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(-) Description

Title :  CRYSTAL STRUCTURE OF BEE VENOM HYALURONIDASE IN COMPLEX WITH HYALURONIC ACID TETRAMER
 
Authors :  Z. Markovic-Housley, G. Miglierini, L. Soldatova, P. J. Rizkallah, U. T. Schirmer
Date :  19 Jul 00  (Deposition) - 01 Oct 01  (Release) - 25 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A
Keywords :  7 Stranded Tim Barrel, Allergen, Glycosidase Family 56, Hyaluronic Acid, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Markovic-Housley, G. Miglierini, L. Soldatova, P. J. Rizkallah, U. Muller, T. Schirmer
Crystal Structure Of Hyaluronidase, A Major Allergen Of Bee Venom.
Structure Fold. Des. V. 8 1025 2000
PubMed-ID: 11080624  |  Reference-DOI: 10.1016/S0969-2126(00)00511-6

(-) Compounds

Molecule 1 - HYALURONOGLUCOSAMINIDASE
    Chains: A
    EC Number: 3.2.1.35
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell: HIGH-FIVE INSECT CELLS
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Expression System Vector: PMELBAC A
    Expression System Vector Type: BACULOVIRUS
    Organism Common: HONEY BEE
    Organism Scientific: APIS MELLIFERA
    Organism Taxid: 7460
    Synonym: HYALURONIDASE, API M II

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1GCU3Ligand/IonD-GLUCURONIC ACID
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:21 , NAG A:402BINDING SITE FOR RESIDUE GCU A 401
2AC2SOFTWAREPHE A:46 , TYR A:55 , ALA A:73 , SER A:304 , GCU A:401 , GCU A:403 , HOH A:537BINDING SITE FOR RESIDUE NAG A 402
3AC3SOFTWARETRP A:301 , SER A:303 , SER A:304 , NAG A:402 , NAG A:404 , HOH A:529 , HOH A:537BINDING SITE FOR RESIDUE GCU A 403
4AC4SOFTWAREASP A:111 , GLU A:113 , TYR A:184 , TYR A:227 , GLN A:271 , GCU A:403 , GCU A:405BINDING SITE FOR RESIDUE NAG A 404
5AC5SOFTWAREGLU A:113 , TYR A:184 , NAG A:404BINDING SITE FOR RESIDUE GCU A 405

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:313
2A:189 -A:201

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:186 -Pro A:187

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1FCV)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1FCV)

(-) 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:324
 aligned with HUGA_APIME | Q08169 from UniProtKB/Swiss-Prot  Length:382

    Alignment length:324
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361    
           HUGA_APIME    42 EFNVYWNVPTFMCHKYGLRFEEVSEKYGILQNWMDKFRGEEIAILYDPGMFPALLKDPNGNVVARNGGVPQLGNLTKHLQVFRDHLINQIPDKSFPGVGVIDFESWRPIFRQNWASLQPYKKLSVEVVRREHPFWDDQRVEQEAKRRFEKYGQLFMEETLKAAKRMRPAANWGYYAYPYCYNLTPNQPSAQCEATTMQENDKMSWLFESEDVLLPSVYLRWNLTSGERVGLVGGRVKEALRIARQMTTSRKKVLPYYWYKYQDRRDTDLSRADLEATLRKITDLGADGFIIWGSSDDINTKAKCLQFREYLNNELGPAVKRIAL 365
               SCOP domains d1fcva_ A: Bee venom hyaluronidase                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1fcvA00 A:10-333 Aldolase class I                                                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee.hhhhhhhhh...hhhhhh.....hhhhh.....eeeee......eeee.....eeeehhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee......hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..................hhhhhhhhhhhhhhhhhh.ee..........hhhhhhhhhhhhhhhhhhhhh.......ee..eee.ee..eeeee.hhhhhhhhhhhhhhhh..eeeee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1fcv A  10 EFNVYWNVPTFMCHKYGLRFEEVSEKYGILQNWMDKFRGEEIAILYDPGMFPALLKDPNGNVVARNGGVPQLGNLTKHLQVFRDHLINQIPDKSFPGVGVIDFESWRPIFRQNWASLQPYKKLSVEVVRREHPFWDDQRVEQEAKRRFEKYGQLFMEETLKAAKRMRPAANWGYYAYPYCYNLTPNQPSAQCEATTMQENDKMSWLFESEDVLLPSVYLRWNLTSGERVGLVGGRVKEALRIARQMTTSRKKVLPYYWYKYQDRRDTDLSRADLEATLRKITDLGADGFIIWGSSDDINTKAKCLQFREYLNNELGPAVKRIAL 333
                                    19        29        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
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1FCV)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HUGA_APIME | Q08169)
molecular function
    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:0004415    hyalurononglucosaminidase activity    Catalysis of the random hydrolysis of (1->4) linkages between N-acetyl-beta-D-glucosamine and D-glucuronate residues in hyaluronate.
    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:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    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.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HUGA_APIME | Q08169: 1fcq 1fcu 2j88

(-) Related Entries Specified in the PDB File

1fcq 1FCQ IS THE SAME PROTEIN WITHOUT LIGAND IN A DIFFERENT CRYSTAL FORM
1fcu 1FCU IS THE SAME PROTEIN WITHOUT LIGAND IN THE SAME CRYSTAL FORM