1VFM - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THERMOACTINOMYCES VULGARIS R-47 ALPHA-AMYLASE 2/ALPHA-CYCLODEXTRIN COMPLEX

Authors :   A. Ohtaki, M. Mizuno, T. Tonozuka, Y. Sakano, S. Kamitori

Date :   16 Apr 04 (Deposition) - 08 Feb 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Amylase, Complex, Cyclodextrin, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Ohtaki, M. Mizuno, T. Tonozuka, Y. Sakano, S. Kamitori
Complex Structures Of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 2 With Acarbose And Cyclodextrins Demonstrate The Multiple Substrate Recognition Mechanism
J. Biol. Chem. V. 279 31033 2004
PubMed-ID: 15138257 | Reference-DOI: 10.1074/JBC.M404311200
(for further references see the PDB file header)

Molecule 1 - NEOPULLULANASE 2
	Chains	:	A, B
	EC Number	:	3.2.1.135
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	THERMOACTINOMYCES VULGARIS
	Organism Taxid	:	2026
	Strain	:	R-47
	Synonym	:	ALPHA-AMYLASE 2, ALPHA-AMYLASE II

		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, 14)

No.	Name	Count	Type	Full Name
1	BGC	1	Ligand/Ion	BETA-D-GLUCOSE
2	CA	2	Ligand/Ion	CALCIUM ION
3	GLC	11	Ligand/Ion	ALPHA-D-GLUCOSE

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	BGC	-1	Ligand/Ion	BETA-D-GLUCOSE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	GLC	6	Ligand/Ion	ALPHA-D-GLUCOSE

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	BGC	1	Ligand/Ion	BETA-D-GLUCOSE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	GLC	5	Ligand/Ion	ALPHA-D-GLUCOSE

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:204 , HIS A:244 , PHE A:286 , ASN A:325 , GLU A:354 , HIS A:420 , ASN A:421 , GLC A:802 , GLC A:806 , HOH A:1084	BINDING SITE FOR RESIDUE GLC A 801
02	AC2	SOFTWARE	TYR A:204 , MET A:293 , ASP A:465 , ARG A:469 , GLC A:801 , GLC A:803	BINDING SITE FOR RESIDUE GLC A 802
03	AC3	SOFTWARE	ASP A:465 , GLC A:802 , GLC A:804	BINDING SITE FOR RESIDUE GLC A 803
04	AC4	SOFTWARE	GLC A:803 , GLC A:805 , GLC A:806 , TYR B:45	BINDING SITE FOR RESIDUE GLC A 804
05	AC5	SOFTWARE	TRP A:356 , GLC A:804 , GLC A:806 , ARG B:44 , TYR B:45	BINDING SITE FOR RESIDUE GLC A 805
06	AC6	SOFTWARE	PHE A:286 , VAL A:326 , GLU A:354 , TRP A:356 , GLC A:801 , GLC A:804 , GLC A:805 , TYR B:45 , HOH B:1005	BINDING SITE FOR RESIDUE GLC A 806
07	AC7	SOFTWARE	TYR B:204 , HIS B:244 , ASN B:325 , GLU B:354 , HIS B:420 , ASN B:421 , GLC B:902 , BGC B:906	BINDING SITE FOR RESIDUE GLC B 901
08	AC8	SOFTWARE	TYR B:204 , ASP B:465 , ARG B:469 , GLC B:901 , GLC B:903	BINDING SITE FOR RESIDUE GLC B 902
09	AC9	SOFTWARE	ASP B:465 , GLC B:902 , GLC B:904	BINDING SITE FOR RESIDUE GLC B 903
10	BC1	SOFTWARE	TYR A:45 , GLC B:903 , GLC B:905 , BGC B:906	BINDING SITE FOR RESIDUE GLC B 904
11	BC2	SOFTWARE	ARG A:44 , TYR A:45 , TRP B:356 , GLC B:904 , BGC B:906	BINDING SITE FOR RESIDUE GLC B 905
12	BC3	SOFTWARE	VAL B:326 , TRP B:356 , GLC B:901 , GLC B:904 , GLC B:905	BINDING SITE FOR RESIDUE BGC B 906
13	BC4	SOFTWARE	ASN A:143 , ASP A:145 , ASN A:148 , ASP A:149 , GLY A:169 , ASP A:171	BINDING SITE FOR RESIDUE CA A 1001
14	BC5	SOFTWARE	ASN B:143 , ASP B:145 , ASN B:148 , ASP B:149 , GLY B:169 , ASP B:171	BINDING SITE FOR RESIDUE CA B 1002

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

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 1VFM)

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

(no "Exon" information available for 1VFM)

