1JIB - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   COMPLEX OF ALPHA-AMYLASE II (TVA II) FROM THERMOACTINOMYCES VULGARIS R-47 WITH MALTOTETRAOSE BASED ON A CRYSTAL SOAKED WITH MALTOHEXAOSE.

Authors :   T. Yokota, T. Tonozuka, Y. Shimura, K. Ichikawa, S. Kamitori, Y. Sakano

Date :   02 Jul 01 (Deposition) - 25 Jul 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.30

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

Keywords :   Pullulan, Cyclodextrin, Neopullulanase, Maltohexaose, Maltotetraose, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Yokota, T. Tonozuka, Y. Shimura, K. Ichikawa, S. Kamitori, Y. Sakano
Structures Of Thermoactinomyces Vulgaris R-47 Alpha-Amylase Ii Complexed With Substrate Analogues.
Biosci. Biotechnol. Biochem. V. 65 619 2001
PubMed-ID: 11330677 | Reference-DOI: 10.1271/BBB.65.619
(for further references see the PDB file header)

Molecule 1 - NEOPULLULANASE
	Chains	:	A, B
	EC Number	:	3.2.1.135
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTND325N
	Expression System Strain	:	MV1184
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	THERMOACTINOMYCES VULGARIS
	Organism Taxid	:	2026

		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 (1, 2)

No.	Name	Count	Type	Full Name
1	MTT	2	Ligand/Ion	MALTOTETRAOSE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	MTT	1	Ligand/Ion	MALTOTETRAOSE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	MTT	1	Ligand/Ion	MALTOTETRAOSE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:202 , TYR A:204 , HIS A:244 , PHE A:286 , ASN A:325 , VAL A:326 , GLU A:354 , TRP A:356 , HIS A:420 , ASP A:421 , ASP A:465 , ARG A:469 , ARG B:44 , TYR B:45 , GLN B:112	BINDING SITE FOR RESIDUE MTT A 601
2	AC2	SOFTWARE	ARG A:44 , TYR A:45 , GLN A:112 , HIS B:202 , TYR B:204 , HIS B:244 , PHE B:286 , ARG B:323 , ASN B:325 , VAL B:326 , GLU B:354 , TRP B:356 , TYR B:374 , HIS B:420 , ASP B:421 , ASP B:465 , ARG B:469	BINDING SITE FOR RESIDUE MTT B 701

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

Asymmetric Unit

No.	Residues
1	Phe A:273	-	Pro A:274
2	Asp A:465	-	Pro A:466
3	Phe B:273	-	Pro B:274
4	Asp B:465	-	Pro B:466

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

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

(no "Exon" information available for 1JIB)

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:585
 aligned with NEPU2_THEVU | Q08751 from UniProtKB/Swiss-Prot  Length:585

