3AZZ - JenaLib

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE LAMINARINASE CATALYTIC DOMAIN FROM THERMOTOGA MARITIMA MSB8 IN COMPLEX WITH GLUCONOLACTONE

Authors :   W. Y. Jeng, N. C. Wang, A. H. J. Wang

Date :   03 Jun 11 (Deposition) - 23 Nov 11 (Release) - 19 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.81

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Beta-Jelly Roll Fold, Glycosyl Hydrolase Family 16, Laminarinase, Endo-1, 3-Beta-Glucanase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Y. Jeng, N. C. Wang, C. T. Lin, L. F. Shyur, A. H. Wang
Crystal Structures Of The Laminarinase Catalytic Domain Fro Thermotoga Maritima Msb8 In Complex With Inhibitors: Essential Residues For Beta-1, 3 And Beta-1, 4 Glucan Selection.
J. Biol. Chem. V. 286 45030 2011
PubMed-ID: 22065588 | Reference-DOI: 10.1074/JBC.M111.271213

Molecule 1 - LAMINARINASE
	Chains	:	A, B, C, D
	EC Number	:	3.2.1.39
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-21A
	Expression System Strain	:	BL-21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 204-466
	Gene	:	TM_0024
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	243274
	Strain	:	MSB8, ATCC43589

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 15)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	LGC	3	Ligand/Ion	(3S,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-ONE
3	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	LGC	1	Ligand/Ion	(3S,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-ONE
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	LGC	1	Ligand/Ion	(3S,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-ONE
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 3)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	LGC	1	Ligand/Ion	(3S,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-ONE
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 4 (1, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	LGC	-1	Ligand/Ion	(3S,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-ONE
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:45 , TRP A:112 , ALA A:114 , TRP A:116 , GLU A:132 , ASP A:134 , GLU A:137 , HIS A:151 , HOH A:850 , HOH A:901	BINDING SITE FOR RESIDUE LGC A 300
02	AC2	SOFTWARE	GLU A:17 , ASP A:19 , GLY A:61 , ASP A:249 , HOH A:779 , HOH A:790	BINDING SITE FOR RESIDUE CA A 301
03	AC3	SOFTWARE	GLY A:33 , ASN A:34 , GLY A:35 , HIS A:36 , ALA A:37 , TYR A:50 , ASP A:74 , TYR A:79 , HOH B:684	BINDING SITE FOR RESIDUE SO4 A 303
04	AC4	SOFTWARE	TYR A:250 , ARG A:252 , HOH A:607 , HOH A:930	BINDING SITE FOR RESIDUE SO4 A 302
05	AC5	SOFTWARE	ASN B:45 , TRP B:112 , ALA B:114 , TRP B:116 , GLU B:132 , ASP B:134 , GLU B:137 , HIS B:151 , HOH B:852 , HOH B:862 , HOH B:933	BINDING SITE FOR RESIDUE LGC B 300
06	AC6	SOFTWARE	GLU B:17 , ASP B:19 , GLY B:61 , ASP B:249 , HOH B:782 , HOH B:785	BINDING SITE FOR RESIDUE CA B 301
07	AC7	SOFTWARE	GLY B:33 , ASN B:34 , GLY B:35 , HIS B:36 , ALA B:37 , TYR B:50 , ASP B:74 , TYR B:76 , TYR B:79 , HOH B:686	BINDING SITE FOR RESIDUE SO4 B 303
08	AC8	SOFTWARE	ARG B:252 , HOH B:531 , HOH B:651	BINDING SITE FOR RESIDUE SO4 B 302
09	AC9	SOFTWARE	ASN C:45 , TRP C:112 , ALA C:114 , TRP C:116 , GLU C:132 , ASP C:134 , GLU C:137 , HIS C:151 , HOH C:849 , HOH C:860 , HOH C:867 , HOH C:900	BINDING SITE FOR RESIDUE LGC C 300
10	BC1	SOFTWARE	GLU C:17 , ASP C:19 , GLY C:61 , ASP C:249 , HOH C:440 , HOH C:797	BINDING SITE FOR RESIDUE CA C 301
11	BC2	SOFTWARE	GLY C:33 , ASN C:34 , GLY C:35 , HIS C:36 , TYR C:50 , ASP C:74 , TYR C:76 , TYR C:79	BINDING SITE FOR RESIDUE SO4 C 303
12	BC3	SOFTWARE	TYR C:250 , ARG C:252 , HOH C:666 , HOH C:842	BINDING SITE FOR RESIDUE SO4 C 302
13	BC4	SOFTWARE	GLU D:17 , ASP D:19 , GLY D:61 , ASP D:249 , HOH D:665 , HOH D:775	BINDING SITE FOR RESIDUE CA D 301
14	BC5	SOFTWARE	GLY D:33 , ASN D:34 , GLY D:35 , HIS D:36 , TYR D:50 , ASP D:74 , TYR D:76 , TYR D:79 , HOH D:871	BINDING SITE FOR RESIDUE SO4 D 303
15	BC6	SOFTWARE	ARG D:252 , HOH D:780 , HOH D:792	BINDING SITE FOR RESIDUE SO4 D 302

