1ODZ - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   EXPANSION OF THE GLYCOSYNTHASE REPERTOIRE TO PRODUCE DEFINED MANNO-OLIGOSACCHARIDES

Authors :   M. Jahn, D. Stoll, R. A. J. Warren, L. Szabo, P. Singh, H. J. Gilbert, V. M. A. Ducros, G. J. Davies, S. G. Withers

Date :   17 Mar 03 (Deposition) - 10 Jul 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Hydrolase, Mannanase, Family 26, Glycoside-Hydrolase, Glycosynthase, Manno-Oligosaccharide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Jahn, D. Stoll, R. A. J. Warren, L. Szabo, P. Singh, H. J. Gilbert, V. M. A. Ducros, G. J. Davies, S. G. Withers
Expansion Of The Glycosynthase Repertoire To Produce Defined Manno-Oligosaccharides
Chem. Commun. (Camb. ) V. 12 1327 2003
PubMed-ID: 12841226 | Reference-DOI: 10.1039/B302380J

Molecule 1 - MANNANASE A
	Chains	:	A, B
	EC Number	:	3.2.1.78
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Fragment	:	RESIDUES 39-423
	Mutation	:	YES
	Organism Common	:	PSEUDOMONAS CELLULOSA
	Organism Scientific	:	CELLVIBRIO JAPONICUS
	Organism Taxid	:	155077
	Other Details	:	COMPLEX WITH MANNOBIOSE
	Synonym	:	ENDO-BETA-MANNANASE

		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 (5, 10)

No.	Name	Count	Type	Full Name
1	BMA	2	Ligand/Ion	BETA-D-MANNOSE
2	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
3	NA	2	Ligand/Ion	SODIUM ION
4	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
5	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
3	NA	-1	Ligand/Ion	SODIUM ION
4	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
3	NA	-1	Ligand/Ion	SODIUM ION
4	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:143 , TRP A:162 , GLU A:212 , TYR A:285 , ALA A:325 , TRP A:360 , TRP A:379 , BMA A:1426 , HOH A:2484 , HOH A:2486 , HOH A:2487 , HOH A:2488 , HOH A:2489	BINDING SITE FOR RESIDUE MAN A1425
02	AC2	SOFTWARE	GLU A:121 , TRP A:360 , ARG A:361 , HIS A:377 , MAN A:1425 , HOH A:2490 , HOH A:2491 , HOH A:2492 , HOH A:2493 , HOH A:2494	BINDING SITE FOR RESIDUE BMA A1426
03	AC3	SOFTWARE	HIS B:143 , GLU B:212 , TYR B:285 , ALA B:325 , TRP B:360 , TRP B:379 , BMA B:1425 , HOH B:2527 , HOH B:2528 , HOH B:2530 , HOH B:2531 , HOH B:2532	BINDING SITE FOR RESIDUE MAN B1424
04	AC4	SOFTWARE	GLU B:121 , TRP B:360 , ARG B:361 , HIS B:377 , MAN B:1424 , HOH B:2155 , HOH B:2533 , HOH B:2534 , HOH B:2535 , HOH B:2536	BINDING SITE FOR RESIDUE BMA B1425
05	AC5	SOFTWARE	GLU A:67 , HIS A:71 , GLU A:239 , TRS A:1424	BINDING SITE FOR RESIDUE ZN A1423
06	AC6	SOFTWARE	ARG A:69 , SER A:72 , ILE A:73 , ARG A:352 , GLU A:353 , ILE A:354	BINDING SITE FOR RESIDUE NA A1427
07	AC7	SOFTWARE	GLU B:67 , HIS B:71 , GLU B:239 , TRS B:1426	BINDING SITE FOR RESIDUE ZN B1423
08	AC8	SOFTWARE	ARG B:69 , SER B:72 , ILE B:73 , ARG B:352 , GLU B:353 , ILE B:354	BINDING SITE FOR RESIDUE NA B1427
09	AC9	SOFTWARE	GLU A:67 , HIS A:71 , GLN A:232 , ARG A:235 , GLU A:239 , TRP A:276 , ZN A:1423 , HOH A:2481 , HOH A:2482 , HOH A:2483	BINDING SITE FOR RESIDUE TRS A1424
10	BC1	SOFTWARE	GLU B:67 , HIS B:71 , GLN B:232 , ARG B:235 , GLU B:239 , TRP B:276 , ZN B:1423 , HOH B:2537 , HOH B:2538 , HOH B:2539	BINDING SITE FOR RESIDUE TRS B1426

(no "SS Bond" information available for 1ODZ)

