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(-) Description

Title :  THE SULFOTRANSFERASE DOMAIN OF HUMAN HAPARIN SULFATE N-DEACETYLASE/N-SULFOTRANSFERASE
 
Authors :  Y. Kakuta, L. C. Pedersen, M. Negishi
Date :  07 Sep 98  (Deposition) - 16 Sep 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Sulfotransferase, Pap, Haparin Sulfate, Haparin Sulfate Biosynthesis, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Kakuta, T. Sueyoshi, M. Negishi, L. C. Pedersen
Crystal Structure Of The Sulfotransferase Domain Of Human Heparan Sulfate N-Deacetylase/ N-Sulfotransferase 1.
J. Biol. Chem. V. 274 10673 1999
PubMed-ID: 10196134  |  Reference-DOI: 10.1074/JBC.274.16.10673
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEPARAN SULFATE N-DEACETYLASE/N-SULFOTRANSFERASE
    Cellular LocationGOLGI MEMBRANE
    ChainsA
    EC Number2.8.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Cellular LocationCYTOPLASM
    Expression System PlasmidPGEX-4T3
    Expression System StrainDH5A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSULFOTRANSFERASE DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNST1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1A3P1Ligand/IonADENOSINE-3'-5'-DIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:7 , HOH A:10 , HOH A:28 , HOH A:29 , HOH A:38 , HOH A:41 , LYS A:614 , THR A:615 , GLY A:616 , THR A:617 , THR A:618 , SER A:712 , PHE A:816 , TRP A:817 , LEU A:829 , LYS A:833 , GLY A:834 , ARG A:835 , TYR A:837BINDING SITE FOR RESIDUE A3P A 301

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:818 -A:828

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:611 -Pro A:612

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_072646G611SNDST1_HUMANDisease (MRT46)606231459AG611S
2UniProtVAR_072647F640LNDST1_HUMANDisease (MRT46)606231458AF640L
3UniProtVAR_072648E642DNDST1_HUMANDisease (MRT46)606231457AE642D
4UniProtVAR_072649R709QNDST1_HUMANDisease (MRT46)606231456AR709Q

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.5aENST000002617975aENSE00001607679chr5:149887674-149887788115NDST1_HUMAN-00--
1.7eENST000002617977eENSE00001171009chr5:149900430-149901329900NDST1_HUMAN1-1711710--
1.8ENST000002617978ENSE00000972942chr5:149907366-149907860495NDST1_HUMAN172-3361650--
1.9ENST000002617979ENSE00000841211chr5:149912507-14991259488NDST1_HUMAN337-366300--
1.10ENST0000026179710ENSE00000439232chr5:149914429-149914583155NDST1_HUMAN366-417520--
1.11ENST0000026179711ENSE00000841214chr5:149915262-149915447186NDST1_HUMAN418-479620--
1.12aENST0000026179712aENSE00001198482chr5:149918790-149918918129NDST1_HUMAN480-522430--
1.13ENST0000026179713ENSE00001475127chr5:149919644-149919826183NDST1_HUMAN523-583611A:579-5835
1.14ENST0000026179714ENSE00001507093chr5:149921132-14992122897NDST1_HUMAN584-616331A:584-616 (gaps)33
1.15ENST0000026179715ENSE00001475124chr5:149922410-149922533124NDST1_HUMAN616-657421A:616-65742
1.16ENST0000026179716ENSE00001475122chr5:149924874-149925048175NDST1_HUMAN657-715591A:657-715 (gaps)59
1.17ENST0000026179717ENSE00001475121chr5:149927780-149927950171NDST1_HUMAN716-772571A:716-77257
1.18ENST0000026179718ENSE00001475119chr5:149929240-149929349110NDST1_HUMAN773-809371A:773-80937
1.20ENST0000026179720ENSE00001475118chr5:149931315-149931417103NDST1_HUMAN809-843351A:809-84335
1.22cENST0000026179722cENSE00001475116chr5:149932775-1499377734999NDST1_HUMAN844-882391A:844-87936

(-) Sequences/Alignments

Asymmetric/Biological 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:282
 aligned with NDST1_HUMAN | P52848 from UniProtKB/Swiss-Prot  Length:882

