3BC9 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   ALPHA-AMYLASE B IN COMPLEX WITH ACARBOSE

Authors :   T. -C. Tan, B. N. Mijts, K. Swaminathan, B. K. C. Patel, C. Divne

Date :   12 Nov 07 (Deposition) - 22 Apr 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.35

Chains :   Asym./Biol. Unit : A

Keywords :   Alpha-Amylase, Acarbose, Thermostable, Halophilic, N Domain, Raw Starch Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. -C. Tan, B. N. Mijts, K. Swaminathan, B. K. C. Patel, C. Divne
Crystal Structure Of The Polyextremophilic Alpha-Amylase Amyb From Halothermothrix Orenii: Details Of A Productive Enzyme-Substrate Complex And An N Domain With A Role In Binding Raw Starch
J. Mol. Biol. V. 378 850 2008
PubMed-ID: 18387632 | Reference-DOI: 10.1016/J.JMB.2008.02.041

Molecule 1 - ALPHA AMYLASE, CATALYTIC REGION
	Chains	:	A
	EC Number	:	3.2.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-19B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	AMYB
	Organism Scientific	:	HALOTHERMOTHRIX ORENII
	Organism Taxid	:	373903
	Strain	:	H 168
	Synonym	:	AMYB

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (8, 17)

No.	Name	Count	Type	Full Name
1	ACI	2	Ligand/Ion	6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL
2	ACR	1	Ligand/Ion	ALPHA-ACARBOSE
3	BGC	1	Ligand/Ion	BETA-D-GLUCOSE
4	CA	4	Ligand/Ion	CALCIUM ION
5	G6D	1	Ligand/Ion	6-DEOXY-ALPHA-D-GLUCOSE
6	GLC	5	Ligand/Ion	ALPHA-D-GLUCOSE
7	GLD	2	Ligand/Ion	4,6-DIDEOXYGLUCOSE
8	NA	1	Ligand/Ion	SODIUM ION

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:198 , GLY A:236 , ALA A:237 , TRP A:260 , HOH A:1508	BINDING SITE FOR RESIDUE G6D A 801
02	AC2	SOFTWARE	MET A:235 , GLY A:236 , ALA A:237 , TRP A:260 , HOH A:1406 , HOH A:1554	BINDING SITE FOR RESIDUE GLC A 802
03	AC3	SOFTWARE	ASP A:286 , MET A:316 , GLY A:317 , HOH A:1429	BINDING SITE FOR RESIDUE ACI A 803
04	AC4	SOFTWARE	HOH A:1485 , HOH A:1528	BINDING SITE FOR RESIDUE GLD A 804
05	AC5	SOFTWARE	TRP A:131 , TYR A:184 , ARG A:450 , TYR A:455 , HOH A:1076 , HOH A:1291	BINDING SITE FOR RESIDUE GLC A 805
06	AC6	SOFTWARE	TYR A:184 , HIS A:233 , ARG A:348 , ASP A:350 , GLU A:380 , HIS A:446 , ASP A:447	BINDING SITE FOR RESIDUE ACI A 806
07	AC7	SOFTWARE	ALA A:351 , HIS A:354 , GLU A:380 , TYR A:455	BINDING SITE FOR RESIDUE GLD A 807
08	AC8	SOFTWARE	LYS A:353 , TYR A:455 , HOH A:1530	BINDING SITE FOR RESIDUE GLC A 808
09	AC9	SOFTWARE	TRP A:382 , GLU A:384 , HOH A:1094 , HOH A:1537	BINDING SITE FOR RESIDUE BGC A 809
10	BC1	SOFTWARE	ASP A:449 , SER A:458 , ILE A:459 , TYR A:460 , SER A:461 , ARG A:462 , LYS A:463 , TRP A:488 , GLU A:588 , ASP A:589 , HOH A:1045 , HOH A:1218 , HOH A:1449 , HOH A:1468	BINDING SITE FOR RESIDUE ACR A 901
11	BC2	SOFTWARE	TRP A:304 , TRP A:306 , THR A:307 , TRP A:310 , ASP A:311 , HOH A:1014	BINDING SITE FOR RESIDUE GLC A 1001
12	BC3	SOFTWARE	TYR A:239 , ASN A:264 , ASP A:394 , HOH A:1316	BINDING SITE FOR RESIDUE GLC A 1002
13	BC4	SOFTWARE	ASP A:283 , SER A:303 , ASP A:305 , ASP A:321 , GLU A:323 , HOH A:1021	BINDING SITE FOR RESIDUE CA A 701
14	BC5	SOFTWARE	ASN A:232 , ASP A:313 , ASP A:319 , HIS A:354 , HOH A:1029	BINDING SITE FOR RESIDUE CA A 702
15	BC6	SOFTWARE	ASN A:77 , ALA A:419 , ALA A:517 , ASP A:518 , ASP A:541 , HOH A:1083	BINDING SITE FOR RESIDUE CA A 703
16	BC7	SOFTWARE	ASP A:283 , ASP A:305 , ASP A:313 , ASP A:319	BINDING SITE FOR RESIDUE NA A 704
17	BC8	SOFTWARE	PHE A:527 , ASP A:533 , HOH A:1400 , HOH A:1404 , HOH A:1409	BINDING SITE FOR RESIDUE CA A 705

