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(-) Description

Title :  CRYSTAL STRUCTURE OF HEPARINASE II COMPLEXED WITH A DISACCHARIDE PRODUCT
 
Authors :  D. Shaya, M. Cygler
Date :  27 Jan 06  (Deposition) - 18 Apr 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha Plus Beta, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Shaya, A. Tocilj, Y. Li, J. Myette, G. Venkataraman, R. Sasisekharan, M. Cygler
Crystal Structure Of Heparinase Ii From Pedobacter Heparinu And Its Complex With A Disaccharide Product.
J. Biol. Chem. V. 281 15525 2006
PubMed-ID: 16565082  |  Reference-DOI: 10.1074/JBC.M512055200

(-) Compounds

Molecule 1 - HEPARINASE II PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HEP B
    Organism Scientific: PEDOBACTER HEPARINUS
    Organism Taxid: 984

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 44)

Asymmetric/Biological Unit (3, 44)
No.NameCountTypeFull Name
1H1S2Ligand/IonHEPARIN DISACCHARIDE I-S
2MSE40Mod. Amino AcidSELENOMETHIONINE
3ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:408 , ASP A:425 , HIS A:451 , HOH A:893 , HOH A:1101 , HOH A:1275BINDING SITE FOR RESIDUE ZN A 1
2AC2SOFTWAREHIS B:408 , ASP B:425 , HIS B:451 , HOH B:900 , HOH B:992 , HOH B:1006BINDING SITE FOR RESIDUE ZN B 2
3AC3SOFTWAREASP A:145 , ARG A:148 , GLY A:201 , HIS A:202 , GLU A:205 , TYR A:257 , ARG A:261 , ASN A:405 , HIS A:406 , TYR A:429 , TYR A:436 , ASN A:437 , GLY A:469 , GLY A:470 , SER A:471 , ILE A:491 , HOH A:895 , HOH A:905 , HOH A:918 , HOH A:1046BINDING SITE FOR RESIDUE H1S A 801
4AC4SOFTWAREASP B:145 , ARG B:148 , GLY B:201 , HIS B:202 , GLU B:205 , TYR B:257 , ARG B:261 , ASN B:405 , HIS B:406 , TYR B:429 , TYR B:436 , ASN B:437 , GLY B:470 , SER B:471 , ILE B:491 , HOH B:867 , HOH B:873 , HOH B:1007BINDING SITE FOR RESIDUE H1S B 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FUT)

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1His A:48 -Pro A:49
2Tyr A:191 -Pro A:192
3Ser A:376 -Pro A:377
4Gly A:515 -Pro A:516
5Leu A:610 -Pro A:611
6His B:48 -Pro B:49
7Tyr B:191 -Pro B:192
8Ser B:376 -Pro B:377
9Leu B:610 -Pro B:611

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FUT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2FUT)

(-) Exons   (0, 0)

(no "Exon" information available for 2FUT)

(-) 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:743
 aligned with HEPB_PEDHD | C6XZB6 from UniProtKB/Swiss-Prot  Length:772

