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(-) Description

Title :  HEVAMINE MUTANT D125A/E127A/Y183F IN COMPLEX WITH TETRA-NAG
 
Authors :  H. J. Rozeboom, B. W. Dijkstra
Date :  08 Jan 02  (Deposition) - 23 Jan 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Chitinase/Lysozyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Bokma, H. J. Rozeboom, M. Sibbald, B. W. Dijkstra, J. J. Beintema
Expression And Characterization Of Active Site Mutants Of Hevamine, A Chitinase From The Rubber Tree Hevea Brasiliensis.
Eur. J. Biochem. V. 269 893 2002
PubMed-ID: 11846790  |  Reference-DOI: 10.1046/J.0014-2956.2001.02721.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEVAMINE A
    Chains: A
    EC Number: 3.2.1.14, 3.2.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGELAF+
    Expression System Strain: BL21(DE3)TRXB
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: HEVEA BRASILIENSIS
    Organism Taxid: 3981

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:11 , ALA A:47 , GLY A:48 , HOH A:364 , NAG A:902BINDING SITE FOR RESIDUE NAG A 901
2AC2SOFTWAREGLN A:9 , ASN A:34 , ASN A:45 , ALA A:47 , LYS A:245 , HOH A:411 , NAG A:901 , NAG A:903BINDING SITE FOR RESIDUE NAG A 902
3AC3SOFTWAREGLN A:9 , GLY A:81 , ILE A:82 , GLU A:223 , ALA A:224 , LYS A:245 , TRP A:255 , TYR A:259 , HOH A:302 , HOH A:329 , HOH A:442 , NAG A:902 , NAG A:904BINDING SITE FOR RESIDUE NAG A 903
4AC4SOFTWARETYR A:6 , PHE A:32 , GLY A:81 , GLN A:181 , ASN A:184 , ALA A:224 , ALA A:225 , TRP A:255 , NAG A:903BINDING SITE FOR RESIDUE NAG A 904

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:20 -A:67
2A:50 -A:57
3A:159 -A:188

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ala A:31 -Phe A:32
2Phe A:161 -Pro A:162
3Trp A:255 -Ser A:256

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CHLY_HEVBR_001 *L296RCHLY_HEVBR  ---  ---AL270R
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHITINASE_18PS01095 Chitinases family 18 active site.CHLY_HEVBR145-153  1A:119-126

(-) Exons   (0, 0)

(no "Exon" information available for 1KQZ)

(-) 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:273
 aligned with CHLY_HEVBR | P23472 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:273
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296   
           CHLY_HEVBR    27 GGIAIYWGQNGNEGTLTQTCSTRKYSYVNIAFLNKFGNGQTPQINLAGHCNPAAGGCTIVSNGIRSCQIQGIKVMLSLGGGIGSYTLASQADAKNVADYLWNNFLGGKSSSRPLGDAVLDGIDFDIEHGSTLYWDDLARYLSAYSKQGKKVYLTAAPQCPFPDRYLGTALNTGLFDYVWVQFYNNPPCQYSSGNINNIINSWNRWTTSINAGKIFLGLPAAPEAAGSGYVPPDVLISRILPEIKKSPKYGGVMLWSKFYDDKNGYSSSILDSV 299
               SCOP domains d1kqza_ A: Hevamine A (chitinase/lysozyme)                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1kqzA00 A:1-273 Glycosidases                                                                                                                                                                                                                                                      CATH domains
               Pfam domains Glyco_hydro_18-1kqzA01 A:1-233                                                                                                                                                                                                           ---------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......hhhhhhhh....eeeeeee.eee..eeee........hhhhhhhhhhhhhhhhhhh..eeeeeee.........hhhhhhhhhhhhhhhh................eeeee.......hhhhhhhhhhhhhhhh...eeee..........hhhhhhh....eeeee...hhhhh.....hhhhhhhhhhhhhhh...eeeeeee.hhhhh.....hhhhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R--- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------CHITINASE-------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kqz A   1 GGIAIYWGQNGNEGTLTQTCSTRKYSYVNIAFLNKFGNGQTPQINLAGHCNPAAGGCTIVSNGIRSCQIQGIKVMLSLGGGIGSYTLASQADAKNVADYLWNNFLGGKSSSRPLGDAVLDGIDFAIAHGSTLYWDDLARYLSAYSKQGKKVYLTAAPQCPFPDRYLGTALNTGLFDYVWVQFFNNPPCQYSSGNINNIINSWNRWTTSINAGKIFLGLPAAPEAAGSGYVPPDVLISRILPEIKKSPKYGGVMLWSKFYDDKNGYSSSILDSV 273
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CHLY_HEVBR | P23472)
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:0004568    chitinase activity    Catalysis of the hydrolysis of (1->4)-beta linkages of N-acetyl-D-glucosamine (GlcNAc) polymers of chitin and chitodextrins.
    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.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0003796    lysozyme activity    Catalysis of the hydrolysis of the beta-(1->4) linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan.
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:0006032    chitin catabolic process    The chemical reactions and pathways resulting in the breakdown of chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
    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.
    GO:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
cellular component
    GO:0005773    vacuole    A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

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  CHLY_HEVBR | P23472
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 Related Entries

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

UniProtKB/Swiss-Prot
        CHLY_HEVBR | P23472: 1hvq 1kqy 1kr0 1kr1 1llo 2hvm

(-) Related Entries Specified in the PDB File

1hvq 1HVQ IS CRYSTAL STRUCTURES OF HEVAMINE, A PLANT DEFENCE PROTEIN WITH CHITINASE AND LYSOZYME ACTIVITY, AND ITS COMPLEX WITH AN INHIBITOR.
1kqy 1KQY IS HEVAMINE MUTANT D125A/E127A/Y183F IN COMPLEX WITH PENTA-NAG.
1kr0 1KR0 IS HEVAMINE MUTANT D125A/Y183F IN COMPLEX WITH TETRA- NAG.
1kr1 1KR1 IS HEVAMINE MUTANT D125A/E127A IN COMPLEX WITH TETRA- NAG.
1llo 1LLO IS HEVAMINE A (A PLANT ENDOCHITINASE/LYSOZYME) COMPLEXED WITH ALLOSAMIDIN.
2hvm 2HVM IS HEVAMINE A AT 1.8 ANGSTROM RESOLUTION.