(no "SS Bond" information available for 3AZZ)

Asymmetric Unit

No.	Residues
1	Trp A:127	-	Pro A:128
2	Phe A:242	-	Pro A:243
3	Trp B:127	-	Pro B:128
4	Phe B:242	-	Pro B:243
5	Trp C:127	-	Pro C:128
6	Phe C:242	-	Pro C:243
7	Trp D:127	-	Pro D:128
8	Phe D:242	-	Pro D:243

(no "SAP(SNP)/Variant" information available for 3AZZ)

(no "PROSITE Motif" information available for 3AZZ)

(no "Exon" information available for 3AZZ)

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:250
 aligned with Q9WXN1_THEMA | Q9WXN1 from UniProtKB/TrEMBL  Length:642

    Alignment length:250
                                   219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459
         Q9WXN1_THEMA   210 EDWQLVWSQEFDDGVIDPNIWNFEIGNGHAKGIPGWGNGELEYYTDENAFVENGCLVIEARKEQVSDEYGTYDYTSARMTTEGKFEIKYGKIEIRAKLPKGKGIWPALWMLGNNIGEVGWPTCGEIDIMEMLGHDTRTVYGTAHGPGYSGGASIGVAYHLPEGVPDFSEDFHIFSIEWDEDEVEWYVDGQLYHVLSKDELAELGLEWVFDHPFFLILNVAVGGYWPGYPDETTQFPQRMYIDYIRVYKDM 459
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee............ee....hhhhhhhhhhh....ee....eeee..eeeeeeeeeeee....eeeeee.eee.....ee..eeeeeeee......eeeeeeeee.hhhhhh.....eeeeee.......eeeeeee...........eeee............eeeeeeee..eeeeee..eeeeeeehhhhhhh.........eeeeeeeee...............eeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3azz A   8 EDWQLVWSQEFDDGVIDPNIWNFEIGNGHAKGIPGWGNGELEYYTDENAFVENGCLVIEARKEQVSDEYGTYDYTSARMTTEGKFEIKYGKIEIRAKLPKGKGIWPALWMLGNNIGEVGWPTCGEIDIMEMLGHDTRTVYGTAHGPGYSGGASIGVAYHLPEGVPDFSEDFHIFSIEWDEDEVEWYVDGQLYHVLSKDELAELGLEWVFDHPFFLILNVAVGGYWPGYPDETTQFPQRMYIDYIRVYKDM 257
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257

Chain B from PDB  Type:PROTEIN  Length:250
 aligned with Q9WXN1_THEMA | Q9WXN1 from UniProtKB/TrEMBL  Length:642

    Alignment length:250
                                   219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459
         Q9WXN1_THEMA   210 EDWQLVWSQEFDDGVIDPNIWNFEIGNGHAKGIPGWGNGELEYYTDENAFVENGCLVIEARKEQVSDEYGTYDYTSARMTTEGKFEIKYGKIEIRAKLPKGKGIWPALWMLGNNIGEVGWPTCGEIDIMEMLGHDTRTVYGTAHGPGYSGGASIGVAYHLPEGVPDFSEDFHIFSIEWDEDEVEWYVDGQLYHVLSKDELAELGLEWVFDHPFFLILNVAVGGYWPGYPDETTQFPQRMYIDYIRVYKDM 459
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee............ee.........hhhhhh...eee....eeee..eeeeeeeeeeeee..eeeeeee.eee.........eeeeeeee......eeeeeeeee.hhhhhh.....eeeeee.......eeeeeee.........eeeeee............eeeeeeee..eeeeee..eeeeeeehhhhhhh.........eeeeeeeee...............eeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3azz B   8 EDWQLVWSQEFDDGVIDPNIWNFEIGNGHAKGIPGWGNGELEYYTDENAFVENGCLVIEARKEQVSDEYGTYDYTSARMTTEGKFEIKYGKIEIRAKLPKGKGIWPALWMLGNNIGEVGWPTCGEIDIMEMLGHDTRTVYGTAHGPGYSGGASIGVAYHLPEGVPDFSEDFHIFSIEWDEDEVEWYVDGQLYHVLSKDELAELGLEWVFDHPFFLILNVAVGGYWPGYPDETTQFPQRMYIDYIRVYKDM 257
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257

Chain C from PDB  Type:PROTEIN  Length:250
 aligned with Q9WXN1_THEMA | Q9WXN1 from UniProtKB/TrEMBL  Length:642

