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(-) Description

Title :  CRYSTAL STRUCTURE OF 3-O-SULFOTRANSFERASE (3-OST-1) WITH BOUND PAP AND HEPTASACCHARIDE SUBSTRATE
 
Authors :  A. F. Moon, Y. Xu, S. M. Woody, J. M. Krahn, R. J. Linhardt, J. Liu, L. C. Ped
Date :  21 Oct 11  (Deposition) - 04 Apr 12  (Release) - 25 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Sulfotransferase, Heparan Sulfate, Alpha/Beta Motif, Co-Factor Paps/Pap, Heparan Sulfate Oligosaccharides, Golgi-Localized, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. F. Moon, Y. Xu, S. M. Woody, J. M. Krahn, R. J. Linhardt, J. Liu, L. C. Pedersen
Dissecting The Substrate Recognition Of 3-O-Sulfotransferas For The Biosynthesis Of Anticoagulant Heparin.
Proc. Natl. Acad. Sci. Usa V. 109 5265 2012
PubMed-ID: 22431632  |  Reference-DOI: 10.1073/PNAS.1117923109

(-) Compounds

Molecule 1 - HEPARAN SULFATE GLUCOSAMINE 3-O-SULFOTRANSFERASE 1
    Chains: A, B
    EC Number: 2.8.2.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX4T3
    Expression System Taxid: 562
    Fragment: 3-O-SULFOTRANSFERASE ISOFORM 1
    Gene: HS3ST1, 3OST, 3OST1
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: HEPARAN SULFATE D-GLUCOSAMINYL 3-O-SULFOTRANSFERASE 1, HEPARAN SULFATE 3-O-SULFOTRANSFERASE 1

 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  (5, 14)

