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(-) Description

Title :  CRYSTAL STRUCTURE OF HEPARINASE II
 
Authors :  D. Shaya, M. Cygler
Date :  27 Jan 06  (Deposition) - 18 Apr 06  (Release) - 23 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
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  (8, 17)

Asymmetric/Biological Unit (8, 17)
No.NameCountTypeFull Name
1FMT3Ligand/IonFORMIC ACID
2GCU2Ligand/IonD-GLUCURONIC ACID
3MAN2Ligand/IonALPHA-D-MANNOSE
4PCA2Mod. Amino AcidPYROGLUTAMIC ACID
5PO42Ligand/IonPHOSPHATE ION
6RAM2Ligand/IonALPHA-L-RHAMNOSE
7XYS2Ligand/IonXYLOPYRANOSE
8ZN2Ligand/IonZINC ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:97 , LYS A:102 , LEU A:104 , THR A:105 , MAN A:774 , HOH A:1060 , HOH A:1224 , HOH A:1298BINDING SITE FOR RESIDUE RAM A 773
02AC2SOFTWARETHR A:134 , RAM A:773 , GCU A:775 , XYS A:776BINDING SITE FOR RESIDUE MAN A 774
03AC3SOFTWARETHR A:134 , MAN A:774 , XYS A:776 , FMT A:943BINDING SITE FOR RESIDUE GCU A 775
04AC4SOFTWAREMAN A:774 , GCU A:775BINDING SITE FOR RESIDUE XYS A 776
05AC5SOFTWAREPHE B:97 , LYS B:102 , LEU B:104 , THR B:105 , MAN B:774 , HOH B:1257 , HOH B:1318 , HOH B:1358BINDING SITE FOR RESIDUE RAM B 773
06AC6SOFTWARETHR B:134 , RAM B:773 , GCU B:775BINDING SITE FOR RESIDUE MAN B 774
07AC7SOFTWARETHR B:134 , MAN B:774 , XYS B:776BINDING SITE FOR RESIDUE GCU B 775
08AC8SOFTWAREGCU B:775BINDING SITE FOR RESIDUE XYS B 776
09AC9SOFTWAREHIS A:408 , ASP A:425 , HIS A:451 , HOH A:1319 , HOH A:1320 , HOH A:1339BINDING SITE FOR RESIDUE ZN A 1
10BC1SOFTWAREHIS B:408 , ASP B:425 , HIS B:451 , HOH B:1306 , HOH B:1327 , HOH B:1328BINDING SITE FOR RESIDUE ZN B 2
11BC2SOFTWAREPRO A:611 , ASN A:615 , ASP A:665 , TYR A:666 , HOH A:1283 , HOH A:1404BINDING SITE FOR RESIDUE PO4 A 944
12BC3SOFTWARELEU B:610 , PRO B:611 , ASN B:615 , ASP B:665 , TYR B:666BINDING SITE FOR RESIDUE PO4 B 945
13BC4SOFTWAREPRO A:714 , ARG A:769 , LEU A:771 , HOH A:1103 , HOH A:1171 , HOH A:1232BINDING SITE FOR RESIDUE FMT A 941
14BC5SOFTWAREPRO B:714 , ARG B:769 , LEU B:771 , HOH B:1112 , HOH B:1268BINDING SITE FOR RESIDUE FMT B 942
15BC6SOFTWARELYS A:93 , THR A:139 , GCU A:775BINDING SITE FOR RESIDUE FMT A 943

(-) SS Bonds  (0, 0)

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

(-) 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 2FUQ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2FUQ)

(-) 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:747
 aligned with HEPB_PEDHD | C6XZB6 from UniProtKB/Swiss-Prot  Length:772

