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Transferase activator/transferase PDB id
1nhe
Jmol
Contents
Protein chains
123 a.a. *
272 a.a. *
Ligands
PG4 ×2
UDP ×2
Metals
_CA ×2
Waters ×331
* Residue conservation analysis
PDB id:
1nhe
Name: Transferase activator/transferase
Title: Crystal structure of lactose synthase complex with udp
Structure: Alpha-lactalbumin. Chain: a, c. Fragment: regulatory subunit of lactose synthase. Synonym: lactalbumin, alpha. Engineered: yes. Other_details: chains a and b form first, c and d second lactose synthase complex. Beta-1,4-galactosyltransferase. Chain: b, d.
Source: Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Bos taurus. Cattle. Organism_taxid: 9913.
Biol. unit: Dimer (from PQS)
Resolution:
2.50Å     R-factor:   0.197     R-free:   0.255
Authors: B.Ramakrishnan,P.K.Qasba
Key ref:
B.Ramakrishnan and P.K.Qasba (2001). Crystal structure of lactose synthase reveals a large conformational change in its catalytic component, the beta1,4-galactosyltransferase-I. J Mol Biol, 310, 205-218. PubMed id: 11419947 DOI: 10.1006/jmbi.2001.4757
Date:
19-Dec-02     Release date:   07-Jan-03    
Supersedes: 1j94
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P29752  (LALBA_MOUSE) -  Alpha-lactalbumin
Seq:
Struc: 		143 a.a.
123 a.a.
Protein chains
Pfam   ArchSchema ?
P08037  (B4GT1_BOVIN) -  Beta-1,4-galactosyltransferase 1
Seq:
Struc: 		402 a.a.
272 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 1: Chains B, D: E.C.2.4.1.22  - Lactose synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: UDP-galactose + D-glucose = UDP + lactose
UDP-galactose
 + D-glucose
 =
UDP
Bound ligand (Het Group name = UDP)
corresponds exactly 		+ lactose
   Enzyme class 2: Chains B, D: E.C.2.4.1.38  - Beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: UDP-galactose + N-acetyl-beta-D-glucosaminylglycopeptide = UDP + beta-D- galactosyl-(1->4)-N-acetyl-beta-D-glucosaminylglycopeptide
UDP-galactose
 + N-acetyl-beta-D-glucosaminylglycopeptide
 =
UDP
Bound ligand (Het Group name = UDP)
corresponds exactly 		+ beta-D- galactosyl-(1->4)-N-acetyl-beta-D-glucosaminylglycopeptide
   Enzyme class 3: Chains B, D: E.C.2.4.1.90  - N-acetyllactosamine synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: UDP-galactose + N-acetyl-D-glucosamine = UDP + N-acetyllactosamine
UDP-galactose
 + N-acetyl-D-glucosamine
 =
UDP
Bound ligand (Het Group name = UDP)
corresponds exactly 		+ N-acetyllactosamine
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     carbohydrate metabolic process   2 terms 
  Biochemical function     protein binding     4 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.2001.4757 J Mol Biol 310:205-218 (2001)
PubMed id: 11419947  
 
 
Crystal structure of lactose synthase reveals a large conformational change in its catalytic component, the beta1,4-galactosyltransferase-I.
B.Ramakrishnan, P.K.Qasba.