    Alignment length:743
                                    39        49        59        69        79        89        99       109       119       129       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       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769   
           HEPB_PEDHD    30 DVVWKDVDGVSMPIPPKTHPRLYLREQQVPDLKNRMNDPKLKKVWADMIKMQEDWKPADIPEVKDFRFYFNQKGLTVRVELMALNYLMTKDPKVGREAITSIIDTLETATFKPAGDISRGIGLFMVTGAIVYDWCYDQLKPEEKTRFVKAFVRLAKMLECGYPPVKDKSIVGHASEWMIMRDLLSVGIAIYDEFPEMYNLAAGRFFKEHLVARNWFYPSHNYHQGMSYLNVRFTNDLFALWILDRMGAGNVFNPGQQFILYDAIYKRRPDGQILAGGDVDYSRKKPKYYTMPALLAGSYYKDEYLNYEFLKDPNVEPHCKLFEFLWRDTQLGSRKPDDLPLSRYSGSPFGWMIARTGWGPESVIAEMKVNEYSFLNHQHQDAGAFQIYYKGPLAIDAGSYTGSSGGYNSPHNKNFFKRTIAHNSLLIYDPKETFSSSGYGGSDHTDFAANDGGQRLPGKGWIAPRDLKEMLAGDFRTGKILAQGFGPDNQTPDYTYLKGDITAAYSAKVKEVKRSFLFLNLKDAKVPAAMIVFDKVVASNPDFKKFWLLHSIEQPEIKGNQITIKRTKNGDSGMLVNTALLPDAANSNITSIGGKGKDFWVFGTNYTNDPKPGTDEALERGEWRVEITPKKAAAEDYYLNVIQIADNTQQKLHEVKRIDGDKVVGVQLADRIVTFSKTSETVDRPFGFSVVGKGTFKFVMTDLLPGTWQVLKDGKILYPALSAKGDDGALYFEGTEGTYRFLR 772
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee...........hhhhhhhhhhhhh..hhhhhhhhhhhhh............hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.......hhhhh..eeee.....eeeee.......eeeeee................eeeee..eee..............hhhhhhh..hhhhh..eeee.....................................hhhhhhhh.....eeeeeeee.......eeeeeee.hhhh...eeeeeeeeeeee.......eeeeeeeeeee.....eeeeeeee....eee..eeeee.......eeeeeeeee.hhh.eeeeeee......ee..ee.................eeeeeee.....eeeeeeeeeeee.........eeee...eeeeee..eeeeee.........eeeee.....eeeee.....eeeeeee..eeeeeeeee......eeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fut A  30 DVVWKDVDGVSmPIPPKTHPRLYLREQQVPDLKNRmNDPKLKKVWADmIKmQEDWKPADIPEVKDFRFYFNQKGLTVRVELmALNYLmTKDPKVGREAITSIIDTLETATFKPAGDISRGIGLFmVTGAIVYDWCYDQLKPEEKTRFVKAFVRLAKmLECGYPPVKDKSIVGHASEWmImRDLLSVGIAIYDEFPEmYNLAAGRFFKEHLVARNWFYPSHNYHQGmSYLNVRFTNDLFALWILDRmGAGNVFNPGQQFILYDAIYKRRPDGQILAGGDVDYSRKKPKYYTmPALLAGSYYKDEYLNYEFLKDPNVEPHCKLFEFLWRDTQLGSRKPDDLPLSRYSGSPFGWmIARTGWGPESVIAEmKVNEYSFLNHQHQDAGAFQIYYKGPLAIDAGSYTGSSGGYNSPHNKNFFKRTIAHNSLLIYDPKETFSSSGYGGSDHTDFAANDGGQRLPGKGWIAPRDLKEmLAGDFRTGKILAQGFGPDNQTPDYTYLKGDITAAYSAKVKEVKRSFLFLNLKDAKVPAAmIVFDKVVASNPDFKKFWLLHSIEQPEIKGNQITIKRTKNGDSGmLVNTALLPDAANSNITSIGGKGKDFWVFGTNYTNDPKPGTDEALERGEWRVEITPKKAAAEDYYLNVIQIADNTQQKLHEVKRIDGDKVVGVQLADRIVTFSKTSETVDRPFGFSVVGKGTFKFVmTDLLPGTWQVLKDGKILYPALSAKGDDGALYFEGTEGTYRFLR 772
                                    39 |      49        59     |  69       |79|       89        99       109 |     119       129       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       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599   |   609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769   
                                      41-MSE                  65-MSE      77-MSE                           111-MSE |                                  154-MSE                         186-MSE              207-MSE            226-MSE                      255-MSE             275-MSE                                      320-MSE                                                      381-MSE        396-MSE                                                                                                499-MSE                                                     559-MSE                                     603-MSE                                                                                                                       729-MSE                                       
                                                                             80-MSE                              117-MSE                                                                                     209-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:743
 aligned with HEPB_PEDHD | C6XZB6 from UniProtKB/Swiss-Prot  Length:772

