1E6Z - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CHITINASE B FROM SERRATIA MARCESCENS WILDTYPE IN COMPLEX WITH CATALYTIC INTERMEDIATE

Authors :   D. Komander, B. Synstad, V. G. H. Eijsink, D. M. F. Van Aalten

Date :   23 Aug 00 (Deposition) - 22 Jun 01 (Release) - 12 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.99

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Hydrolase, Chitin Degradation, Catalytic Intermediate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. M. F. Van Aalten, D. Komander, B. Synstad, S. Gseidnes, M. G. Peter, V. G. H. Eijsink
Structural Insights Into The Catalytic Mechanism Of A Famil 18 Exo-Chitinase
Proc. Natl. Acad. Sci. Usa V. 98 8979 2001
PubMed-ID: 11481469 | Reference-DOI: 10.1073/PNAS.151103798

Molecule 1 - CHITINASE B
	Chains	:	A, B
	EC Number	:	3.2.1.14
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	SERRATIA MARCESCENS
	Organism Taxid	:	615
	Synonym	:	1,4-BETA-POLY-N-ACETYLGLUCOSAMINIDASE, CHITODEXTRINASE, POLY-BETA-GLUCOSAMINIDASE, POLY(1,4-(N-ACETYL-BETA-D-GLUCOSAMINIDE)) GLYCANOHYDROLASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	NGO	2	Ligand/Ion	2-METHYL-4,5-DIHYDRO-(1,2-DIDEOXY-ALPHA-D-GLUCOPYRANOSO)[2,1-D]-1,3-OXAZOLE
3	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	NGO	1	Ligand/Ion	2-METHYL-4,5-DIHYDRO-(1,2-DIDEOXY-ALPHA-D-GLUCOPYRANOSO)[2,1-D]-1,3-OXAZOLE
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 5)

No.	Name	Count	Type	Full Name
1	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	NGO	1	Ligand/Ion	2-METHYL-4,5-DIHYDRO-(1,2-DIDEOXY-ALPHA-D-GLUCOPYRANOSO)[2,1-D]-1,3-OXAZOLE
3	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP B:97 , ASP B:215 , TRP B:220 , ASP B:316 , HOH B:626 , HOH B:808 , HOH B:818 , HOH B:602 , HOH B:908	BINDING SITE FOR RESIDUE NAG B1001
2	AC2	SOFTWARE	ARG A:420 , HOH A:649 , HOH A:667 , HOH A:923 , HOH A:828 , LYS B:386 , ARG B:420 , HOH B:776	BINDING SITE FOR RESIDUE SO4 A1500
3	AC3	SOFTWARE	THR B:26 , ARG B:343 , ARG B:410 , HOH B:798 , HOH B:898 , HOH B:717 , HOH B:739	BINDING SITE FOR RESIDUE SO4 B1500
4	AC4	SOFTWARE	LYS A:132 , GLN A:168 , THR A:171 , ASP A:172 , LYS B:115 , HOH B:813	BINDING SITE FOR RESIDUE SO4 B1501
5	AC5	SOFTWARE	ASN A:352 , PRO B:454 , ALA B:455 , HOH B:738 , HOH B:618 , HOH B:670 , HOH B:777	BINDING SITE FOR RESIDUE SO4 B1502
6	AC6	SOFTWARE	TYR A:10 , PHE A:51 , TRP A:97 , ASP A:142 , GLU A:144 , MET A:212 , TYR A:214 , ASP A:215 , TYR A:292 , TRP A:403 , HOH A:697 , HOH A:650	BINDING SITE FOR RESIDUE NGO A 999
7	AC7	SOFTWARE	TYR B:10 , PHE B:51 , TRP B:97 , ASP B:142 , GLU B:144 , ALA B:184 , MET B:212 , TYR B:214 , ASP B:215 , TYR B:292 , TRP B:403 , HOH B:872 , HOH B:932	BINDING SITE FOR RESIDUE NGO B 999
8	AC8	SOFTWARE	TRP A:97 , PHE A:191 , ASP A:215 , TRP A:220 , ASP A:316 , HOH A:617 , HOH A:687 , HOH A:685 , HOH A:724 , HOH A:997 , HOH A:650 , HOH A:841 , HOH A:736 , HOH A:799 , HOH A:896 , HOH A:721 , HOH A:663 , TYR B:481	BINDING SITE FOR CHAIN A OF DI-SACCHARIDE NAG A1001 AND NAG A1002

