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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BOVINE BETA 1,4 GALACTOSYLTRANSFERASE (B4GALT1) CATALYTIC DOMAIN COMPLEXED WITH UMP
 
Authors :  L. N. Gastinel, C. Cambillau, Y. Bourne
Date :  29 Jul 00  (Deposition) - 16 Aug 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Nucleotide Binding Protein, Alpha Beta Alpha Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. N. Gastinel, C. Cambillau, Y. Bourne
Crystal Structures Of The Bovine Beta4Galactosyltransferase Catalytic Domain And Its Complex With Uridine Diphosphogalactose.
Embo J. V. 18 3546 1999
PubMed-ID: 10393171  |  Reference-DOI: 10.1093/EMBOJ/18.13.3546
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA 1,4 GALACTOSYLTRANSFERASE
    Chains: A, B
    EC Number: 2.4.1.38
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell Line: NSO
    Expression System Common: HOUSE MOUSE
    Expression System Plasmid: PEE12
    Expression System Taxid: 10090
    Fragment: CATALYTIC DOMAIN
    Organ: LIVER
    Organism Common: CATTLE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: BETA4GALT1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1U5P1Ligand/IonURIDINE-5'-MONOPHOSPHATE
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1U5P-1Ligand/IonURIDINE-5'-MONOPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1U5P1Ligand/IonURIDINE-5'-MONOPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:189 , ASN B:190 , ARG B:191 , MET B:225 , PHE B:226 , HOH B:615BINDING SITE FOR RESIDUE U5P B 101

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:134 -A:176
2A:247 -A:266
3B:134 -B:176
4B:247 -B:266

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1FGX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1FGX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1FGX)

(-) Exons   (0, 0)

(no "Exon" information available for 1FGX)

(-) 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:272
 aligned with B4GT1_BOVIN | P08037 from UniProtKB/Swiss-Prot  Length:402

    Alignment length:272
                                   140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400  
          B4GT1_BOVIN   131 LTACPEESPLLVGPMLIEFNIPVDLKLVEQQNPKVKLGGRYTPMDCISPHKVAIIIPFRNRQEHLKYWLYYLHPILQRQQLDYGIYVINQAGESMFNRAKLLNVGFKEALKDYDYNCFVFSDVDLIPMNDHNTYRCFSQPRHISVAMDKFGFSLPYVQYFGGVSALSKQQFLSINGFPNNYWGWGGEDDDIYNRLAFRGMSVSRPNAVIGKCRMIRHSRDKKNEPNPQRFDRIAHTKETMLSDGLNSLTYMVLEVQRYPLYTKITVDIGTPS 402
               SCOP domains d1fgxa_ A: beta 1,4 galactosyltransferase (b4GalT1)                                                                                                                                                                                                                              SCOP domains
               CATH domains 1fgxA00 A:131-402 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................hhhhhhhhh.......ee.........eeeeeeee..hhhhhhhhhhhhhhhhhhh..eeeeeeeee......hhhhhhhhhhhhhh......eeeee...eee.............ee...ee.hhh...........eeeeehhhhhhh...........hhhhhhhhhhhhh............eeee.................hhhhhhhhh...hhhhh..eeeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fgx A 131 LTACPEESPLLVGPMLIEFNIPVDLKLIEQQNPKVKLGGRYTPMDCISPHKVAIIIPFRNRQEHLKYWLYYLHPILQRQQLDYGIYVINQAGESMFNRAKLLNVGFKEALKDYDYNCFVFSDVDLIPMNDHNTYRCFSQPRHISVAMDKFGFSLPYVQYFGGVSALSKQQFLSINGFPNNYWGWGGEDDDIYNRLAFRGMSVSRPNAVIGKCRMIRHSRDKKNEPNPQRFDRIAHTKETMLSDGLNSLTYMVLEVQRYPLYTKITVDIGTPS 402
                                   140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400  


Chain B from PDB  Type:PROTEIN  Length:273
 aligned with B4GT1_BOVIN | P08037 from UniProtKB/Swiss-Prot  Length:402