(no "SS Bond" information available for 3BC9)

Asymmetric/Biological Unit

No.	Residues
1	Glu A:22	-	Pro A:23

(no "SAP(SNP)/Variant" information available for 3BC9)

(no "PROSITE Motif" information available for 3BC9)

(no "Exon" information available for 3BC9)

Asymmetric/Biological 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 B8CZ54_HALOH | B8CZ54 from UniProtKB/TrEMBL  Length:623

    Alignment length:585
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618     
         B8CZ54_HALOH    39 SLFLIESEPSTGASVSKNLTEIILIFSNDINKVSQLALTDLITDSDIQGIDYNIEGNKVIINNFSLEPTCNYRLSYEVIDIYDNHLQGYIEFLVNQSNYPQIPDQEVNHTILQAFYWEMNTGEYATEHPEEANLWNLLAERAPELAEAGFTAVWLPPANKGMAGIHDVGYGTYDLWDLGEFDQKGTVRTKYGTKGELENAIDALHNNDIKVYFDAVLNHRMGADYAETVLLDENSRDKPGQYIKAWTGFNFPGRNGEYSNFTWNGQCFDGTDWDDYSKESGKYLFDEKSWDWTYNWDEDYLMGADVDYENEAVQNDVIDWGQWIINNIDFDGFRLDAVKHIDYRFIDKWMSAVQNSSNRDVFFVGEAWVEDVDDLKGFLDTVGNPDLRVFDFPLRSFFVDMLNGAYMADLRNAGLVNSPGYENRAVTFVDNHDTDRDEGSYTVSIYSRKYQAYAYILTRAEGVPTVYWKDYYIWEMKEGLDKLLTARRYYAYGPGYEVDNNDADIYSYVRSGFPDVAGDGLVLMISDGTSGNVAGKWINSRQPDTEFYDLTGHIKEHVTTDSEGYGNFKVIKSEDKGWSIWVPVE 623
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....eee.....eeeeee...eeeeeeeeeee....ee....eeeee..eeeee........eeeeeeeeee....eeeeeeeeee........hhhhh...eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.....ee.hhhhh....eee..................hhhhhhhhhhhhhhh..eeeeee...ee....eeeeee...........eeeeeee...............hhh.eeeeeee....eeeeee...................eee...hhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhh...eeeehhhhhhhhhhhh...hhhhhhh.hhhhh..hhh.eee....................hhhhhhhhhhhh...eeeeehhhhhh..hhhhhhhhhhhhhhh....eee.......eeeeee..........eeeeee......eeeeeee......eeee.......eee.....eeeeeee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bc9 A  15 SLFLIESEPSTGASVSKNLTEIILIFSNDINKVSQLALTDLITDSDIQGIDYNIEGNKVIINNFSLEPTCNYRLSYEVIDIYDNHLQGYIEFLVNQSNYPQIPDQEVNHTILQAFYWEMNTGEYATEHPEEANLWNLLAERAPELAEAGFTAVWLPPANKGMAGIHDVGYGTYDLWDLGEFDQKGTVRTKYGTKGELENAIDALHNNDIKVYFDAVLNHRMGADYAETVLLDENSRDKPGQYIKAWTGFNFPGRNGEYSNFTWNGQCFDGTDWDDYSKESGKYLFDEKSWDWTYNWDEDYLMGADVDYENEAVQNDVIDWGQWIINNIDFDGFRLDAVKHIDYRFIDKWMSAVQNSSNRDVFFVGEAWVEDVDDLKGFLDTVGNPDLRVFDFPLRSFFVDMLNGAYMADLRNAGLVNSPGYENRAVTFVDNHDTDRDEGSYTVSIYSRKYQAYAYILTRAEGVPTVYWKDYYIWEMKEGLDKLLTARRYYAYGPGYEVDNNDADIYSYVRSGFPDVAGDGLVLMISDGTSGNVAGKWINSRQPDTEFYDLTGHIKEHVTTDSEGYGNFKVIKSEDKGWSIWVPVE 599
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594

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 3BC9)

(no "CATH Domain" information available for 3BC9)

(no "Pfam Domain" information available for 3BC9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (B8CZ54_HALOH | B8CZ54)

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:0033927	glucan 1,4-alpha-maltohexaosidase activity	Catalysis of the hydrolysis of (1->4)-alpha-D-glucosidic linkages in amylaceous polysaccharides, to remove successive maltohexaose residues from the non-reducing chain ends.
	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/Biological Unit
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	Cis Peptide Bonds
		Glu A:22 - Pro A:23	[ RasMol ]

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	3bc9
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	3.2.1.1
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UniProtKB/TrEMBL
	B8CZ54_HALOH \| B8CZ54	:	3bcd 3bcf

3bcd	ALPHA-AMYLASE B IN COMPLEX WITH MALTOTETRAOSE AND ALPHA- CYCLODEXTRIN
3bcf	ALPHA-AMYLASE B WITHOUT SUGAR

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (8, 17)

Sites (17, 17)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (8, 8)

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