Asymmetric Unit

No.	Residues
1	A:328	-	A:331
2	B:328	-	B:331

Asymmetric Unit

No.	Residues
1	Ser A:50	-	Phe A:51
2	Glu A:144	-	Tyr A:145
3	Ser A:261	-	Pro A:262
4	Asp A:316	-	Pro A:317
5	Trp A:403	-	His A:404
6	Ser B:50	-	Phe B:51
7	Glu B:144	-	Tyr B:145
8	Ser B:261	-	Pro B:262
9	Asp B:316	-	Pro B:317
10	Trp B:403	-	His B:404

(no "SAP(SNP)/Variant" information available for 1E6Z)

(no "PROSITE Motif" information available for 1E6Z)

(no "Exon" information available for 1E6Z)

Asymmetric 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:498
 aligned with Q54276_SERMA | Q54276 from UniProtKB/TrEMBL  Length:499

    Alignment length:498
                                    11        21        31        41        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       371       381       391       401       411       421       431       441       451       461       471       481       491        
         Q54276_SERMA     2 STRKAVIGYYFIPTNQINNYTETDTSVVPFPVSNITPAKAKQLTHINFSFLDINSNLECAWDPATNDAKARDVVNRLTALKAHNPSLRIMFSIGGWYYSNDLGVSHANYVNAVKTPASRAKFAQSCVRIMKDYGFDGVDIDWEYPQAAEVDGFIAALQEIRTLLNQQTITDGRQALPYQLTIAGAGGAFFLSRYYSKLAQIVAPLDYINLMTYDLAGPWEKVTNHQAALFGDAAGPTFYNALREANLGWSWEELTRAFPSPFSLTVDAAVQQHLMMEGVPSAKIVMGVPFYGRAFKGVSGGNGGQYSSHSTPGEDPYPSTDYWLVGCEECVRDKDPRIASYRQLEQMLQGNYGYQRLWNDKTKTPYLYHAQNGLFVTYDDAESFKYKAKYIKQQQLGGVMFWHLGQDNRNGDLLAALDRYFNAADYDDSQLDMGTGLRYTGVGPGNLPIMTAPAYVPGTTYAQGALVSYQGYVWQTKWGYITSAPGSDSAWLKVGRVA 499
               SCOP domains d1e6za2 A:2-291,A:380-446 Chitinase B, catalytic domain                                                                                                                                                                                                                                           d1e6za3 A:292-379 Chitinase B                                                           d1e6za2 A:2-291,A:380-446 Chitinase B, catalytic domain            d1e6za1 A:447-498 Chitinase B, C-terminal domain    - SCOP domains
               CATH domains 1e6zA01 A:2-290,A:381-448 Glycosidases                                                                                                                                                                                                                                                           1e6zA02 A:291-380  [code=3.10.50.10, no name defined]                                     1e6zA01 A:2-290,A:381-448 Glycosidases                              1e6zA03 A:449-498                                 - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeee.hhhhhh............hhhhhhhhhhhhh.eeeeeeeee.....ee.....hhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhh....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee.hhhhhhhhhhhhhhhhh...eeeee............................hhhhhh....hhhhhhhhh......hhhhhhhhhhh....hhh.eeeeee.eeeeee..............................hhhhhhhh...eeehhhhhhhhhh...eeeeee....eeeeee....eeee..hhhhhhhhhhhhhhh...eeeeehhhhh...hhhhhhhhhhhhh..........................................eeee..eeeee..............eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1e6z A   2 STRKAVIGYYFIPTNQINNYTETDTSVVPFPVSNITPAKAKQLTHINFSFLDINSNLECAWDPATNDAKARDVVNRLTALKAHNPSLRIMFSIGGWYYSNDLGVSHANYVNAVKTPASRAKFAQSCVRIMKDYGFDGVDIDWEYPQAAEVDGFIAALQEIRTLLNQQTITDGRQALPYQLTIAGAGGAFFLSRYYSKLAQIVAPLDYINLMTYDLAGPWEKVTNHQAALFGDAAGPTFYNALREANLGWSWEELTRAFPSPFSLTVDAAVQQHLMMEGVPSAKIVMGVPFYGRAFKGVSGGNGGQYSSHSTPGEDPYPSTDYWLVGCEECVRDKDPRIASYRQLEQMLQGNYGYQRLWNDKTKTPYLYHAQNGLFVTYDDAESFKYKAKYIKQQQLGGVMFWHLGQDNRNGDLLAALDRYFNAADYDDSQLDMGTGLRYTGVGPGNLPIMTAPAYVPGTTYAQGALVSYQGYVWQTKWGYITSAPGSDSAWLKVGRVA 499
                                    11        21        31        41        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       371       381       391       401       411       421       431       441       451       461       471       481       491