    Alignment length:743
                                    39        49        59        69        79        89        99       109       119       129       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       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769   
           HEPB_PEDHD    30 DVVWKDVDGVSMPIPPKTHPRLYLREQQVPDLKNRMNDPKLKKVWADMIKMQEDWKPADIPEVKDFRFYFNQKGLTVRVELMALNYLMTKDPKVGREAITSIIDTLETATFKPAGDISRGIGLFMVTGAIVYDWCYDQLKPEEKTRFVKAFVRLAKMLECGYPPVKDKSIVGHASEWMIMRDLLSVGIAIYDEFPEMYNLAAGRFFKEHLVARNWFYPSHNYHQGMSYLNVRFTNDLFALWILDRMGAGNVFNPGQQFILYDAIYKRRPDGQILAGGDVDYSRKKPKYYTMPALLAGSYYKDEYLNYEFLKDPNVEPHCKLFEFLWRDTQLGSRKPDDLPLSRYSGSPFGWMIARTGWGPESVIAEMKVNEYSFLNHQHQDAGAFQIYYKGPLAIDAGSYTGSSGGYNSPHNKNFFKRTIAHNSLLIYDPKETFSSSGYGGSDHTDFAANDGGQRLPGKGWIAPRDLKEMLAGDFRTGKILAQGFGPDNQTPDYTYLKGDITAAYSAKVKEVKRSFLFLNLKDAKVPAAMIVFDKVVASNPDFKKFWLLHSIEQPEIKGNQITIKRTKNGDSGMLVNTALLPDAANSNITSIGGKGKDFWVFGTNYTNDPKPGTDEALERGEWRVEITPKKAAAEDYYLNVIQIADNTQQKLHEVKRIDGDKVVGVQLADRIVTFSKTSETVDRPFGFSVVGKGTFKFVMTDLLPGTWQVLKDGKILYPALSAKGDDGALYFEGTEGTYRFLR 772
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeeee...............hhhhhhhhhhhhhhhhhhhhhh.............hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.......hhhhh..eeee.....eeeee........eeeee................eeee...eee.......................hhhhh..eeee.....................................hhhhhhhh.....eeeeeee........eeeeeee.hhhh...eeeeeeeeeeee.......eeeeeeeeeee.....eeeeeeee....eee..eeeee.......eeeeeeeee.....eeeeeee......ee..ee.................eeeeeee.....eeeeeeeeeeee.........eeee...eeeeee..eeeeee.........eeeee.....eeeee.....eeeeeee..eeeeeeeee......eeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fut B  30 DVVWKDVDGVSmPIPPKTHPRLYLREQQVPDLKNRmNDPKLKKVWADmIKmQEDWKPADIPEVKDFRFYFNQKGLTVRVELmALNYLmTKDPKVGREAITSIIDTLETATFKPAGDISRGIGLFmVTGAIVYDWCYDQLKPEEKTRFVKAFVRLAKmLECGYPPVKDKSIVGHASEWmImRDLLSVGIAIYDEFPEmYNLAAGRFFKEHLVARNWFYPSHNYHQGmSYLNVRFTNDLFALWILDRmGAGNVFNPGQQFILYDAIYKRRPDGQILAGGDVDYSRKKPKYYTmPALLAGSYYKDEYLNYEFLKDPNVEPHCKLFEFLWRDTQLGSRKPDDLPLSRYSGSPFGWmIARTGWGPESVIAEmKVNEYSFLNHQHQDAGAFQIYYKGPLAIDAGSYTGSSGGYNSPHNKNFFKRTIAHNSLLIYDPKETFSSSGYGGSDHTDFAANDGGQRLPGKGWIAPRDLKEmLAGDFRTGKILAQGFGPDNQTPDYTYLKGDITAAYSAKVKEVKRSFLFLNLKDAKVPAAmIVFDKVVASNPDFKKFWLLHSIEQPEIKGNQITIKRTKNGDSGmLVNTALLPDAANSNITSIGGKGKDFWVFGTNYTNDPKPGTDEALERGEWRVEITPKKAAAEDYYLNVIQIADNTQQKLHEVKRIDGDKVVGVQLADRIVTFSKTSETVDRPFGFSVVGKGTFKFVmTDLLPGTWQVLKDGKILYPALSAKGDDGALYFEGTEGTYRFLR 772
                                    39 |      49        59     |  69       |79|       89        99       109 |     119       129       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       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599   |   609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769   
                                      41-MSE                  65-MSE      77-MSE                           111-MSE |                                  154-MSE                         186-MSE              207-MSE            226-MSE                      255-MSE             275-MSE                                      320-MSE                                                      381-MSE        396-MSE                                                                                                499-MSE                                                     559-MSE                                     603-MSE                                                                                                                       729-MSE                                       
                                                                             80-MSE                              117-MSE                                                                                     209-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 2FUT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2FUT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FUT)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (HEPB_PEDHD | C6XZB6)
molecular function
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    GO:0047488    heparin lyase activity    Catalysis of the eliminative cleavage of polysaccharides containing 1,4-linked D-glucuronate or L-iduronate residues and 1,4-alpha-linked 2-sulfoamino-2-deoxy-6-sulfo-D-glucose residues to give oligosaccharides with terminal 4-deoxy-alpha-D-gluc-4-enuronosyl groups at their nonreducing ends.
    GO:0015021    heparin-sulfate lyase activity    Catalysis of the elimination of sulfate; appears to act on linkages between N-acetyl-D-glucosamine and uronate. Product is an unsaturated sugar.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0030211    heparin catabolic process    The chemical reactions and pathways resulting in the breakdown 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.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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  2fut
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 Related Entries

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

UniProtKB/Swiss-Prot
        HEPB_PEDHD | C6XZB6: 2fuq 3e7j 3e80

(-) Related Entries Specified in the PDB File

2fuq NATIVE HEPARINASE II WITHOUT SUBSTRATE