    Alignment length:250
                                   219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459
         Q9WXN1_THEMA   210 EDWQLVWSQEFDDGVIDPNIWNFEIGNGHAKGIPGWGNGELEYYTDENAFVENGCLVIEARKEQVSDEYGTYDYTSARMTTEGKFEIKYGKIEIRAKLPKGKGIWPALWMLGNNIGEVGWPTCGEIDIMEMLGHDTRTVYGTAHGPGYSGGASIGVAYHLPEGVPDFSEDFHIFSIEWDEDEVEWYVDGQLYHVLSKDELAELGLEWVFDHPFFLILNVAVGGYWPGYPDETTQFPQRMYIDYIRVYKDM 459
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee............ee....hhhhhhhhhhh...eee....eeee..eeeeeeeeeeee....eeeeee.eee.........eeeeeeee......eeeeeeeee.hhhhhh.....eeeeeee......eeeeeee.........eeeeee............eeeeeeee..eeeeee..eeeeeeehhhhhhhh........eeeeeeeee...............eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3azz C   8 EDWQLVWSQEFDDGVIDPNIWNFEIGNGHAKGIPGWGNGELEYYTDENAFVENGCLVIEARKEQVSDEYGTYDYTSARMTTEGKFEIKYGKIEIRAKLPKGKGIWPALWMLGNNIGEVGWPTCGEIDIMEMLGHDTRTVYGTAHGPGYSGGASIGVAYHLPEGVPDFSEDFHIFSIEWDEDEVEWYVDGQLYHVLSKDELAELGLEWVFDHPFFLILNVAVGGYWPGYPDETTQFPQRMYIDYIRVYKDM 257
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257

Chain D from PDB  Type:PROTEIN  Length:250
 aligned with Q9WXN1_THEMA | Q9WXN1 from UniProtKB/TrEMBL  Length:642

    Alignment length:250
                                   219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459
         Q9WXN1_THEMA   210 EDWQLVWSQEFDDGVIDPNIWNFEIGNGHAKGIPGWGNGELEYYTDENAFVENGCLVIEARKEQVSDEYGTYDYTSARMTTEGKFEIKYGKIEIRAKLPKGKGIWPALWMLGNNIGEVGWPTCGEIDIMEMLGHDTRTVYGTAHGPGYSGGASIGVAYHLPEGVPDFSEDFHIFSIEWDEDEVEWYVDGQLYHVLSKDELAELGLEWVFDHPFFLILNVAVGGYWPGYPDETTQFPQRMYIDYIRVYKDM 459
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee............ee....hhhhhhhhhhh...eee....eeee..eeeeeeeeeeeee..eeeeeee.eee.........eeeeeeee......eeeeeeeee.hhhhhh.....eeeeeee......eeeeeee.........eeeeee............eeeeeeee..eeeeee..eeeeeeehhhhhhh.........eeeeeeeee...............eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3azz D   8 EDWQLVWSQEFDDGVIDPNIWNFEIGNGHAKGIPGWGNGELEYYTDENAFVENGCLVIEARKEQVSDEYGTYDYTSARMTTEGKFEIKYGKIEIRAKLPKGKGIWPALWMLGNNIGEVGWPTCGEIDIMEMLGHDTRTVYGTAHGPGYSGGASIGVAYHLPEGVPDFSEDFHIFSIEWDEDEVEWYVDGQLYHVLSKDELAELGLEWVFDHPFFLILNVAVGGYWPGYPDETTQFPQRMYIDYIRVYKDM 257
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257

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 '\|'

(no "SCOP Domain" information available for 3AZZ)

(no "CATH Domain" information available for 3AZZ)

(no "Pfam Domain" information available for 3AZZ)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q9WXN1_THEMA | Q9WXN1)

molecular function
	GO:0042973	glucan endo-1,3-beta-D-glucosidase activity	Catalysis of the hydrolysis of (1->3)-beta-D-glucosidic linkages in (1->3)-beta-D-glucans.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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: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.

Asymmetric Unit
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	Cis Peptide Bonds
		Phe A:242 - Pro A:243	[ RasMol ]
		Phe B:242 - Pro B:243	[ RasMol ]
		Phe C:242 - Pro C:243	[ RasMol ]
		Phe D:242 - Pro D:243	[ RasMol ]
		Trp A:127 - Pro A:128	[ RasMol ]
		Trp B:127 - Pro B:128	[ RasMol ]
		Trp C:127 - Pro C:128	[ RasMol ]
		Trp D:127 - Pro D:128	[ RasMol ]

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		Biological Unit 4	[ Jena3D ]

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Access by PDB/NDB ID
	3azz
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	3.2.1.39
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UniProtKB/TrEMBL
	Q9WXN1_THEMA \| Q9WXN1	:	1gui 3azx 3azy 3b00 3b01

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 15)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (7, 7)

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