Chain B from PDB  Type:PROTEIN  Length:498
 aligned with Q54276_SERMA | Q54276 from UniProtKB/TrEMBL  Length:499

    Alignment length:498
                                    11        21        31        41        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       371       381       391       401       411       421       431       441       451       461       471       481       491        
         Q54276_SERMA     2 STRKAVIGYYFIPTNQINNYTETDTSVVPFPVSNITPAKAKQLTHINFSFLDINSNLECAWDPATNDAKARDVVNRLTALKAHNPSLRIMFSIGGWYYSNDLGVSHANYVNAVKTPASRAKFAQSCVRIMKDYGFDGVDIDWEYPQAAEVDGFIAALQEIRTLLNQQTITDGRQALPYQLTIAGAGGAFFLSRYYSKLAQIVAPLDYINLMTYDLAGPWEKVTNHQAALFGDAAGPTFYNALREANLGWSWEELTRAFPSPFSLTVDAAVQQHLMMEGVPSAKIVMGVPFYGRAFKGVSGGNGGQYSSHSTPGEDPYPSTDYWLVGCEECVRDKDPRIASYRQLEQMLQGNYGYQRLWNDKTKTPYLYHAQNGLFVTYDDAESFKYKAKYIKQQQLGGVMFWHLGQDNRNGDLLAALDRYFNAADYDDSQLDMGTGLRYTGVGPGNLPIMTAPAYVPGTTYAQGALVSYQGYVWQTKWGYITSAPGSDSAWLKVGRVA 499
               SCOP domains d1e6zb2 B:2-291,B:380-446 Chitinase B, catalytic domain                                                                                                                                                                                                                                           d1e6zb3 B:292-379 Chitinase B                                                           d1e6zb2 B:2-291,B:380-446 Chitinase B, catalytic domain            d1e6zb1 B:447-499 Chitinase B, C-terminal domain      SCOP domains
               CATH domains 1e6zB01 B:2-290,B:381-448 Glycosidases                                                                                                                                                                                                                                                           1e6zB02 B:291-380  [code=3.10.50.10, no name defined]                                     1e6zB01 B:2-290,B:381-448 Glycosidases                              1e6zB03 B:449-499                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeee.hhhhhhh...........hhhhhhhhhhhhh.eeeeeeeee.....ee.....hhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhh....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee.hhhhhhhhhhhhhhhhh...eeeee............................hhhhhh....hhhhhhhhh......hhhhhhhhhhhh...hhh.eeeeee.eeeeee..............................hhhhhhh....eeehhhhhhhhh....eeeeee....eeeeee....eeee..hhhhhhhhhhhhhhh...eeeeehhhhh...hhhhhhhhhhhhh..........................................eeee..eeeee..............eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1e6z B   2 STRKAVIGYYFIPTNQINNYTETDTSVVPFPVSNITPAKAKQLTHINFSFLDINSNLECAWDPATNDAKARDVVNRLTALKAHNPSLRIMFSIGGWYYSNDLGVSHANYVNAVKTPASRAKFAQSCVRIMKDYGFDGVDIDWEYPQAAEVDGFIAALQEIRTLLNQQTITDGRQALPYQLTIAGAGGAFFLSRYYSKLAQIVAPLDYINLMTYDLAGPWEKVTNHQAALFGDAAGPTFYNALREANLGWSWEELTRAFPSPFSLTVDAAVQQHLMMEGVPSAKIVMGVPFYGRAFKGVSGGNGGQYSSHSTPGEDPYPSTDYWLVGCEECVRDKDPRIASYRQLEQMLQGNYGYQRLWNDKTKTPYLYHAQNGLFVTYDDAESFKYKAKYIKQQQLGGVMFWHLGQDNRNGDLLAALDRYFNAADYDDSQLDMGTGLRYTGVGPGNLPIMTAPAYVPGTTYAQGALVSYQGYVWQTKWGYITSAPGSDSAWLKVGRVA 499
                                    11        21        31        41        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       371       381       391       401       411       421       431       441       451       461       471       481       491