Asymmetric Unit (5, 14)
No.NameCountTypeFull Name
1A3P2Ligand/IonADENOSINE-3'-5'-DIPHOSPHATE
2BDP4Ligand/IonBETA-D-GLUCOPYRANURONIC ACID
3IDS2Ligand/Ion2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID
4NGY2Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-6-O-SULFO-ALPHA-D-GLUCOPYRANOSE
5SGN4Ligand/IonN,O6-DISULFO-GLUCOSAMINE
Biological Unit 1 (5, 7)
No.NameCountTypeFull Name
1A3P1Ligand/IonADENOSINE-3'-5'-DIPHOSPHATE
2BDP2Ligand/IonBETA-D-GLUCOPYRANURONIC ACID
3IDS1Ligand/Ion2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID
4NGY1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-6-O-SULFO-ALPHA-D-GLUCOPYRANOSE
5SGN2Ligand/IonN,O6-DISULFO-GLUCOSAMINE
Biological Unit 2 (5, 7)
No.NameCountTypeFull Name
1A3P1Ligand/IonADENOSINE-3'-5'-DIPHOSPHATE
2BDP2Ligand/IonBETA-D-GLUCOPYRANURONIC ACID
3IDS1Ligand/Ion2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID
4NGY1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-6-O-SULFO-ALPHA-D-GLUCOPYRANOSE
5SGN2Ligand/IonN,O6-DISULFO-GLUCOSAMINE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:7 , HOH A:16 , HOH A:18 , HOH A:23 , LYS A:68 , GLY A:69 , GLY A:70 , THR A:71 , ARG A:72 , ALA A:73 , ARG A:151 , SER A:159 , ILE A:225 , PHE A:258 , TYR A:259 , LEU A:270 , LYS A:274 , GLY A:275 , ARG A:276 , HIS A:278 , HOH A:312 , HOH A:316 , HOH A:357BINDING SITE FOR RESIDUE A3P A 603
02AC2SOFTWAREHOH B:21 , HOH B:28 , HOH B:33 , LYS B:68 , GLY B:69 , GLY B:70 , THR B:71 , ARG B:72 , ALA B:73 , ARG B:151 , SER B:159 , ILE B:225 , PHE B:258 , TYR B:259 , LEU B:270 , LYS B:274 , GLY B:275 , ARG B:276 , HIS B:278 , HOH B:321 , HOH B:324 , HOH B:335 , HOH B:382BINDING SITE FOR RESIDUE A3P B 603
03AC3SOFTWAREBDP A:2 , ARG A:72 , GLU A:76 , ARG A:268 , LEU A:270 , HIS A:271 , HOH A:323 , HOH A:393 , HOH A:410BINDING SITE FOR RESIDUE NGY A 1
04AC4SOFTWARENGY A:1 , SGN A:3 , ARG A:72 , GLU A:90 , LYS A:123 , SER A:273 , LYS A:274 , HOH A:356BINDING SITE FOR RESIDUE BDP A 2
05AC5SOFTWAREBDP A:2 , IDS A:4 , HOH A:23 , ARG A:67 , GLU A:90 , HIS A:92 , PRO A:125 , ALA A:126 , GLN A:163 , HOH A:317 , HOH A:318 , HOH A:323 , HOH A:325BINDING SITE FOR RESIDUE SGN A 3
06AC6SOFTWARESGN A:3 , SGN A:5 , ARG A:67 , GLN A:163 , ASN A:167 , ARG A:197 , HOH A:317 , HOH A:318 , HOH A:356BINDING SITE FOR RESIDUE IDS A 4
07AC7SOFTWAREIDS A:4 , BDP A:6 , ASN A:167 , HIS A:168 , LYS A:171 , LYS A:173 , ARG A:197 , HOH A:352BINDING SITE FOR RESIDUE SGN A 5
08AC8SOFTWARESGN A:5BINDING SITE FOR RESIDUE BDP A 6
09AC9SOFTWAREBDP B:2 , ARG B:72 , GLU B:76 , LEU B:270 , HIS B:271BINDING SITE FOR RESIDUE NGY B 1
10BC1SOFTWARENGY B:1 , SGN B:3 , ARG B:72 , GLU B:90 , LYS B:123 , SER B:273 , LYS B:274BINDING SITE FOR RESIDUE BDP B 2
11BC2SOFTWAREBDP B:2 , IDS B:4 , HOH B:33 , ARG B:67 , GLU B:90 , HIS B:92 , PRO B:125 , ALA B:126 , HOH B:383 , HOH B:384BINDING SITE FOR RESIDUE SGN B 3
12BC3SOFTWARESGN B:3 , SGN B:5 , ARG B:67 , GLN B:163 , ASN B:167 , ARG B:197 , HOH B:383BINDING SITE FOR RESIDUE IDS B 4
13BC4SOFTWAREIDS B:4 , BDP B:6 , ASN B:167 , HIS B:168 , ARG B:197 , HOH B:348 , HOH B:353 , HOH B:361BINDING SITE FOR RESIDUE SGN B 5
14BC5SOFTWARESGN B:5BINDING SITE FOR RESIDUE BDP B 6

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:260 -A:269
2B:260 -B:269

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:65 -Val A:66
2Gly B:65 -Val B:66

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3UAN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3UAN)

(-) Exons   (0, 0)

(no "Exon" information available for 3UAN)

