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Description

Title :   HEVAMINE MUTANT D125A/E127A/Y183F IN COMPLEX WITH PENTA-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 (3, 13)

Asymmetric/Biological Unit (3, 13)

No.	Name	Count	Type	Full Name
1	GOL	5	Ligand/Ion	GLYCEROL
2	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SO4	3	Ligand/Ion	SULFATE ION

Sites (13, 13)

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:65 , HOH A:506 , HOH A:507 , HOH A:556 , HOH A:593 , NAG A:901	BINDING SITE FOR RESIDUE NAG A 900
02	AC2	SOFTWARE	GLY A:11 , ASN A:45 , ALA A:47 , GLY A:48 , HOH A:418 , HOH A:487 , HOH A:571 , NAG A:900 , NAG A:902	BINDING SITE FOR RESIDUE NAG A 901
03	AC3	SOFTWARE	GLN A:9 , ASN A:34 , ASN A:45 , ALA A:47 , LYS A:245 , HOH A:525 , NAG A:901 , NAG A:903	BINDING SITE FOR RESIDUE NAG A 902
04	AC4	SOFTWARE	GLN A:9 , PHE A:32 , GLY A:81 , ILE A:82 , GLU A:223 , ALA A:224 , LYS A:245 , TRP A:255 , TYR A:259 , HOH A:309 , HOH A:361 , HOH A:565 , NAG A:902 , NAG A:904	BINDING SITE FOR RESIDUE NAG A 903
05	AC5	SOFTWARE	TYR A:6 , PHE A:32 , GLY A:81 , GLN A:181 , PHE A:183 , ASN A:184 , ALA A:224 , ALA A:225 , TRP A:255 , HOH A:336 , NAG A:903 , GOL A:950	BINDING SITE FOR RESIDUE NAG A 904
06	AC6	SOFTWARE	ARG A:23 , SER A:89 , GLN A:90 , ALA A:91 , ARG A:204 , HOH A:460 , HOH A:483 , HOH A:491	BINDING SITE FOR RESIDUE SO4 A 800
07	AC7	SOFTWARE	THR A:15 , LEU A:16 , THR A:17 , ILE A:59 , VAL A:60 , GLY A:63	BINDING SITE FOR RESIDUE SO4 A 801
08	AC8	SOFTWARE	LYS A:149 , LYS A:150 , SER A:192 , HOH A:392 , HOH A:471	BINDING SITE FOR RESIDUE SO4 A 802
09	AC9	SOFTWARE	GLY A:1 , GLY A:81 , ALA A:127 , ASN A:184 , LYS A:244 , VAL A:273 , HOH A:318 , HOH A:334 , NAG A:904	BINDING SITE FOR RESIDUE GOL A 950
10	BC1	SOFTWARE	GLN A:68 , GLY A:71 , ILE A:72 , LYS A:73 , ASP A:120 , SER A:191 , HOH A:346 , HOH A:534	BINDING SITE FOR RESIDUE GOL A 951
11	BC2	SOFTWARE	LYS A:24 , ALA A:143 , TYR A:144 , GLN A:147 , ASP A:261 , SER A:267 , HOH A:333 , HOH A:347 , HOH A:568	BINDING SITE FOR RESIDUE GOL A 952
12	BC3	SOFTWARE	THR A:58 , SER A:61 , ASN A:62 , ARG A:65 , GLY A:115 , ASP A:116 , HOH A:403 , HOH A:509	BINDING SITE FOR RESIDUE GOL A 953
13	BC4	SOFTWARE	GLN A:158 , ASN A:185 , LEU A:270 , ASP A:271 , HOH A:343 , HOH A:374 , HOH A:399 , HOH A:438	BINDING SITE FOR RESIDUE GOL A 954

SS Bonds (3, 3)

Asymmetric/Biological Unit

No.	Residues
1	A:20	-	A:67
2	A:50	-	A:57
3	A:159	-	A:188

Cis Peptide Bonds (3, 3)

Asymmetric/Biological Unit

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CHLY_HEVBR_001 *	L	296	R	CHLY_HEVBR	---	---	A	L	270	R
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (1, 1)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHITINASE_18	PS01095	Chitinases family 18 active site.	CHLY_HEVBR	145-153	1	A:119-126

Exons (0, 0)

(no "Exon" information available for 1KQY)

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 d1kqya_ A: Hevamine A (chitinase/lysozyme)                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1kqyA00 A:1-273 Glycosidases                                                                                                                                                                                                                                                      CATH domains
               Pfam domains Glyco_hydro_18-1kqyA01 A:1-233                                                                                                                                                                                                           ---------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......hhhhhhhh....eeeeeee.eee..eeee........hhhhhhhhhhhhhhhhhhh..eeeeeee.........hhhhhhhhhhhhhhhhh...............eeeee.......hhhhhhhhhhhhhhhh...eeee..........hhhhhh.....eeeee...hhhhh.....hhhhhhhhhhhhh.....eeeeeee.hhhhh.....hhhhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R--- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------CHITINASE-------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kqy 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

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: (Trans)glycosidases (1191)

Family: Type II chitinase (131)

Protein domain: Hevamine A (chitinase/lysozyme) (7)

Rubber tree (Hevea brasiliensis) [TaxId: 3981] (7)

d1kqya_

CATH Domains (1, 1)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Glycosidases (843)

Hevea brasiliensis. Organism_taxid: 3981. (4)

1kqyA00

A:1-273

Pfam Domains (1, 1)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Glyco_hydro_tim (488)

Family: Glyco_hydro_18 (72)

Hevea brasiliensis (Para rubber tree) (Siphonia brasiliensis) (5)

Glyco_hydro_18-1kqyA01

A:1-233

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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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	CHLY_HEVBR \| P23472	:	1hvq 1kqz 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.
1kqz	1KQZ IS HEVAMINE MUTANT D125A/E127A/Y183F IN COMPLEX WITH TETRA-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.