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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN M340H-BETA-1,4-GALACTOSYLTRANSFERASE-1 (M340H-B4GAL-T1) IN COMPLEX WITH TRISACCHARIDE FROM LACTO-N-NEOTETRAOSE
 
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  (2x)
Biol. Unit 5:  A,B,C  (1x)
Keywords :  Protein-Carbohydrate Interactions, Gt-A Fold, Glycosyltransferase, 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, 30)

Asymmetric Unit (7, 30)
No.NameCountTypeFull Name
1BGC3Ligand/IonBETA-D-GLUCOSE
2GAL3Ligand/IonBETA-D-GALACTOSE
3GOL4Ligand/IonGLYCEROL
4MN3Ligand/IonMANGANESE (II) ION
5NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO411Ligand/IonSULFATE ION
7UDP3Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 1 (6, 9)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2GAL1Ligand/IonBETA-D-GALACTOSE
3GOL1Ligand/IonGLYCEROL
4MN-1Ligand/IonMANGANESE (II) ION
5NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO44Ligand/IonSULFATE ION
7UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 2 (6, 11)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2GAL1Ligand/IonBETA-D-GALACTOSE
3GOL2Ligand/IonGLYCEROL
4MN-1Ligand/IonMANGANESE (II) ION
5NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO45Ligand/IonSULFATE ION
7UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 3 (6, 7)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2GAL1Ligand/IonBETA-D-GALACTOSE
3GOL1Ligand/IonGLYCEROL
4MN-1Ligand/IonMANGANESE (II) ION
5NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO42Ligand/IonSULFATE ION
7UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 4 (6, 54)
No.NameCountTypeFull Name
1BGC6Ligand/IonBETA-D-GLUCOSE
2GAL6Ligand/IonBETA-D-GALACTOSE
3GOL8Ligand/IonGLYCEROL
4MN-1Ligand/IonMANGANESE (II) ION
5NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO422Ligand/IonSULFATE ION
7UDP6Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 5 (6, 27)
No.NameCountTypeFull Name
1BGC3Ligand/IonBETA-D-GLUCOSE
2GAL3Ligand/IonBETA-D-GALACTOSE
3GOL4Ligand/IonGLYCEROL
4MN-1Ligand/IonMANGANESE (II) ION
5NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO411Ligand/IonSULFATE ION
7UDP3Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (30, 30)