    Alignment length:585
                                    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       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580     
          NEPU2_THEVU     1 MLLEAIFHEAKGSYAYPISETQLRVRLRAKKGDVVRCEVLYADRYASPEEELAHALAGKAGSDERFDYFEALLECSTKRVKYVFLLTGPQGEAVYFGETGFSAERSKAGVFQYAYIHRSEVFTTPEWAKEAVIYQIFPERFANGDPSNDPPGTEQWAKDARPRHDSFYGGDLKGVIDRLPYLEELGVTALYFTPIFASPSHHKYDTADYLAIDPQFGDLPTFRRLVDEAHRRGIKIILDAVFNHAGDQFFAFRDVLQKGEQSRYKDWFFIEDFPVSKTSRTNYETFAVQVPAMPKLRTENPEVKEYLFDVARFWMEQGIDGWRLDVANEVDHAFWREFRRLVKSLNPDALIVGEIWHDASGWLMGDQFDSVMNYLFRESVIRFFATGEIHAERFDAELTRARMLYPEQAAQGLWNLLDSHDTERFLTSCGGNEAKFRLAVLFQMTYLGTPLIYYGDEIGMAGATDPDCRRPMIWEEKEQNRGLFEFYKELIRLRHRLASLTRGNVRSWHADKQANLYAFVRTVQDQHVGVVLNNRGEKQTVLLQVPESGGKTWLDCLTGEEVHGKQGQLKLTLRPYQGMILWNGR 585
               SCOP domains d1jiba1 A:1-120 Maltogenic amylase, N-terminal domain N                                                                 d1jiba3 A:121-502 Maltogenic amylase, central domain                                                                                                                                                                                                                                                                                                                                          d1jiba2 A:503-585 Maltogenic amylase                                                SCOP domains
               CATH domains 1jibA01 A:1-121 Immunoglobulins                                                                                          1jibA02 A:122-242,A:298-502 Glycosidases                                                                                 -------------------------------------------------------1jibA02 A:122-242,A:298-502 Glycosidases                                                                                                                                                                     1jibA04 A:503-585 Golgi alpha-mannosidase II                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh........eeeee..eeeeeeeee.....eeeeeee..........eeee..eeee...eeeeeeeee.....eeeeeeee.....eeeee..eee........eee...hhhhh...hhhhhh..eeeehhhhh.............................hhhhhhhhhhhhhhhh..eeee...ee..........eeeee.....hhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhh.hhhhh...............................hhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhh...eeee................ee.hhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhh..eee.......hhhhhh..hhhhhhhhhhhhh....eeeee.hhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee....eeeeeeee..eeeeeeee......eeeee.........ee........ee..eeeee.....eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jib A   1 MLLEAIFHEAKGSYAYPISETQLRVRLRAKKGDVVRCEVLYADRYASPEEELAHALAGKAGSDERFDYFEALLECSTKRVKYVFLLTGPQGEAVYFGETGFSAERSKAGVFQYAYIHRSEVFTTPEWAKEAVIYQIFPERFANGDPSNDPPGTEQWAKDARPRHDSFYGGDLKGVIDRLPYLEELGVTALYFTPIFASPSHHKYDTADYLAIDPQFGDLPTFRRLVDEAHRRGIKIILDAVFNHAGDQFFAFRDVLQKGEQSRYKDWFFIEDFPVSKTSRTNYETFAVQVPAMPKLRTENPEVKEYLFDVARFWMEQGIDGWRLNVANEVDHAFWREFRRLVKSLNPDALIVGEIWHDASGWLMGDQFDSVMNYLFRESVIRFFATGEIHAERFDAELTRARMLYPEQAAQGLWNLLDSHDTERFLTSCGGNEAKFRLAVLFQMTYLGTPLIYYGDEIGMAGATDPDCRRPMIWEEKEQNRGLFEFYKELIRLRHRLASLTRGNVRSWHADKQANLYAFVRTVQDQHVGVVLNNRGEKQTVLLQVPESGGKTWLDCLTGEEVHGKQGQLKLTLRPYQGMILWNGR 585
                                    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       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580

Chain B from PDB  Type:PROTEIN  Length:585
 aligned with NEPU2_THEVU | Q08751 from UniProtKB/Swiss-Prot  Length:585