    Alignment length:747
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       
           HEPB_PEDHD    26 QTKADVVWKDVDGVSMPIPPKTHPRLYLREQQVPDLKNRMNDPKLKKVWADMIKMQEDWKPADIPEVKDFRFYFNQKGLTVRVELMALNYLMTKDPKVGREAITSIIDTLETATFKPAGDISRGIGLFMVTGAIVYDWCYDQLKPEEKTRFVKAFVRLAKMLECGYPPVKDKSIVGHASEWMIMRDLLSVGIAIYDEFPEMYNLAAGRFFKEHLVARNWFYPSHNYHQGMSYLNVRFTNDLFALWILDRMGAGNVFNPGQQFILYDAIYKRRPDGQILAGGDVDYSRKKPKYYTMPALLAGSYYKDEYLNYEFLKDPNVEPHCKLFEFLWRDTQLGSRKPDDLPLSRYSGSPFGWMIARTGWGPESVIAEMKVNEYSFLNHQHQDAGAFQIYYKGPLAIDAGSYTGSSGGYNSPHNKNFFKRTIAHNSLLIYDPKETFSSSGYGGSDHTDFAANDGGQRLPGKGWIAPRDLKEMLAGDFRTGKILAQGFGPDNQTPDYTYLKGDITAAYSAKVKEVKRSFLFLNLKDAKVPAAMIVFDKVVASNPDFKKFWLLHSIEQPEIKGNQITIKRTKNGDSGMLVNTALLPDAANSNITSIGGKGKDFWVFGTNYTNDPKPGTDEALERGEWRVEITPKKAAAEDYYLNVIQIADNTQQKLHEVKRIDGDKVVGVQLADRIVTFSKTSETVDRPFGFSVVGKGTFKFVMTDLLPGTWQVLKDGKILYPALSAKGDDGALYFEGTEGTYRFLR 772
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee..eeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhhhhhhhh...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
                 2fuq A  26 xTKADVVWKDVDGVSMPIPPKTHPRLYLREQQVPDLKNRMNDPKLKKVWADMIKMQEDWKPADIPEVKDFRFYFNQKGLTVRVELMALNYLMTKDPKVGREAITSIIDTLETATFKPAGDISRGIGLFMVTGAIVYDWCYDQLKPEEKTRFVKAFVRLAKMLECGYPPVKDKSIVGHASEWMIMRDLLSVGIAIYDEFPEMYNLAAGRFFKEHLVARNWFYPSHNYHQGMSYLNVRFTNDLFALWILDRMGAGNVFNPGQQFILYDAIYKRRPDGQILAGGDVDYSRKKPKYYTMPALLAGSYYKDEYLNYEFLKDPNVEPHCKLFEFLWRDTQLGSRKPDDLPLSRYSGSPFGWMIARTGWGPESVIAEMKVNEYSFLNHQHQDAGAFQIYYKGPLAIDAGSYTGSSGGYNSPHNKNFFKRTIAHNSLLIYDPKETFSSSGYGGSDHTDFAANDGGQRLPGKGWIAPRDLKEMLAGDFRTGKILAQGFGPDNQTPDYTYLKGDITAAYSAKVKEVKRSFLFLNLKDAKVPAAMIVFDKVVASNPDFKKFWLLHSIEQPEIKGNQITIKRTKNGDSGMLVNTALLPDAANSNITSIGGKGKDFWVFGTNYTNDPKPGTDEALERGEWRVEITPKKAAAEDYYLNVIQIADNTQQKLHEVKRIDGDKVVGVQLADRIVTFSKTSETVDRPFGFSVVGKGTFKFVMTDLLPGTWQVLKDGKILYPALSAKGDDGALYFEGTEGTYRFLR 772
                            |       35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       
                            |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
                           26-PCA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:747
 aligned with HEPB_PEDHD | C6XZB6 from UniProtKB/Swiss-Prot  Length:772

