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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN M340H-BETA-1,4-GALACTOSYLTRANSFERASE-1 (M340H-B4GAL-T1) IN COMPLEX WITH PENTASACCHARIDE
 
Authors :  B. Ramakrishnan, P. K. Qasba
Date :  28 Mar 12  (Deposition) - 04 Jul 12  (Release) - 02 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
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 Complex, 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, BETA4GAL-T1, 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, 42)

Asymmetric Unit (7, 42)
No.NameCountTypeFull Name
1BGC3Ligand/IonBETA-D-GLUCOSE
2GAL6Ligand/IonBETA-D-GALACTOSE
3GOL3Ligand/IonGLYCEROL
4MN3Ligand/IonMANGANESE (II) ION
5NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO418Ligand/IonSULFATE ION
7UDH3Ligand/Ion6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE
Biological Unit 1 (6, 15)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2GAL2Ligand/IonBETA-D-GALACTOSE
3GOL1Ligand/IonGLYCEROL
4MN-1Ligand/IonMANGANESE (II) ION
5NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO48Ligand/IonSULFATE ION
7UDH1Ligand/Ion6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE
Biological Unit 2 (6, 13)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2GAL2Ligand/IonBETA-D-GALACTOSE
3GOL1Ligand/IonGLYCEROL
4MN-1Ligand/IonMANGANESE (II) ION
5NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO46Ligand/IonSULFATE ION
7UDH1Ligand/Ion6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE
Biological Unit 3 (6, 11)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2GAL2Ligand/IonBETA-D-GALACTOSE
3GOL1Ligand/IonGLYCEROL
4MN-1Ligand/IonMANGANESE (II) ION
5NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO44Ligand/IonSULFATE ION
7UDH1Ligand/Ion6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE
Biological Unit 4 (6, 78)
No.NameCountTypeFull Name
1BGC6Ligand/IonBETA-D-GLUCOSE
2GAL12Ligand/IonBETA-D-GALACTOSE
3GOL6Ligand/IonGLYCEROL
4MN-1Ligand/IonMANGANESE (II) ION
5NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO436Ligand/IonSULFATE ION
7UDH6Ligand/Ion6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE
Biological Unit 5 (6, 39)
No.NameCountTypeFull Name
1BGC3Ligand/IonBETA-D-GLUCOSE
2GAL6Ligand/IonBETA-D-GALACTOSE
3GOL3Ligand/IonGLYCEROL
4MN-1Ligand/IonMANGANESE (II) ION
5NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO418Ligand/IonSULFATE ION
7UDH3Ligand/Ion6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE

(-) Sites  (30, 30)