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 d1vfma1 A:1-120 automated matches                                                                                       d1vfma3 A:121-502 automated matches                                                                                                                                                                                                                                                                                                                                                           d1vfma2 A:503-585 automated matches                                                 SCOP domains
               CATH domains 1vfmA01 A:1-121 Immunoglobulins                                                                                          1vfmA02 A:122-242,A:298-502 Glycosidases                                                                                 -------------------------------------------------------1vfmA02 A:122-242,A:298-502 Glycosidases                                                                                                                                                                     1vfmA04 A:503-585 Golgi alpha-mannosidase II                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh........eee....eeeeeeeee.....eeeeeee...............eeee....eeeeeeeee.....eeeeeeee.......ee....ee..hhhhh.eee...hhhhh....hhhhhh.eeeehhhhhh............................hhhhhhhhhhhhhhhh..eeee.........................hhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhh.hhhhh...............................hhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhh...eeee.....hhhhh......ee.hhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhh..eee.......hhhhhh..hhhhhhhhhhhhh....eeeee.hhhhh......hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee....eeeeeeee..eeeeeeee.....eeeeee.hhhhh.eeee.....eee....eeeeee....eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vfm A   1 MLLEAIFHEAKGSYAYPISETQLRVRLRAKKGDVVRCEVLYADRYASPEEELAHALAGKAGSDERFDYFEALLECSTKRVKYVFLLTGPQGEAVYFGETGFSAERSKAGVFQYAYIHRSEVFTTPEWAKEAVIYQIFPERFANGDPSNDPPGTEQWAKDARPRHDSFYGGDLKGVIDRLPYLEELGVTALYFTPIFASPSHHKYDTADYLAIDPQFGDLPTFRRLVDEAHRRGIKIILDAVFNHAGDQFFAFRDVLQKGEQSRYKDWFFIEDFPVSKTSRTNYETFAVQVPAMPKLRTENPEVKEYLFDVARFWMEQGIDGWRLNVANEVDHAFWREFRRLVKSLNPDALIVGEIWHDASGWLMGDQFDSVMNYLFRESVIRFFATGEIHAERFDAELTRARMLYPEQAAQGLWNLLDSHNTERFLTSCGGNEAKFRLAVLFQMTYLGTPLIYYGDEIGMAGATDPDCRRPMIWEEKEQNRGLFEFYKELIRLRHRLASLTRGNVRSWHADKQANLYAFVRTVQDQHVGVVLNNRGEKQTVLLQVPESGGKTWLDCLTGEEVHGKQGQLKLTLRPYQGMILWNGR 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 d1vfmb1 B:1-120 automated matches                                                                                       d1vfmb3 B:121-502 automated matches                                                                                                                                                                                                                                                                                                                                                           d1vfmb2 B:503-585 automated matches                                                 SCOP domains
               CATH domains 1vfmB01 B:1-121 Immunoglobulins                                                                                          1vfmB02 B:122-242,B:298-502 Glycosidases                                                                                 -------------------------------------------------------1vfmB02 B:122-242,B:298-502 Glycosidases                                                                                                                                                                     1vfmB04 B:503-585 Golgi alpha-mannosidase II                                        CATH domains
           Pfam domains (1) Alpha-amylase_N-1vfmB05 B:1-117                                                                                      ----------------------------------------------------Alpha-amylase-1vfmB03 B:170-466                                                                                                                                                                                                                                                                          -----------------------------------------Alpha-amylase_C-1vfmB01 B:508-583                                           -- Pfam domains (1)
           Pfam domains (2) Alpha-amylase_N-1vfmB06 B:1-117                                                                                      ----------------------------------------------------Alpha-amylase-1vfmB04 B:170-466                                                                                                                                                                                                                                                                          -----------------------------------------Alpha-amylase_C-1vfmB02 B:508-583                                           -- Pfam domains (2)
         Sec.struct. author .hhhhh........eee....eeeeeeeee.....eeeeeee................eeee...eeeeeeeee.....eeeeeeee.....eeee....ee.hhhhh..eee...hhhhh...hhhhhhh.eeeehhhhh.............................hhhhhhhhhhhhhhhh..eeee.........................hhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhh.hhhhh...............................hhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhh...eeee.....hhhhh......ee.hhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhh..eee.......hhhhhh..hhhhhhhhhhhhh....eeeee..........................hhhhhhhhhhhhhhhhhhhhhhhheeeeeeee....eeeeeeee..eeeeeeee......eeee........eeee.....eee.....eeee.....eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vfm B   1 MLLEAIFHEAKGSYAYPISETQLRVRLRAKKGDVVRCEVLYADRYASPEEELAHALAGKAGSDERFDYFEALLECSTKRVKYVFLLTGPQGEAVYFGETGFSAERSKAGVFQYAYIHRSEVFTTPEWAKEAVIYQIFPERFANGDPSNDPPGTEQWAKDARPRHDSFYGGDLKGVIDRLPYLEELGVTALYFTPIFASPSHHKYDTADYLAIDPQFGDLPTFRRLVDEAHRRGIKIILDAVFNHAGDQFFAFRDVLQKGEQSRYKDWFFIEDFPVSKTSRTNYETFAVQVPAMPKLRTENPEVKEYLFDVARFWMEQGIDGWRLNVANEVDHAFWREFRRLVKSLNPDALIVGEIWHDASGWLMGDQFDSVMNYLFRESVIRFFATGEIHAERFDAELTRARMLYPEQAAQGLWNLLDSHNTERFLTSCGGNEAKFRLAVLFQMTYLGTPLIYYGDEIGMAGATDPDCRRPMIWEEKEQNRGLFEFYKELIRLRHRLASLTRGNVRSWHADKQANLYAFVRTVQDQHVGVVLNNRGEKQTVLLQVPESGGKTWLDCLTGEEVHGKQGQLKLTLRPYQGMILWNGR 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. Strain: r-47. (23)

1a	1vfmA02	A:122-242,A:298-502
1b	1vfmB02	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. Strain: r-47. (23)

2a	1vfmA04	A:503-585
2b	1vfmB04	B:503-585

Homologous Superfamily: Immunoglobulins (2282)

Thermoactinomyces vulgaris. Organism_taxid: 2026. Strain: r-47. (23)

3a	1vfmA01	A:1-121
3b	1vfmB01	B:1-121

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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	1vfm
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	NEPU2_THEVU \| Q08751
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	3.2.1.135
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1ji2
1vfk	THE SAME PROTEIN COMPLEXED WITH ACARBOSE
1vfo	THE SAME PROTEIN COMPLEXED WITH BETA-CYCLODEXTRIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 14)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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 (3, 6)

Gene Ontology (8, 8)

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Related Entries

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Related Entries Specified in the PDB File