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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN HEPARANASE NUCLEOPHILE MUTANT (E343Q), IN COMPLEX WITH UNREACTED GLUCURONIC ACID CONFIGURED AZIRIDINE PROBE JJB355
 
Authors :  L. Wu, Y. Jin, G. J. Davies
Date :  13 Jun 16  (Deposition) - 31 May 17  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Heparanase, Probe, Gh79, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Wu, J. Jiang, Y. Jin, W. W. Kallemeijn, C. L. Kuo, M. Artola, W. Dai, C. Van Elk, M. Van Eijk, G. A. Van Der Marel, J. D. C. Codee, B. I. Florea, J. M. F. G. Aerts, H. S. Overkleeft, G. J. Davies
Activity-Based Probes For Functional Interrogation Of Retaining Beta-Glucuronidases.
Nat. Chem. Biol. 2017
PubMed-ID: 28581485  |  Reference-DOI: 10.1038/NCHEMBIO.2395

(-) Compounds

Molecule 1 - HEPARANASE
    Chains: A
    EC Number: 3.2.1.166
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Fragment: UNP RESIDUES 158-543
    Gene: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ENDO-GLUCORONIDASE,HEPARANASE-1,HPA1
 
Molecule 2 - HEPARANASE
    Chains: B
    EC Number: 3.2.1.166
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Fragment: UNP RESIDUES 36-109
    Gene: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ENDO-GLUCORONIDASE,HEPARANASE-1,HPA1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric/Biological Unit (4, 15)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2EDO7Ligand/Ion1,2-ETHANEDIOL
3GUX1Ligand/Ion(1~{R},2~{S},3~{R},4~{S},5~{S},6~{R})-7-[8-[(AZANYLIDENE-{4}-AZANYLIDENE)AMINO]OCTYL]-3,4,5-TRIS(OXIDANYL)-7-AZABICYCLO[4.1.0]HEPTANE-2-CARBOXYLICACID
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:415 , THR A:416 , ASN A:439 , THR A:440 , HOH A:730 , HOH A:922binding site for residue EDO A 605
02AC2SOFTWAREPHE A:327 , MET A:375 , HOH A:889 , HOH A:935 , HOH A:950 , HIS B:50binding site for residue EDO A 606
03AC3SOFTWAREARG A:307 , HIS A:486 , LEU A:488 , LEU A:489 , HOH A:741binding site for residue EDO A 607
04AC4SOFTWAREGLN A:324 , HOH A:715 , HOH A:722 , HOH A:784 , HOH A:954binding site for residue EDO A 608
05AC5SOFTWARELYS A:477 , ASN A:496 , LYS A:514 , HOH A:723binding site for residue EDO A 609
06AC6SOFTWAREPRO A:353 , HOH A:882binding site for residue EDO A 610
07AC7SOFTWARELYS A:337 , HOH A:989binding site for residue CL A 611
08AC8SOFTWAREGLY A:239 , MET A:278 , HOH A:726 , HOH A:896binding site for residue CL A 612
09AC9SOFTWAREALA A:388 , HOH B:346 , HOH B:360binding site for residue CL A 613
10AD1SOFTWAREASN A:224 , GLU A:225 , GLN A:270 , TYR A:298 , GLN A:343 , TYR A:348 , GLY A:349 , GLY A:350 , GLN A:383 , TYR A:391 , HOH A:708 , HOH A:908 , ASP B:62 , GLY B:96 , THR B:97 , HOH B:304binding site for residue GUX A 614
11AD2SOFTWARECYS A:179 , PRO B:78 , ARG B:81 , ARG B:85 , HOH B:301binding site for residue EDO B 201
12AD3SOFTWAREASN A:200 , SER A:202 , HOH A:812 , HOH A:894 , HOH A:937binding site for Mono-Saccharide NAG A 601 bound to ASN A 200
13AD4SOFTWAREASN A:217binding site for Mono-Saccharide NAG A 604 bound to ASN A 217
14AD5SOFTWAREASN A:238 , GLN A:241 , HOH A:703 , HOH A:710 , HOH A:718 , HOH A:795 , HOH A:825binding site for Mono-Saccharide NAG A 602 bound to ASN A 238
15AD6SOFTWAREASN A:459 , HOH A:756 , HOH A:803 , HOH A:834 , HOH A:932 , HOH A:956binding site for Mono-Saccharide NAG A 603 bound to ASN A 459

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:437 -A:542

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Gly A:265 -Pro A:266
2Gln A:383 -Val A:384
3Tyr A:468 -Pro A:469
4Gly A:484 -Pro A:485
5Ser B:88 -Pro B:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5L9Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5L9Z)

(-) Exons   (0, 0)

(no "Exon" information available for 5L9Z)

(-) 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:385
                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeehhhhhhhhhhhhhhh.eeeeeee............hhhhhhhhhhhhhh....eeee..hhhhhhhhhh...hhhhhhhhhhhhhhhhhh.......eeeeee...hhhhhhhhhhhhhhhhhhh.eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeee.........hhhhhhhhhhhhhhhhhhh...eee..................hhhhhhhhhhhhheeeee.eeee.......eeeeeeee...........eeeeeee.....eeee.........eeeeeeee...hhhhh..eee..ee..............ee......eee...eeeeeee....hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l9z A 159 KFKNSTYSRSSVDVLYTFANCSGLDLIFGLNALLRTADLQWNSSNAQLLLDYCSSKGYNISWELGNEPNSFLKKADIFINGSQLGEDFIQLHKLLRKSTFKNAKLYGPDVGQPRRKTAKMLKSFLKAGGEVIDSVTWHHYYLNGRTATREDFLNPDVLDIFISSVQKVFQVVESTRPGKKVWLGQTSSAYGGGAPLLSDTFAAGFMWLDKLGLSARMGIEVVMRQVFFGAGNYHLVDENFDPLPDYWLSLLFKKLVGTKVLMASVQGSKRRKLRVYLHCTNTDNPRYKEGDLTLYAINLHNVTKYLRLPYPFSNKQVDKYLLRPLGPHGLLSKSVQLNGLTLKMVDDQTLPPLMEKPLRPGSSLGLPAFSYSFFVIRNAKVAACI 543
                                   168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538     


Chain B from PDB  Type:PROTEIN  Length:74
                                                                                                          
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....ee.....eeeeehhhhhhh.hhhhhhhhhhhhhhhhhh..eeeee.hhhhh.eee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 5l9z B  36 QDVVDLDFFTQEPLHLVSPSFLSVTIDANLATDPRFLILLGSPKLRTLARGLSPAYLRFGGTKTDFLIFDPKKE 109
                                    45        55        65        75        85        95       105
   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 5L9Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5L9Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5L9Z)

(-) Gene Ontology  (31, 31)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gln A:383 - Val A:384   [ RasMol ]  
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    Gly A:484 - Pro A:485   [ RasMol ]  
    Ser B:88 - Pro B:89   [ RasMol ]  
    Tyr A:468 - Pro A:469   [ RasMol ]  
 

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  3.2.1.166
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 Related Entries

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

UniProtKB/Swiss-Prot
        HPSE_HUMAN | Q9Y251: 5e8m 5e97 5e98 5e9b 5e9c 5l9y 5la4 5la7

(-) Related Entries Specified in the PDB File

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