    Alignment length:273
                                   139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399   
          B4GT1_BOVIN   130 SLTACPEESPLLVGPMLIEFNIPVDLKLVEQQNPKVKLGGRYTPMDCISPHKVAIIIPFRNRQEHLKYWLYYLHPILQRQQLDYGIYVINQAGESMFNRAKLLNVGFKEALKDYDYNCFVFSDVDLIPMNDHNTYRCFSQPRHISVAMDKFGFSLPYVQYFGGVSALSKQQFLSINGFPNNYWGWGGEDDDIYNRLAFRGMSVSRPNAVIGKCRMIRHSRDKKNEPNPQRFDRIAHTKETMLSDGLNSLTYMVLEVQRYPLYTKITVDIGTPS 402
               SCOP domains d1fgxb_ B: beta 1,4 galactosyltransferase (b4GalT1)                                                                                                                                                                                                                               SCOP domains
               CATH domains 1fgxB00 B:130-402 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................hhhhhhhhh.......ee.........eeeeeeee..hhhhhhhhhhhhhhhhhhhh.eeeeeeeee......hhhhhhhhhhhhhhhhh...eeeee...eee.............ee...ee.hhh...........eeeeehhhhhhh...........hhhhhhhhhhhhh............eeee.................hhhhhhhhh...hhhhh..eeeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fgx B 130 SLTACPEESPLLVGPMLIEFNIPVDLKLIEQQNPKVKLGGRYTPMDCISPHKVAIIIPFRNRQEHLKYWLYYLHPILQRQQLDYGIYVINQAGESMFNRAKLLNVGFKEALKDYDYNCFVFSDVDLIPMNDHNTYRCFSQPRHISVAMDKFGFSLPYVQYFGGVSALSKQQFLSINGFPNNYWGWGGEDDDIYNRLAFRGMSVSRPNAVIGKCRMIRHSRDKKNEPNPQRFDRIAHTKETMLSDGLNSLTYMVLEVQRYPLYTKITVDIGTPS 402
                                   139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1FGX)