Asymmetric Unit

No.	Residues
1	Ala A:117	-	Pro A:118
2	Trp A:156	-	Pro A:157
3	Ala B:117	-	Pro B:118
4	Trp B:156	-	Pro B:157

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GH26	PS51764	Glycosyl hydrolases family 26 (GH26) domain profile.	MANA_CELJU	56-409	2	A:56-409 B:56-409

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GH26	PS51764	Glycosyl hydrolases family 26 (GH26) domain profile.	MANA_CELJU	56-409	1	A:56-409 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GH26	PS51764	Glycosyl hydrolases family 26 (GH26) domain profile.	MANA_CELJU	56-409	1	- B:56-409

(no "Exon" information available for 1ODZ)

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:379
 aligned with MANA_CELJU | P49424 from UniProtKB/Swiss-Prot  Length:423

    Alignment length:381
                                    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 
           MANA_CELJU    42 VKPVTVKLVDSQATMETRSLFAFMQEQRRHSIMFGHQHETTQGLTITRTDGTQSDTFNAVGDFAAVYGWDTLSIVAPKAEGDIVAQVKKAYARGGIITVSSHFDNPKTDTQKGVWPVGTSWDQTPAVVDSLPGGAYNPVLNGYLDQVAEWANNLKDEQGRLIPVIFRLYHENTGSWFWWGDKQSTPEQYKQLFRYSVEYLRDVKGVRNFLYAYSPNNFWDVTEANYLERYPGDEWVDVLGFDTYGPVADNADWFRNVVANAALVARMAEARGKIPVISEIGIRAPDIEAGLYDNQWYRKLISGLKADPDAREIAFLLVWRNAPQGVPGPNGTQVPHYWVPANRPENINNGTLEDFQAFYADEFTAFNRDIEQVYQRPTLIV 422
               SCOP domains d1odza_ A: Mannanase A, ManA                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1odzA00 A:42-422 Glycosidases                                                                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee........hhhhhhhhhhhhhhh...eeeeee................hhhhhhhh....eeeee.hhh........hhhhhhhhhhh..eeeee.......hhhhh.......................hhhhhhhhhhhhhhhhhh..........eeee.................hhhhhhhhhhhhhhhhhh......eeeee........hhhhhhh.........ee..eeee....hhhhhhhhhhhhhhhhhhhhhhh.ee...eeeehhhhhhh.....hhhhhhhhhhhhh.hhhhh.eeee.......ee.--..ee........hhhhhhhhhhhhhhhhhhh..eehhhhh.......ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------GH26  PDB: A:56-409 UniProt: 56-409                                                                                                                                                                                                                                                                                                                               ------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1odz A  42 VKPVTVKLVDSQATMETRSLFAFMQEQRRHSIMFGHQHETTQGLTITRTDGTQSDTFNAVGDFAAVYGWDTLSIVAPKAEGDIVAQVKKAYARGGIITVSSHFDNPKTDTQKGVWPVGTSWDQTPAVVDSLPGGAYNPVLNGYLDQVAEWANNLKDEQGRLIPVIFRLYHENTGSWFWWGDKQSTPEQYKQLFRYSVEYLRDVKGVRNFLYAYSPNNFWDVTEANYLERYPGDEWVDVLGFDTYGPVADNADWFRNVVANAALVARMAEARGKIPVISGIGIRAPDIEAGLYDNQWYRKLISGLKADPDAREIAFLLVWRNAPQGVPG--GTQVPHYWVPANRPENINNGTLEDFQAFYADEFTAFNRDIEQVYQRPTLIV 422
                                    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       | -|      381       391       401       411       421 
                                                                                                                                                                                                                                                                                                                                                                 369  |                                                  
                                                                                                                                                                                                                                                                                                                                                                    372

Chain B from PDB  Type:PROTEIN  Length:379
 aligned with MANA_CELJU | P49424 from UniProtKB/Swiss-Prot  Length:423