 
  ABSTRACT  
 
The lactose synthase (LS) enzyme is a 1:1 complex of a catalytic component, beta1,4-galactosyltransferse (beta4Gal-T1) and a regulatory component, alpha-lactalbumin (LA), a mammary gland-specific protein. LA promotes the binding of glucose (Glc) to beta4Gal-T1, thereby altering its sugar acceptor specificity from N-acetylglucosamine (GlcNAc) to glucose, which enables LS to synthesize lactose, the major carbohydrate component of milk. The crystal structures of LS bound with various substrates were solved at 2 A resolution. These structures reveal that upon substrate binding to beta4Gal-T1, a large conformational change occurs in the region comprising residues 345 to 365. This repositions His347 in such a way that it can participate in the coordination of a metal ion, and creates a sugar and LA-binding site. At the sugar-acceptor binding site, a hydrophobic N-acetyl group-binding pocket is found, formed by residues Arg359, Phe360 and Ile363. In the Glc-bound structure, this hydrophobic pocket is absent. For the binding of Glc to LS, a reorientation of the Arg359 side-chain occurs, which blocks the hydrophobic pocket and maximizes the interactions with the Glc molecule. Thus, the role of LA is to hold Glc by hydrogen bonding with the O-1 hydroxyl group in the acceptor-binding site on beta4Gal-T1, while the N-acetyl group-binding pocket in beta4Gal-T1 adjusts to maximize the interactions with the Glc molecule. This study provides details of a structural basis for the partially ordered kinetic mechanism proposed for lactose synthase.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The molecular structure of LS, a 1:1 complex between the catalytic domain of bovine b4Gal-T1 (residue 130 to 402)[26] and mouse LA. The complex is shown with the acceptor GlcNAc. The interaction of LA with b4Gal-T1 is mostly near the acceptor site, away from both the N and C termini of b4Gal-T1. 		Figure 9.
Figure 9. Molecular surface diagram and interactions showing differences in the acceptor binding pocket at the second exo-cyclic position of GlcNAc and Glc. (a) In the LS·UDP·Mn2+ complex, which does not contain any sugar acceptor, the N-acetyl group binding pocket is still present. (b) In the LS-GlcNAc complex, when the GlcNAc molecule is preset the hydrophobic pocket is completely occupied by the N-acetyl group of GlcNAc. In the absence of the N-acetyl group, this pocket will remain empty if Glc were to bind in this site. (c) and (d) In the LS-Glc complex, Glc binds in this region where the side-chain conformation of Arg359 adopts an orientation that closes the hydrophobic pocket.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 310, 205-218) copyright 2001.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20030628 R.Hurtado-Guerrero, T.Zusman, S.Pathak, A.F.Ibrahim, S.Shepherd, A.Prescott, G.Segal, and D.M.van Aalten (2010).
Molecular mechanism of elongation factor 1A inhibition by a Legionella pneumophila glycosyltransferase.
  Biochem J, 426, 281-292.
PDB codes: 2wzf 2wzg
18712827 A.D.Schuyler, R.L.Jernigan, P.K.Qasba, B.Ramakrishnan, and G.S.Chirikjian (2009).
Iterative cluster-NMA: A tool for generating conformational transitions in proteins.
  Proteins, 74, 760-776.  
18673333 E.A.Landers, H.R.Burkin, G.T.Bleck, L.Howell-Skalla, and D.J.Miller (2009).
Porcine beta1,4-galactosyltransferase-I sequence and expression.
  Reprod Domest Anim, 44, 228-234.  
18694425 G.T.Bleck, M.B.Wheeler, L.B.Hansen, H.Chester-Jones, and D.J.Miller (2009).
Lactose synthase components in milk: concentrations of alpha-lactalbumin and beta1,4-galactosyltransferase in milk of cows from several breeds at various stages of lactation.
  Reprod Domest Anim, 44, 241-247.  
19106107 J.R.Brown, F.Yang, A.Sinha, B.Ramakrishnan, Y.Tor, P.K.Qasba, and J.D.Esko (2009).
Deoxygenated Disaccharide Analogs as Specific Inhibitors of {beta}1-4-Galactosyltransferase 1 and Selectin-mediated Tumor Metastasis.
  J Biol Chem, 284, 4952-4959.
PDB code: 3ee5
19179461 P.Bojarová, K.Krenek, K.Wetjen, K.Adamiak, H.Pelantová, K.Bezouska, L.Elling, and V.Kren (2009).
Synthesis of LacdiNAc-terminated glycoconjugates by mutant galactosyltransferase--a way to new glycodrugs and materials.
  Glycobiology, 19, 509-517.  
18518825 L.L.Lairson, B.Henrissat, G.J.Davies, and S.G.Withers (2008).
Glycosyltransferases: structures, functions, and mechanisms.
  Annu Rev Biochem, 77, 521-555.  