    Alignment length:747
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       
           HEPB_PEDHD    26 QTKADVVWKDVDGVSMPIPPKTHPRLYLREQQVPDLKNRMNDPKLKKVWADMIKMQEDWKPADIPEVKDFRFYFNQKGLTVRVELMALNYLMTKDPKVGREAITSIIDTLETATFKPAGDISRGIGLFMVTGAIVYDWCYDQLKPEEKTRFVKAFVRLAKMLECGYPPVKDKSIVGHASEWMIMRDLLSVGIAIYDEFPEMYNLAAGRFFKEHLVARNWFYPSHNYHQGMSYLNVRFTNDLFALWILDRMGAGNVFNPGQQFILYDAIYKRRPDGQILAGGDVDYSRKKPKYYTMPALLAGSYYKDEYLNYEFLKDPNVEPHCKLFEFLWRDTQLGSRKPDDLPLSRYSGSPFGWMIARTGWGPESVIAEMKVNEYSFLNHQHQDAGAFQIYYKGPLAIDAGSYTGSSGGYNSPHNKNFFKRTIAHNSLLIYDPKETFSSSGYGGSDHTDFAANDGGQRLPGKGWIAPRDLKEMLAGDFRTGKILAQGFGPDNQTPDYTYLKGDITAAYSAKVKEVKRSFLFLNLKDAKVPAAMIVFDKVVASNPDFKKFWLLHSIEQPEIKGNQITIKRTKNGDSGMLVNTALLPDAANSNITSIGGKGKDFWVFGTNYTNDPKPGTDEALERGEWRVEITPKKAAAEDYYLNVIQIADNTQQKLHEVKRIDGDKVVGVQLADRIVTFSKTSETVDRPFGFSVVGKGTFKFVMTDLLPGTWQVLKDGKILYPALSAKGDDGALYFEGTEGTYRFLR 772
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee..eeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh......................hhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhh.......hhhhh..eeee.....eeeee.......eeeeee................eeeee..eee..............hhhhhhh..hhhhh..eee......................................hhhhhhhh.....eeeeeee........eeeeeee.hhhh...eeeeeeeeeeee.......eeeeeeeeeee......eeeeeee....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
                 2fuq B  26 xTKADVVWKDVDGVSMPIPPKTHPRLYLREQQVPDLKNRMNDPKLKKVWADMIKMQEDWKPADIPEVKDFRFYFNQKGLTVRVELMALNYLMTKDPKVGREAITSIIDTLETATFKPAGDISRGIGLFMVTGAIVYDWCYDQLKPEEKTRFVKAFVRLAKMLECGYPPVKDKSIVGHASEWMIMRDLLSVGIAIYDEFPEMYNLAAGRFFKEHLVARNWFYPSHNYHQGMSYLNVRFTNDLFALWILDRMGAGNVFNPGQQFILYDAIYKRRPDGQILAGGDVDYSRKKPKYYTMPALLAGSYYKDEYLNYEFLKDPNVEPHCKLFEFLWRDTQLGSRKPDDLPLSRYSGSPFGWMIARTGWGPESVIAEMKVNEYSFLNHQHQDAGAFQIYYKGPLAIDAGSYTGSSGGYNSPHNKNFFKRTIAHNSLLIYDPKETFSSSGYGGSDHTDFAANDGGQRLPGKGWIAPRDLKEMLAGDFRTGKILAQGFGPDNQTPDYTYLKGDITAAYSAKVKEVKRSFLFLNLKDAKVPAAMIVFDKVVASNPDFKKFWLLHSIEQPEIKGNQITIKRTKNGDSGMLVNTALLPDAANSNITSIGGKGKDFWVFGTNYTNDPKPGTDEALERGEWRVEITPKKAAAEDYYLNVIQIADNTQQKLHEVKRIDGDKVVGVQLADRIVTFSKTSETVDRPFGFSVVGKGTFKFVMTDLLPGTWQVLKDGKILYPALSAKGDDGALYFEGTEGTYRFLR 772
                            |       35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       
                           26-PCA
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 2FUQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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  2fuq
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2FUQ)