Asymmetric Unit (30, 30)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO 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:407 , HOH A:522 , HOH A:568 , HOH A:572 , HOH A:586 , HOH A:627BINDING SITE FOR RESIDUE UDH A 406
02AC2SOFTWAREASP A:250 , HIS A:340 , HIS A:343 , UDH A:406 , HOH A:522BINDING SITE FOR RESIDUE MN A 407
03AC3SOFTWAREGLU A:144 , PHE A:145 , ASN A:146 , ARG A:339BINDING SITE FOR RESIDUE SO4 A 408
04AC4SOFTWAREASN A:160 , TYR A:167 , PRO A:169 , ARG A:170 , HOH A:602 , HOH A:603 , HOH A:669BINDING SITE FOR RESIDUE SO4 A 409
05AC5SOFTWARETHR A:375 , TYR A:376 , HOH A:671 , ASP B:393 , HOH B:617BINDING SITE FOR RESIDUE SO4 A 410
06AC6SOFTWAREPHE A:263 , ARG A:267 , HOH A:647BINDING SITE FOR RESIDUE SO4 A 411
07AC7SOFTWARESER A:368 , ARG B:185 , ASN B:186 , ASN B:215BINDING SITE FOR RESIDUE SO4 A 412
08AC8SOFTWAREPHE A:263 , SER A:264BINDING SITE FOR RESIDUE SO4 A 413
09AC9SOFTWAREHIS A:343 , SER A:344BINDING SITE FOR RESIDUE SO4 A 414
10BC1SOFTWAREPHE A:318 , SER A:327 , ILE A:328 , PHE B:318 , SER B:327 , ILE B:328BINDING SITE FOR RESIDUE SO4 A 415
11BC2SOFTWAREARG A:224 , ASP A:248 , GLY A:288 , TRP A:310 , GLY A:311 , GLU A:313 , NAG A:403 , HOH A:571 , HOH A:635BINDING SITE FOR RESIDUE GOL A 416
12BC3SOFTWAREPRO 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:407 , GOL B:415 , HOH B:529 , HOH B:556 , HOH B:559 , HOH B:570 , HOH B:616BINDING SITE FOR RESIDUE UDH B 406
13BC4SOFTWAREASP B:250 , HIS B:340 , HIS B:343 , UDH B:406 , HOH B:559BINDING SITE FOR RESIDUE MN B 407
14BC5SOFTWAREASN B:160 , TYR B:167 , PRO B:169 , ARG B:170 , HOH B:585 , HOH B:587 , HOH B:603BINDING SITE FOR RESIDUE SO4 B 408
15BC6SOFTWAREGLU B:144 , PHE B:145 , ARG B:339BINDING SITE FOR RESIDUE SO4 B 409
16BC7SOFTWAREASN B:306 , TRP B:308 , ARG B:358 , SER B:398BINDING SITE FOR RESIDUE SO4 B 410
17BC8SOFTWAREHIS B:343 , SER B:344 , HOH B:598BINDING SITE FOR RESIDUE SO4 B 411
18BC9SOFTWAREARG B:267 , PRO B:331BINDING SITE FOR RESIDUE SO4 B 412
19CC1SOFTWAREASP B:150 , LEU B:151 , LYS B:192 , HOH B:579BINDING SITE FOR RESIDUE SO4 B 413
20CC2SOFTWAREARG B:224 , TRP B:310 , GLY B:311 , GLU B:313 , ASP B:314 , NAG B:403 , UDH B:406 , HOH B:650 , HOH B:668BINDING SITE FOR RESIDUE GOL B 415
21CC3SOFTWAREPRO 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 , ARG C:342 , HIS C:343 , ASP C:346 , MN C:407 , GOL C:412 , HOH C:524 , HOH C:550 , HOH C:599 , HOH C:605 , HOH C:650BINDING SITE FOR RESIDUE UDH C 406
22CC4SOFTWAREASP C:250 , HIS C:340 , HIS C:343 , UDH C:406 , HOH C:524BINDING SITE FOR RESIDUE MN C 407
23CC5SOFTWAREASN C:160 , TYR C:167 , PRO C:169 , ARG C:170 , HOH C:519 , HOH C:602 , HOH C:625BINDING SITE FOR RESIDUE SO4 C 408
24CC6SOFTWAREPHE C:263 , SER C:264BINDING SITE FOR RESIDUE SO4 C 409
25CC7SOFTWAREASN C:306 , TRP C:308 , PRO C:397 , SER C:398BINDING SITE FOR RESIDUE SO4 C 410
26CC8SOFTWAREGLU C:144 , PHE C:145 , ASN C:146 , ARG C:339BINDING SITE FOR RESIDUE SO4 C 411
27CC9SOFTWAREASP C:248 , GLY C:288 , TRP C:310 , GLY C:311 , GLU C:313 , NAG C:403 , UDH C:406 , HOH C:572BINDING SITE FOR RESIDUE GOL C 412
28DC1SOFTWAREPHE 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 , PHE A:356 , GOL A:416 , HOH A:586BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 401 TO 405
29DC2SOFTWAREPHE B:276 , TYR B:282 , TYR B:285 , TRP B:310 , GLY B:311 , GLY B:312 , ASP B:314 , ASP B:315 , ARG B:355 , PHE B:356 , GOL B:415 , HOH B:542 , HOH B:666BINDING SITE FOR CHAIN B OF POLYSACCHARIDE RESIDUES 401 TO 405
30DC3SOFTWAREPHE 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 , GOL C:412 , HOH C:550 , HOH C:564 , HOH C:580 , HOH C:615BINDING SITE FOR CHAIN C OF POLYSACCHARIDE RESIDUES 401 TO 405

(-) 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 4EE3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EE3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EE3)

(-) Exons   (0, 0)

(no "Exon" information available for 4EE3)

(-) 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 d4ee3a_ A: 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..eeeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ee3 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 d4ee3b_ 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..eeeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ee3 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 d4ee3c_ 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
                 4ee3 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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  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  (1, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EE3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EE3)

(-) Gene Ontology  (60, 60)

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

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

(-) Related Entries Specified in the PDB File

2aec CRYSTAL STRUCTURE OF THE M344H-B4GAL-T1 COMPLEX WITHTHE TRISACCHARIDE FROM N-GLYCAN
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
4eem M340H-B4GAL-T1 COMPLEX WITH GLCNAC-BETA1,6-MAN-ALPHA-METHYL
4eeo M340H-B4GAL-T1 COMPLEX WITH GLCNAC-BETA1,6-GLCNAC-ALPHA- BENZYL