18550823 O.Halskau, R.Perez-Jimenez, B.Ibarra-Molero, J.Underhaug, V.Muñoz, A.Martinez, and J.M.Sanchez-Ruiz (2008).
Large-scale modulation of thermodynamic protein folding barriers linked to electrostatics.
  Proc Natl Acad Sci U S A, 105, 8625-8630.  
18393823 P.K.Qasba, B.Ramakrishnan, and E.Boeggeman (2008).
Structure and function of beta -1,4-galactosyltransferase.
  Curr Drug Targets, 9, 292-309.  
17850816 A.L.Milac, N.V.Buchete, T.A.Fritz, G.Hummer, and L.A.Tabak (2007).
Substrate-induced conformational changes and dynamics of UDP-N-acetylgalactosamine:polypeptide N-acetylgalactosaminyltransferase-2.
  J Mol Biol, 373, 439-451.  
17084860 B.Ramakrishnan, and P.K.Qasba (2007).
Role of a single amino acid in the evolution of glycans of invertebrates and vertebrates.
  J Mol Biol, 365, 570-576.  
17685523 C.Leimkuhler, M.Fridman, T.Lupoli, S.Walker, C.T.Walsh, and D.Kahne (2007).
Characterization of rhodosaminyl transfer by the AknS/AknT glycosylation complex and its use in reconstituting the biosynthetic pathway of aclacinomycin A.
  J Am Chem Soc, 129, 10546-10550.  
17883281 M.C.Hartman, S.Jiang, J.S.Rush, C.J.Waechter, and J.K.Coward (2007).
Glycosyltransferase mechanisms: impact of a 5-fluoro substituent in acceptor and donor substrates on catalysis.
  Biochemistry, 46, 11630-11638.  
17006644 I.Brockhausen, M.Benn, S.Bhat, S.Marone, J.G.Riley, P.Montoya-Peleaz, J.Z.Vlahakis, H.Paulsen, J.S.Schutzbach, and W.A.Szarek (2006).
UDP-Gal: GlcNAc-R beta1,4-galactosyltransferase--a target enzyme for drug design. Acceptor specificity and inhibition of the enzyme.
  Glycoconj J, 23, 525-541.  
16829524 J.E.Pak, P.Arnoux, S.Zhou, P.Sivarajah, M.Satkunarajah, X.Xing, and J.M.Rini (2006).
X-ray crystal structure of leukocyte type core 2 beta1,6-N-acetylglucosaminyltransferase. Evidence for a convergence of metal ion-independent glycosyltransferase mechanism.
  J Biol Chem, 281, 26693-26701.
PDB codes: 2gak 2gam
16741984 S.K.Singh, and N.Kishore (2006).
Elucidating the binding thermodynamics of 8-anilino-1-naphthalene sulfonic acid with the A-state of alpha-lactalbumin: an isothermal titration calorimetric investigation.
  Biopolymers, 83, 205-212.  
15861407 A.Vanhooren, A.Chedad, V.Farkas, Z.Majer, M.Joniau, H.Van Dael, and I.Hanssens (2005).
Tryptophan to phenylalanine substitutions allow differentiation of short- and long-range conformational changes during denaturation of goat alpha-lactalbumin.
  Proteins, 60, 118-130.  
15987364 M.H.Yazer, G.A.Denomme, N.L.Rose, and M.M.Palcic (2005).
Amino-acid substitution in the disordered loop of blood group B-glycosyltransferase enzyme causes weak B phenotype.
  Transfusion, 45, 1178-1182.  
15653326 P.K.Qasba, B.Ramakrishnan, and E.Boeggeman (2005).
Substrate-induced conformational changes in glycosyltransferases.
  Trends Biochem Sci, 30, 53-62.  
15465321 B.Ramakrishnan, E.Boeggeman, V.Ramasamy, and P.K.Qasba (2004).
Structure and catalytic cycle of beta-1,4-galactosyltransferase.
  Curr Opin Struct Biol, 14, 593-600.  
14760744 K.Gunasekaran, and R.Nussinov (2004).
Modulating functional loop movements: the role of highly conserved residues in the correlated loop motions.
  Chembiochem, 5, 224-230.  