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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Glycosidases (843)

Serratia marcescens. Organism_taxid: 615. (19)

1a	1e6zA01	A:2-290,A:381-448
1b	1e6zB01	B:2-290,B:381-448

Architecture: Roll (3276)

Topology: Chitinase A; domain 3 (225)

Homologous Superfamily: [code=3.10.50.10, no name defined] (121)

Serratia marcescens. Organism_taxid: 615. (17)

2a	1e6zA02	A:291-380
2b	1e6zB02	B:291-380

Class: Mainly Beta (13760)

Architecture: Ribbon (789)

Topology: Seminal Fluid Protein PDC-109 (Domain B) (33)

Homologous Superfamily: [code=2.10.10.20, no name defined] (20)

Serratia marcescens. Organism_taxid: 615. (13)

3a	1e6zB03	B:449-499
3b	1e6zA03	A:449-498

(no "Pfam Domain" information available for 1E6Z)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q54276_SERMA | Q54276)

molecular function
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	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.
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.
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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Asp A:316 - Pro A:317	[ RasMol ]
		Asp B:316 - Pro B:317	[ RasMol ]
		Glu A:144 - Tyr A:145	[ RasMol ]
		Glu B:144 - Tyr B:145	[ RasMol ]
		Ser A:261 - Pro A:262	[ RasMol ]
		Ser A:50 - Phe A:51	[ RasMol ]
		Ser B:261 - Pro B:262	[ RasMol ]
		Ser B:50 - Phe B:51	[ RasMol ]
		Trp A:403 - His A:404	[ RasMol ]
		Trp B:403 - His B:404	[ RasMol ]

Biological Units
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Access by PDB/NDB ID
	1e6z
		Family and Domain Information	:	ProDom \| SYSTERS
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	Q54276_SERMA \| Q54276
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	3.2.1.14
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	Q54276_SERMA \| Q54276
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UniProtKB/Swiss-Prot
	Q54276_SERMA \| Q54276	:	1e6n 1goi 1ogb
UniProtKB/TrEMBL
	Q54276_SERMA \| Q54276	:	1e15 1e6p 1e6r 1gpf 1ur8 1ur9 1w1p 1w1t 1w1v 1w1y

1ctn	CHITINASE A (E.C.3.2.1.14) (PH 5.5, 4 DEGREES C) SERRATIA MARCESCENS RECOMBINANT FORM EXPRESSED IN ESCHERICHIA COLI
1e15	CHITINASE B FROM SERRATIA MARCESCENS
1e6n	CHITINASE B FROM SERRATIA MARCESCENS INACTIVE MUTANT E144Q IN COMPLEX WITH N-ACETYLGLUCOSAMINE-PENTAMER
1e6p	CHITINASE B FROM SERRATIA MARCESCENS INACTIVE MUTANT E144Q
1e6r	CHITINASE B FROM SERRATIA MARCESCENS WILDTYPE IN COMPLEX WITH INHIBITOR ALLOSAMIDIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (8, 8)

SS Bonds (2, 2)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 6)

CATH Domains (3, 6)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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Related Entries Specified in the PDB File