(-) Gene Ontology  (57, 57)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (B4GT1_BOVIN | P08037)
molecular function
    GO:0003945    N-acetyllactosamine synthase activity    Catalysis of the reaction: UDP-galactose + N-acetyl-D-glucosamine = UDP + N-acetyllactosamine.
    GO:0035250    UDP-galactosyltransferase activity    Catalysis of the transfer of a galactose group from UDP-galactose to an acceptor molecule.
    GO:0043014    alpha-tubulin binding    Interacting selectively and non-covalently with the microtubule constituent protein alpha-tubulin.
    GO:0003831    beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity    Catalysis of the reaction: UDP-galactose + N-acetyl-beta-D-glucosaminylglycopeptide = UDP + beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminylglycopeptide.
    GO:0048487    beta-tubulin binding    Interacting selectively and non-covalently with the microtubule constituent protein beta-tubulin.
    GO:0008092    cytoskeletal protein binding    Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton).
    GO:0008378    galactosyltransferase activity    Catalysis of the transfer of a galactosyl group to an acceptor molecule, typically another carbohydrate or a lipid.
    GO:0004461    lactose synthase activity    Catalysis of the reaction: UDP-galactose + D-glucose = UDP + lactose.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0002526    acute inflammatory response    Inflammation which comprises a rapid, short-lived, relatively uniform response to acute injury or antigenic challenge and is characterized by accumulations of fluid, plasma proteins, and granulocytic leukocytes. An acute inflammatory response occurs within a matter of minutes or hours, and either resolves within a few days or becomes a chronic inflammatory response.
    GO:0060055    angiogenesis involved in wound healing    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels and contribute to the series of events that restore integrity to a damaged tissue, following an injury.
    GO:0007339    binding of sperm to zona pellucida    The process in which the sperm binds to the zona pellucida glycoprotein layer of the egg. The process begins with the attachment of the sperm plasma membrane to the zona pellucida and includes attachment of the acrosome inner membrane to the zona pellucida after the acrosomal reaction takes place.
    GO:0048754    branching morphogenesis of an epithelial tube    The process in which the anatomical structures of branches in an epithelial tube are generated and organized. A tube is a long hollow cylinder.
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0045136    development of secondary sexual characteristics    The process whose specific outcome is the progression of the secondary sexual characteristics over time, from their formation to the mature structures. In humans, these include growth of axillary, chest, and pubic hair, voice changes, testicular/penile enlargement, breast development and menstrual periods. Development occurs in response to sex hormone secretion.
    GO:0002064    epithelial cell development    The process whose specific outcome is the progression of an epithelial cell over time, from its formation to the mature structure. An epithelial cell is a cell usually found in a two-dimensional sheet with a free surface.
    GO:0030198    extracellular matrix organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
    GO:0006012    galactose metabolic process    The chemical reactions and pathways involving galactose, the aldohexose galacto-hexose. D-galactose is widely distributed in combined form in plants, animals and microorganisms as a constituent of oligo- and polysaccharides; it also occurs in galactolipids and as its glucoside in lactose and melibiose.
    GO:0009101    glycoprotein biosynthetic process    The chemical reactions and pathways resulting in the formation of glycoproteins, any protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide.
    GO:0005989    lactose biosynthetic process    The chemical reactions and pathways resulting in the formation of lactose, the disaccharide galactopyranosyl-glucose.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:0030879    mammary gland development    The process whose specific outcome is the progression of the mammary gland over time, from its formation to the mature structure. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk. Its development starts with the formation of the mammary line and ends as the mature gland cycles between nursing and weaning stages.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0009312    oligosaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of oligosaccharides, molecules with between two and (about) 20 monosaccharide residues connected by glycosidic linkages.
    GO:0007341    penetration of zona pellucida    The infiltration by sperm of the zona pellucida to reach the oocyte. The process involves digestive enzymes from a modified lysosome called the acrosome, situated at the head of the sperm.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0060058    positive regulation of apoptotic process involved in mammary gland involution    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process of mammary epithelial cells during mammary gland involution.
    GO:0060054    positive regulation of epithelial cell proliferation involved in wound healing    Any process that activates or increases the rate or extent of epithelial cell proliferation, contributing to the restoration of integrity to a damaged tissue following an injury.
    GO:0006487    protein N-linked glycosylation    A protein glycosylation process in which a carbohydrate or carbohydrate derivative unit is added to a protein via the N4 atom of peptidyl-asparagine, the omega-N of arginine, or the N1' atom peptidyl-tryptophan.
    GO:0006486    protein glycosylation    A protein modification process that results in the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid, e.g. the addition of glycan chains to proteins.
    GO:0060046    regulation of acrosome reaction    Any process that modulates the frequency, rate or extent of the acrosome reaction.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:0051270    regulation of cellular component movement    Any process that modulates the frequency, rate or extent of the movement of a cellular component.
    GO:0042060    wound healing    The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0032580    Golgi cisterna membrane    The lipid bilayer surrounding any of the thin, flattened compartments that form the central portion of the Golgi complex.
    GO:0000138    Golgi trans cisterna    The Golgi cisterna farthest from the endoplasmic reticulum; the final processing compartment through which proteins pass before exiting the Golgi apparatus; the compartment in which N-linked protein glycosylation is completed.
    GO:0016323    basolateral plasma membrane    The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    GO:0031526    brush border membrane    The portion of the plasma membrane surrounding the brush border.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0030057    desmosome    A cell-cell junction in which: on the cytoplasmic surface of each interacting plasma membrane is a dense plaque composed of a mixture of intracellular anchor proteins; a bundle of keratin intermediate filaments is attached to the surface of each plaque; transmembrane adhesion proteins of the cadherin family bind to the plaques and interact through their extracellular domains to hold the adjacent membranes together by a Ca2+-dependent mechanism.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0030175    filopodium    Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft.
    GO:0030112    glycocalyx    A viscous, carbohydrate rich layer at the outermost periphery of a cell.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        B4GT1_BOVIN | P08037: 1fr8 1nf5 1nhe 1nkh 1nmm 1nqi 1nwg 1o0r 1o23 1oqm 1pzt 1pzy 1tvy 1tw1 1tw5 1yro 2fyc 2fyd 4krv

(-) Related Entries Specified in the PDB File

1fr8 1FR8 CONTAINS THE SAME PROTEIN COMPLEXED WITH URIDINE DIPHOSPHOGALACTOSE