Asymmetric Unit (30, 30)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGAL A:402BINDING SITE FOR RESIDUE BGC A 401
02AC2SOFTWAREBGC A:401 , NAG A:403 , HOH A:547 , HOH A:644BINDING 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 , GAL A:402 , GOL A:406 , HOH A:644BINDING 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 , TRP A:310 , HIS A:340 , HIS A:343 , ASP A:346 , MN A:405 , GOL A:406 , HOH A:551 , HOH A:563 , HOH A:586 , HOH A:619BINDING SITE FOR RESIDUE UDP A 404
05AC5SOFTWAREASP A:250 , HIS A:340 , HIS A:343 , UDP A:404 , HOH A:551BINDING 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:549BINDING SITE FOR RESIDUE GOL A 406
07AC7SOFTWAREGLU A:144 , PHE A:145 , ASN A:146 , ARG A:339 , HOH A:618BINDING SITE FOR RESIDUE SO4 A 407
08AC8SOFTWARETYR A:167 , PRO A:169 , ARG A:170 , HOH A:648 , HOH A:654 , HOH A:671BINDING SITE FOR RESIDUE SO4 A 408
09AC9SOFTWAREARG A:267BINDING SITE FOR RESIDUE SO4 A 409
10BC1SOFTWARETHR A:375 , TYR A:376 , ASP B:393BINDING SITE FOR RESIDUE SO4 A 410
11BC2SOFTWAREGAL B:402BINDING SITE FOR RESIDUE BGC B 401
12BC3SOFTWAREBGC B:401 , NAG B:403 , HOH B:607BINDING SITE FOR RESIDUE GAL B 402
13BC4SOFTWAREPHE B:276 , TYR B:282 , TYR B:285 , GLY B:311 , GLY B:312 , ASP B:314 , ASP B:315 , ARG B:355 , GAL B:402 , GOL B:406 , HOH B:619 , HOH B:667BINDING SITE FOR RESIDUE NAG B 403
14BC5SOFTWAREPRO 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:520 , HOH B:585 , HOH B:609 , HOH B:627 , HOH B:667BINDING SITE FOR RESIDUE UDP B 404
15BC6SOFTWAREASP B:250 , HIS B:340 , HIS B:343 , UDP B:404BINDING SITE FOR RESIDUE MN B 405
16BC7SOFTWAREARG B:224 , TRP B:310 , GLY B:311 , GLU B:313 , NAG B:403 , UDP B:404 , HOH B:594 , HOH B:691 , HOH B:692BINDING SITE FOR RESIDUE GOL B 406
17BC8SOFTWARESER A:368 , ASP A:369 , ARG B:185 , ASN B:186 , ASN B:215 , HOH B:688BINDING SITE FOR RESIDUE GOL B 407
18BC9SOFTWAREGLU B:144 , PHE B:145 , ASN B:146 , ARG B:339 , ARG B:342 , HOH B:583BINDING SITE FOR RESIDUE SO4 B 408
19CC1SOFTWAREHIS B:343 , SER B:344 , HOH B:650BINDING SITE FOR RESIDUE SO4 B 409
20CC2SOFTWAREARG B:267 , PRO B:331BINDING SITE FOR RESIDUE SO4 B 410
21CC3SOFTWAREASN B:160 , TYR B:167 , PRO B:169 , ARG B:170 , HOH B:603 , HOH B:635BINDING SITE FOR RESIDUE SO4 B 411
22CC4SOFTWAREASP B:150 , LEU B:151 , GLU B:152 , LYS B:192 , HOH B:666BINDING SITE FOR RESIDUE SO4 B 412
23CC5SOFTWAREGAL C:402BINDING SITE FOR RESIDUE BGC C 401
24CC6SOFTWAREBGC C:401 , NAG C:403BINDING SITE FOR RESIDUE GAL C 402
25CC7SOFTWAREPHE C:276 , TYR C:282 , TYR C:285 , GLY C:311 , GLY C:312 , ASP C:314 , ASP C:315 , ARG C:355 , GAL C:402 , GOL C:406BINDING SITE FOR RESIDUE NAG C 403
26CC8SOFTWAREPRO 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 , ASN C:349 , MN C:405 , GOL C:406 , HOH C:595 , HOH C:597BINDING SITE FOR RESIDUE UDP C 404
27CC9SOFTWAREASP C:250 , HIS C:340 , HIS C:343 , UDP C:404 , HOH C:584BINDING SITE FOR RESIDUE MN C 405
28DC1SOFTWARETRP C:310 , GLY C:311 , GLU C:313 , ASP C:314 , NAG C:403 , UDP C:404BINDING SITE FOR RESIDUE GOL C 406
29DC2SOFTWAREPHE C:145 , ASN C:146 , ARG C:339BINDING SITE FOR RESIDUE SO4 C 407
30DC3SOFTWAREASN C:160 , TYR C:167 , PRO C:169 , ARG C:170 , HOH C:507 , HOH C:542 , HOH C:559BINDING SITE FOR RESIDUE SO4 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 4EE5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EE5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EE5)

(-) Exons   (0, 0)

(no "Exon" information available for 4EE5)

(-) 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 d4ee5a_ 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
                 4ee5 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 d4ee5b_ B: automated matches                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................hhhhhhhhh.......ee.........eeeeeeee..hhhhhhhhhhhhhhhhhhh..eeeeeeeee......hhhhhhhhhhhhhhh.....eeeee...eee.............ee...ee.hhh...........eeeeehhhhhhh...........hhhhhhhhhhhhh............eeee.............hhhhhhhhhhhhh...hhhhh..eeeeeeee..eeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ee5 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 d4ee5c_ 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
                 4ee5 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 4EE5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EE5)

(-) Gene Ontology  (60, 60)

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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 4eea 4eeg 4eem 4eeo 4l41

(-) Related Entries Specified in the PDB File

2ah9 M344H-B4GAL-T1 COMPLEX WITH CHITOTRIOSE
4ee3 M340H-B4GAL-T1 COMPLEX WITH A PENTASACCHARIDE
4ee4 M340H-B4GAL-T1 COMPLEX WITH A TETRASACCHARIDE
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
4eem M340H-B4GAL-T1 COMPLEX WITH GLCNAC-BETA1,6-MAN-ALPHA-METHYL
4eeo M340H-B4GAL-T1 COMPLEX WITH GLCNAC-BETA1,6-GLCNAC-ALPHA- BENZYL