    Alignment length:381
                                    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 
           MANA_CELJU    42 VKPVTVKLVDSQATMETRSLFAFMQEQRRHSIMFGHQHETTQGLTITRTDGTQSDTFNAVGDFAAVYGWDTLSIVAPKAEGDIVAQVKKAYARGGIITVSSHFDNPKTDTQKGVWPVGTSWDQTPAVVDSLPGGAYNPVLNGYLDQVAEWANNLKDEQGRLIPVIFRLYHENTGSWFWWGDKQSTPEQYKQLFRYSVEYLRDVKGVRNFLYAYSPNNFWDVTEANYLERYPGDEWVDVLGFDTYGPVADNADWFRNVVANAALVARMAEARGKIPVISEIGIRAPDIEAGLYDNQWYRKLISGLKADPDAREIAFLLVWRNAPQGVPGPNGTQVPHYWVPANRPENINNGTLEDFQAFYADEFTAFNRDIEQVYQRPTLIV 422
               SCOP domains d1odzb_ B: Mannanase A, ManA                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1odzB00 B:42-422 Glycosidases                                                                                                                                                                                                                                                                                                                                                                 CATH domains
           Pfam domains (1) --------Glyco_hydro_26-1odzB01 B:50-350                                                                                                                                                                                                                                                                              ------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) --------Glyco_hydro_26-1odzB02 B:50-350                                                                                                                                                                                                                                                                              ------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ...ee........hhhhhhhhhhhhhhh...eeeeee................hhhhhhhh....eeeee.hhh........hhhhhhhhhhh..eeeee.......hhhhh..............hhhhh....hhhhhhhhhhhhhhhhhh..........eeee.................hhhhhhhhhhhhhhhhhh......eeeee........hhhhhhh.........ee..eeee....hhhhhhhhhhhhhhhhhhhhhhh.ee...eeeehhhhhhh.....hhhhhhhhhhhhh.hhhhh.eeee.......ee.--..ee........hhhhhhhhhhhhhhhhhhh..eehhhhh.......ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------GH26  PDB: B:56-409 UniProt: 56-409                                                                                                                                                                                                                                                                                                                               ------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1odz B  42 VKPVTVKLVDSQATMETRSLFAFMQEQRRHSIMFGHQHETTQGLTITRTDGTQSDTFNAVGDFAAVYGWDTLSIVAPKAEGDIVAQVKKAYARGGIITVSSHFDNPKTDTQKGVWPVGTSWDQTPAVVDSLPGGAYNPVLNGYLDQVAEWANNLKDEQGRLIPVIFRLYHENTGSWFWWGDKQSTPEQYKQLFRYSVEYLRDVKGVRNFLYAYSPNNFWDVTEANYLERYPGDEWVDVLGFDTYGPVADNADWFRNVVANAALVARMAEARGKIPVISGIGIRAPDIEAGLYDNQWYRKLISGLKADPDAREIAFLLVWRNAPQGVPG--GTQVPHYWVPANRPENINNGTLEDFQAFYADEFTAFNRDIEQVYQRPTLIV 422
                                    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       | -|      381       391       401       411       421 
                                                                                                                                                                                                                                                                                                                                                                 369  |                                                  
                                                                                                                                                                                                                                                                                                                                                                    372

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(

)

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: beta-glycanases (284)

Protein domain: Mannanase A, ManA (7)

Pseudomonas cellulosa (Cellvibrio japonicus) [TaxId: 155077] (5)

1a	d1odza_	A:
1b	d1odzb_	B:

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)

Pseudomonas cellulosa (Cellvibrio japonicus) (1)

1a	1odzA00	A:42-422
1b	1odzB00	B:42-422

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Glyco_hydro_tim (488)

Family: Glyco_hydro_26 (6)

Cellvibrio japonicus (strain Ueda107) (Pseudomonas fluorescens subsp. cellulosa) (3)

1a	Glyco_hydro_26-1odzB01	B:50-350
1b	Glyco_hydro_26-1odzB02	B:50-350

Asymmetric Unit(hide GO term definitions)

Chain A,B (MANA_CELJU | P49424)

molecular function
	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:0016985	mannan endo-1,4-beta-mannosidase activity	Catalysis of the random hydrolysis of (1->4)-beta-D-mannosidic linkages in mannans, galactomannans, glucomannans, and galactoglucomannans.
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:0051069	galactomannan metabolic process	The chemical reactions and pathways involving galactomannan, a polysaccharide composed of D-galactose and D-mannose. The mannose units form the backbone structure (a linear main chain) with the D-galactose as single side units.
	GO:0010391	glucomannan metabolic process	The chemical reactions and pathways involving glucomannan, a polysaccharide composed of D-glucose and D-mannose. The mannose units form the backbone structure (a linear main chain) with the D-glucose as single side-units.
	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.
	GO:0006080	substituted mannan metabolic process	The chemical reactions and pathways involving a mannan backbone composed of D-mannose unites, substituted with D-glucose and/or D-galactose units.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:117 - Pro A:118	[ RasMol ]
		Ala B:117 - Pro B:118	[ RasMol ]
		Trp A:156 - Pro A:157	[ RasMol ]
		Trp B:156 - Pro B:157	[ RasMol ]

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	MANA_CELJU \| P49424	:	1gvy 1gw1 1j9y 1r7o 2whm

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