14997539 M.S.Sujatha, and P.V.Balaji (2004).
Identification of common structural features of binding sites in galactose-specific proteins.
  Proteins, 55, 44-65.  
15473011 R.Tatsumi, Y.Fukunishi, and H.Nakamura (2004).
A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor.
  J Comput Chem, 25, 1995-2005.  
12590131 H.Takemae, R.Ueda, R.Okubo, H.Nakato, S.Izumi, K.Saigo, and S.Nishihara (2003).
Proteoglycan UDP-galactose:beta-xylose beta 1,4-galactosyltransferase I is essential for viability in Drosophila melanogaster.
  J Biol Chem, 278, 15571-15578.  
12966086 T.Sato, M.Gotoh, K.Kiyohara, A.Kameyama, T.Kubota, N.Kikuchi, Y.Ishizuka, H.Iwasaki, A.Togayachi, T.Kudo, T.Ohkura, H.Nakanishi, and H.Narimatsu (2003).
Molecular cloning and characterization of a novel human beta 1,4-N-acetylgalactosaminyltransferase, beta 4GalNAc-T3, responsible for the synthesis of N,N'-diacetyllactosediamine, galNAc beta 1-4GlcNAc.
  J Biol Chem, 278, 47534-47544.  
11916963 B.Ramakrishnan, and P.K.Qasba (2002).
Structure-based design of beta 1,4-galactosyltransferase I (beta 4Gal-T1) with equally efficient N-acetylgalactosaminyltransferase activity: point mutation broadens beta 4Gal-T1 donor specificity.
  J Biol Chem, 277, 20833-20839.
PDB codes: 1l7w 1oqm
12011052 E.Boix, Y.Zhang, G.J.Swaminathan, K.Brew, and K.R.Acharya (2002).
Structural basis of ordered binding of donor and acceptor substrates to the retaining glycosyltransferase, alpha-1,3-galactosyltransferase.
  J Biol Chem, 277, 28310-28318.
PDB codes: 1gwv 1gww 1gx0 1gx4
12001221 I.Halperin, B.Ma, H.Wolfson, and R.Nussinov (2002).
Principles of docking: An overview of search algorithms and a guide to scoring functions.
  Proteins, 47, 409-443.  
11950836 L.C.Pedersen, T.A.Darden, and M.Negishi (2002).
Crystal structure of beta 1,3-glucuronyltransferase I in complex with active donor substrate UDP-GlcUA.
  J Biol Chem, 277, 21869-21873.
PDB code: 1kws
12163485 M.Gotoh, T.Sato, T.Akashima, H.Iwasaki, A.Kameyama, H.Mochizuki, T.Yada, N.Inaba, Y.Zhang, N.Kikuchi, Y.D.Kwon, A.Togayachi, T.Kudo, S.Nishihara, H.Watanabe, K.Kimata, and H.Narimatsu (2002).
Enzymatic synthesis of chondroitin with a novel chondroitin sulfate N-acetylgalactosaminyltransferase that transfers N-acetylgalactosamine to glucuronic acid in initiation and elongation of chondroitin sulfate synthesis.
  J Biol Chem, 277, 38189-38196.  
11943783 P.E.Pummill, and P.L.DeAngelis (2002).
Evaluation of critical structural elements of UDP-sugar substrates and certain cysteine residues of a vertebrate hyaluronan synthase.
  J Biol Chem, 277, 21610-21616.  
12167666 Z.S.Kawar, I.Van Die, and R.D.Cummings (2002).
Molecular cloning and enzymatic characterization of a UDP-GalNAc:GlcNAc(beta)-R beta1,4-N-acetylgalactosaminyltransferase from Caenorhabditis elegans.
  J Biol Chem, 277, 34924-34932.  
  11592969 E.Boix, G.J.Swaminathan, Y.Zhang, R.Natesh, K.Brew, and K.R.Acharya (2001).
Structure of UDP complex of UDP-galactose:beta-galactoside-alpha -1,3-galactosyltransferase at 1.53-A resolution reveals a conformational change in the catalytically important C terminus.
  J Biol Chem, 276, 48608-48614.
PDB code: 1k4v
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.