    Alignment length:585
                                    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       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580     
          NEPU2_THEVU     1 MLLEAIFHEAKGSYAYPISETQLRVRLRAKKGDVVRCEVLYADRYASPEEELAHALAGKAGSDERFDYFEALLECSTKRVKYVFLLTGPQGEAVYFGETGFSAERSKAGVFQYAYIHRSEVFTTPEWAKEAVIYQIFPERFANGDPSNDPPGTEQWAKDARPRHDSFYGGDLKGVIDRLPYLEELGVTALYFTPIFASPSHHKYDTADYLAIDPQFGDLPTFRRLVDEAHRRGIKIILDAVFNHAGDQFFAFRDVLQKGEQSRYKDWFFIEDFPVSKTSRTNYETFAVQVPAMPKLRTENPEVKEYLFDVARFWMEQGIDGWRLDVANEVDHAFWREFRRLVKSLNPDALIVGEIWHDASGWLMGDQFDSVMNYLFRESVIRFFATGEIHAERFDAELTRARMLYPEQAAQGLWNLLDSHDTERFLTSCGGNEAKFRLAVLFQMTYLGTPLIYYGDEIGMAGATDPDCRRPMIWEEKEQNRGLFEFYKELIRLRHRLASLTRGNVRSWHADKQANLYAFVRTVQDQHVGVVLNNRGEKQTVLLQVPESGGKTWLDCLTGEEVHGKQGQLKLTLRPYQGMILWNGR 585
               SCOP domains d1jibb1 B:1-120 Maltogenic amylase, N-terminal domain N                                                                 d1jibb3 B:121-502 Maltogenic amylase, central domain                                                                                                                                                                                                                                                                                                                                          d1jibb2 B:503-585 Maltogenic amylase                                                SCOP domains
               CATH domains 1jibB01 B:1-121 Immunoglobulins                                                                                          1jibB02 B:122-242,B:298-502 Glycosidases                                                                                 -------------------------------------------------------1jibB02 B:122-242,B:298-502 Glycosidases                                                                                                                                                                     1jibB04 B:503-585 Golgi alpha-mannosidase II                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh........eeeee..eeeeeeeee.....eeeeeee..........eeeeeeeeee...eeeeeeeee.....eeeeeeee.....eeee....ee..hhhhh.eee...hhhhh...hhhhhh..eeeehhhhhh............................hhhhhhhhhhhhhhhh..eeee.........................hhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhh.hhhhh...............................hhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhh...eeee.....hhhhh......ee.hhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhh..eee.......hhhhhh..hhhhhhhhhhhhhhh..eeeee.hhhhh......hhhhh....hhhhhhhhhhhhhhhhhhhhhh.hhhhhheeeeeeee....eeeeeeee..eeeeeeee.....eeeeee.hhhhh...ee........ee..eeeeee....eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jib B   1 MLLEAIFHEAKGSYAYPISETQLRVRLRAKKGDVVRCEVLYADRYASPEEELAHALAGKAGSDERFDYFEALLECSTKRVKYVFLLTGPQGEAVYFGETGFSAERSKAGVFQYAYIHRSEVFTTPEWAKEAVIYQIFPERFANGDPSNDPPGTEQWAKDARPRHDSFYGGDLKGVIDRLPYLEELGVTALYFTPIFASPSHHKYDTADYLAIDPQFGDLPTFRRLVDEAHRRGIKIILDAVFNHAGDQFFAFRDVLQKGEQSRYKDWFFIEDFPVSKTSRTNYETFAVQVPAMPKLRTENPEVKEYLFDVARFWMEQGIDGWRLNVANEVDHAFWREFRRLVKSLNPDALIVGEIWHDASGWLMGDQFDSVMNYLFRESVIRFFATGEIHAERFDAELTRARMLYPEQAAQGLWNLLDSHDTERFLTSCGGNEAKFRLAVLFQMTYLGTPLIYYGDEIGMAGATDPDCRRPMIWEEKEQNRGLFEFYKELIRLRHRLASLTRGNVRSWHADKQANLYAFVRTVQDQHVGVVLNNRGEKQTVLLQVPESGGKTWLDCLTGEEVHGKQGQLKLTLRPYQGMILWNGR 585
                                    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       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580

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)

Thermoactinomyces vulgaris. Organism_taxid: 2026. (2)

1a	1jibA02	A:122-242,A:298-502
1b	1jibB02	B:122-242,B:298-502

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Golgi alpha-mannosidase II (346)

Thermoactinomyces vulgaris. Organism_taxid: 2026. (2)

2a	1jibA04	A:503-585
2b	1jibB04	B:503-585

Homologous Superfamily: Immunoglobulins (2282)

Thermoactinomyces vulgaris. Organism_taxid: 2026. (2)

3a	1jibA01	A:1-121
3b	1jibB01	B:1-121

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (NEPU2_THEVU | Q08751)

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: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.
	GO:0031216	neopullulanase activity	Catalysis of the hydrolysis of pullulan to panose (6-alpha-D-glucosylmaltose).
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
		Asp A:465 - Pro A:466	[ RasMol ]
		Asp B:465 - Pro B:466	[ RasMol ]
		Phe A:273 - Pro A:274	[ RasMol ]
		Phe B:273 - Pro B:274	[ RasMol ]

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	1jib
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	NEPU2_THEVU \| Q08751
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	3.2.1.135
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1bvz	1BVZ CONTAINS CRYSTAL STRUCTURE OF UNLIGANDED ALPHA-AMYLASE II (TVA II) FROM THERMOACTINOMYCES VULGARIS R-47
1g1y	1G1Y CONTAINS CRYSTAL STRUCTURE OF ALPHA-AMYLASE II (TVA II) FROM THERMOACTINOMYCES VULGARIS R-47 COMPLEXED WITH BETA-CYCLODEXTRIN

Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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