    Alignment length:301
                                   588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878 
          NDST1_HUMAN   579 DPLWQDPCEDKRHKDIWSKEKTCDRFPKLLIIGPQKTGTTALYLFLGMHPDLSSNYPSSETFEEIQFFNGHNYHKGIDWYMEFFPIPSNTTSDFYFEKSANYFDSEVAPRRAAALLPKAKVLTILINPADRAYSWYQHQRAHDDPVALKYTFHEVITAGSDASSKLRALQNRCLVPGWYATHIERWLSAYHANQILVLDGKLLRTEPAKVMDMVQKFLGVTNTIDYHKTLAFDPKKGFWCQLLEGGKTKCLGKSKGRKYPEMDLDSRAFLKDYYRDHNIELSKLLYKMGQTLPTWLREDLQ 879
               SCOP domains d1nsta_               A: Heparan sulfate N-deacetylase/N-sulfotransferase domain                                                                                                                                                                                                                              SCOP domains
               CATH domains 1nstA00               A:579-879 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                          CATH domains
               Pfam domains --------              ---Sulfotransfer_1-1nstA01 A:604-869                                                                                                                                                                                                                                         ---------- Pfam domains
         Sec.struct. author ........--------------....eeeee.......hhhhhhhhhh...eee................hhhhh.hhhhhhh...-----..eeeee..hhhh...hhhhhhhh....eeeeee..hhhhhhhhhhhhhh...hhhhh..hhhhh.......hhhhhhhhhhhhhh.hhhhhhhhh....hhheeeeehhhhhh.hhhhhhhhhhhh........hhheeee....eeee......................hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------S----------------------------L-D------------------------------------------------------------------Q-------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.13 Exon 1.14  PDB: A:584-616 (gaps) ----------------------------------------Exon 1.16  PDB: A:657-715 (gaps) UniProt: 657-715          Exon 1.17  PDB: A:716-772 UniProt: 716-772               Exon 1.18  PDB: A:773-809            ----------------------------------Exon 1.22c  PDB: A:844-879           Transcript 1 (1)
           Transcript 1 (2) -------------------------------------Exon 1.15  PDB: A:616-657 UniProt: 616-657-------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.20  PDB: A:809-843          ------------------------------------ Transcript 1 (2)
                 1nst A 579 DPLWQDPC--------------CDRFPKLLIIGPQKTGTTALYLFLGMHPDLSSNYPSSETFEEIQFFNGHNYHKGIDWYMEFFPI-----SDFYFEKSANYFDSEVAPRRAAALLPKAKVLTILINPADRAYSWYQHQRAHDDPVALKYTFHEVITAGSDASSKLRALQNRCLVPGWYATHIERWLSAYHANQILVLDGKLLRTEPAKVMDMVQKFLGVTNTIDYHKTLAFDPKKGFWCQLLEGGKTKCLGKSKGRKYPEMDLDSRAFLKDYYRDHNIELSKLLYKMGQTLPTWLREDLQ 879
                                   | -         -  |    608       618       628       638       648       658     |   - |     678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878 
                                 586            601                                                            664   670                                                                                                                                                                                                                 

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NDST1_HUMAN | P52848)
molecular function
    GO:0050119    N-acetylglucosamine deacetylase activity    Catalysis of the reaction: N-acetyl-D-glucosamine + H(2)O = D-glucosamine + acetate.
    GO:0015016    [heparan sulfate]-glucosamine N-sulfotransferase activity    Catalysis of the reaction: 3'-phosphoadenylyl sulfate + [heparan sulfate]-glucosamine = adenosine 3',5'-bisphosphate + [heparan sulfate]-N-sulfoglucosamine.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0019213    deacetylase activity    Catalysis of the hydrolysis of an acetyl group or groups from a substrate molecule.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008146    sulfotransferase activity    Catalysis of the transfer of a sulfate group from 3'-phosphoadenosine 5'-phosphosulfate to the hydroxyl group of an acceptor, producing the sulfated derivative and 3'-phosphoadenosine 5'-phosphate.
    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.
biological process
    GO:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0009887    animal organ morphogenesis    Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    GO:0035904    aorta development    The progression of the aorta over time, from its initial formation to the mature structure. An aorta is an artery that carries blood from the heart to other parts of the body.
    GO:0003279    cardiac septum development    The progression of a cardiac septum over time, from its initial formation to the mature structure.
    GO:0060976    coronary vasculature development    The process whose specific outcome is the progression of the blood vessels of the heart over time, from its formation to the mature structure.
    GO:0048702    embryonic neurocranium morphogenesis    The process in which the anatomical structures of the neurocranium are generated and organized during the embryonic phase. The neurocranium is the portion of the vertebrate skull surrounding the brain.
    GO:0048703    embryonic viscerocranium morphogenesis    The process in which the anatomical structures of the viscerocranium are generated and organized during the embryonic phase. The viscerocranium is the part of the skull comprising the facial bones.
    GO:0008543    fibroblast growth factor receptor signaling pathway    The series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands.
    GO:0030900    forebrain development    The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions).
    GO:0006024    glycosaminoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of glycosaminoglycans, any of a group of polysaccharides that contain amino sugars.
    GO:0030203    glycosaminoglycan metabolic process    The chemical reactions and pathways involving glycosaminoglycans, any one of a group of polysaccharides that contain amino sugars. Formerly known as mucopolysaccharides, they include hyaluronic acid and chondroitin, which provide lubrication in joints and form part of the matrix of cartilage. The three-dimensional structure of these molecules enables them to trap water, which forms a gel and gives glycosaminoglycans their elastic properties.
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0015012    heparan sulfate proteoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of the heparan sulfate proteoglycan, a glycosaminoglycan with repeat unit consisting of alternating alpha-(1->4)-linked hexuronic acid and glucosamine residues; the former are a mixture of sulfated and nonsulfated D-glucuronic acid and L-iduronic acid; the L-iduronic acid is either sulfated or acetylated on its amino group as well as being sulfated on one of its hydroxyl groups; heparan sulfate chains are covalently linked to peptidyl-serine by a glycosidic attachment through the trisaccharide galactosyl-galactosyl-xylosyl to serine residues.
    GO:0030210    heparin biosynthetic process    The chemical reactions and pathways resulting in the formation of heparin, any member of a group of glycosaminoglycans of average Mr (6000-20000), consisting predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0030901    midbrain development    The process whose specific outcome is the progression of the midbrain over time, from its formation to the mature structure. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles).
    GO:0000271    polysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
    GO:0006477    protein sulfation    The addition of a sulfate group as an ester to a protein amino acid.
    GO:0007585    respiratory gaseous exchange    The process of gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
    GO:0007224    smoothened signaling pathway    A series of molecular signals generated as a consequence of activation of the transmembrane protein Smoothened.
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:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    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.

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