIDUE NAG C 403
31DC4SOFTWAREPRO 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:405 , GOL C:406 , HOH C:587BINDING SITE FOR RESIDUE UDP C 404
32DC5SOFTWAREASP C:250 , HIS C:340 , HIS C:343 , UDP C:404 , HOH C:587BINDING SITE FOR RESIDUE MN C 405
33DC6SOFTWAREARG C:224 , TRP C:310 , GLY C:311 , GLU C:313 , ASP C:314 , NAG C:403 , UDP C:404 , HOH C:577BINDING SITE FOR RESIDUE GOL C 406
34DC7SOFTWAREASN C:160 , TYR C:167 , PRO C:169 , ARG C:170 , HOH C:527 , HOH C:534 , HOH C:572 , HOH C:647 , HOH C:663BINDING SITE FOR RESIDUE SO4 C 407
35DC8SOFTWAREGLU C:234 , LYS C:237 , TYR C:376 , GLN C:377 , VAL C:378BINDING SITE FOR RESIDUE SO4 C 408
36DC9SOFTWAREGLU C:144 , PHE C:145 , ASN C:146 , ARG C:339BINDING SITE FOR RESIDUE SO4 C 409
37EC1SOFTWAREHIS C:343 , SER C:344BINDING SITE FOR RESIDUE SO4 C 410
38EC2SOFTWAREARG C:267 , PRO C:331BINDING SITE FOR RESIDUE SO4 C 411
39EC3SOFTWAREPHE C:263 , SER C:264 , HOH C:512BINDING SITE FOR RESIDUE SO4 C 412

(-) 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 4EEA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EEA)

(-) 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 d4eeaa_ A: 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..eeeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eea 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 d4eeab_ B: 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
                 4eea 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 d4eeac_ 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..eeeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eea 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
   Legend:   → Mismatch (orange background)
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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 4EEA)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (60, 60)

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  2.4.1.22
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  2.4.1.38
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  2.4.1.90
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
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    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
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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 4eeg 4eem 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
4eeg M340H-B4GAL-T1 COMPLEX WITH GLCNAC-BETA1,6-GAL-BETA
4eem M340H-B4GAL-T1 COMPLEX WITH GLCNAC-BETA1,6-MAN-ALPHA-METHYL
4eeo M340H-B4GAL-T1 COMPLEX WITH GLCNAC-BETA1,6-GLCNAC-ALPHA- BENZYL