(-) 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:256
 aligned with HS3S1_MOUSE | O35310 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:258
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303        
          HS3S1_MOUSE    54 STQQLPQTIIIGVRKGGTRALLEMLSLHPDVAAAENEVHFFDWEEHYSQGLGWYLTQMPFSSPHQLTVEKTPAYFTSPKVPERIHSMNPTIRLLLILRDPSERVLSDYTQVLYNHLQKHKPYPPIEDLLMRDGRLNLDYKALNRSLYHAHMLNWLRFFPLGHIHIVDGDRLIRDPFPEIQKVERFLKLSPQINASNFYFNKTKGFYCLRDSGKDRCLHESKGRAHPQVDPKLLDKLHEYFHEPNKKFFKLVGRTFDWH 311
               SCOP domains d3uana_ A: automated matches                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee....eee......hhhhhhhhhh....eee.........hhhhhh.hhhhhhhh..ee....eeeee.hhhh...hhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhh.....hhhhhhh.--.....hhhhhhhhhhhhhhhhhh..hhh.eeeeehhhhhhhhhhhhhhhhhhh......hhh.eeee....eeeeee..eee.............hhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3uan A  54 STQQLPQTIIIGVRKGGTRALLEMLSLHPDVAAAENEVHFFDWEEHYSQGLGWYLTQMPFSSPHQLTVEKTPAYFTSPKVPERIHSMNPTIRLLLILRDPSERVLSDYTQVLYNHLQKHKPYPPIEDLLMR--RLNLDYKALNRSLYHAHMLNWLRFFPLGHIHIVDGDRLIRDPFPEIQKVERFLKLSPQINASNFYFNKTKGFYCLRDSGKDRCLHESKGRAHPQVDPKLLDKLHEYFHEPNKKFFKLVGRTFDWH 311
                                    63        73        83        93       103       113       123       133       143       153       163       173       183|  |   193       203       213       223       233       243       253       263       273       283       293       303        
                                                                                                                                                            184  |                                                                                                                            
                                                                                                                                                               187                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:254
 aligned with HS3S1_MOUSE | O35310 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:257
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       
          HS3S1_MOUSE    55 TQQLPQTIIIGVRKGGTRALLEMLSLHPDVAAAENEVHFFDWEEHYSQGLGWYLTQMPFSSPHQLTVEKTPAYFTSPKVPERIHSMNPTIRLLLILRDPSERVLSDYTQVLYNHLQKHKPYPPIEDLLMRDGRLNLDYKALNRSLYHAHMLNWLRFFPLGHIHIVDGDRLIRDPFPEIQKVERFLKLSPQINASNFYFNKTKGFYCLRDSGKDRCLHESKGRAHPQVDPKLLDKLHEYFHEPNKKFFKLVGRTFDWH 311
               SCOP domains d3uanb_ B: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee....hhhhhhhhhh....eee.........hhhhhh.hhhhhhhh........eeeee.hhhhhh.hhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhh.....hhhhhhh.--.....hhhhhhhhhhhhhhhhhh..hhh.eeeeehhhhhhhhhhhhhhhhhhh......hhh.eeee....eeeeee..eee...........-.hhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uan B  55 TQQLPQTIIIGVRKGGTRALLEMLSLHPDVAAAENEVHFFDWEEHYSQGLGWYLTQMPFSSPHQLTVEKTPAYFTSPKVPERIHSMNPTIRLLLILRDPSERVLSDYTQVLYNHLQKHKPYPPIEDLLMR--RLNLDYKALNRSLYHAHMLNWLRFFPLGHIHIVDGDRLIRDPFPEIQKVERFLKLSPQINASNFYFNKTKGFYCLRDSGKDRCLHESKGRAHP-VDPKLLDKLHEYFHEPNKKFFKLVGRTFDWH 311
                                    64        74        84        94       104       114       124       134       144       154       164       174       184  |    194       204       214       224       234       244       254       264       274    | |284       294       304       
                                                                                                                                                           184  |                                                                                         279 |                              
                                                                                                                                                              187                                                                                           281
   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  (0, 0)

(no "CATH Domain" information available for 3UAN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UAN)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HS3S1_MOUSE | O35310)
molecular function
    GO:0008467    [heparan sulfate]-glucosamine 3-sulfotransferase 1 activity    Catalysis of the reaction: 3'-phosphoadenylyl sulfate + [heparan sulfate]-glucosamine = adenosine 3',5'-bisphosphate + [heparan sulfate]-glucosamine 3-sulfate. The [heparan sulfate]-glucosamine 3-sulfate has a substrate consensus sequence of Glc(N2S>NAc)+/-6S GlcA GlcN2S*+/-6S GlcA>IdoA+/-2S Glc(N2S/NAc)+/-6S.
    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.
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:0005796    Golgi lumen    The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.

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  2.8.2.23
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 Related Entries

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

UniProtKB/Swiss-Prot
        HS3S1_MOUSE | O35310: 1vkj

(-) Related Entries Specified in the PDB File

1t8t 3-OST-3A WITH BOUND PAP
1t8u 3-OST-3A WITH BOUND TETRASACCHARIDE SUBSTRATE AND PAP
1zrh 3-OST-1 WITH BOUND PAP