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Asym./Biol. Unit (Jmol Viewer)

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

Title :   ALKALINE ALPHA-AMYLASE AMYK FROM BACILLUS SP. KSM-1378

Authors :   T. Shirai, K. Igarashi, T. Ozawa, H. Hagihara, T. Kobayashi, K. Ozaki, S. Ito

Date :   29 Mar 06 (Deposition) - 13 Feb 07 (Release) - 06 May 08 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A

Keywords :   Beta-Alpha-Barrels, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Shirai, K. Igarashi, T. Ozawa, H. Hagihara, T. Kobayashi, K. Ozaki, S. Ito
Ancestral Sequence Evolutionary Trace And Crystal Structure Analyses Of Alkaline Alpha-Amylase From Bacillus Sp. Ksm-1378 To Clarify The Alkaline Adaptation Process Of Proteins
Proteins V. 66 600 2007
PubMed-ID: 17154418 | Reference-DOI: 10.1002/PROT.21255
(for further references see the PDB file header)

Molecule 1 - AMYLASE
	Chains	:	A
	EC Number	:	3.2.1.1
	Engineered	:	YES
	Expression System	:	BACILLUS SUBTILIS
	Expression System Plasmid	:	PHSP64
	Expression System Strain	:	ISW1214
	Expression System Taxid	:	1423
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-485
	Organism Scientific	:	BACILLUS SP.
	Organism Taxid	:	1409
	Strain	:	KSM-1378
	Synonym	:	ALKLAINE ALPHA-AMYLASE AMYK

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CA	3	Ligand/Ion	CALCIUM ION
2	NA	1	Ligand/Ion	SODIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:163 , ALA A:186 , ASP A:188 , ASP A:207 , HOH A:635	BINDING SITE FOR RESIDUE CA A 778
2	AC2	SOFTWARE	ASN A:106 , ASP A:199 , ASP A:205 , HIS A:240 , HOH A:707	BINDING SITE FOR RESIDUE CA A 779
3	AC3	SOFTWARE	GLY A:305 , PHE A:307 , HIS A:408 , ASP A:409 , ASP A:432 , HOH A:765	BINDING SITE FOR RESIDUE CA A 780
4	AC4	SOFTWARE	ASP A:163 , ASP A:188 , ASP A:199 , ASP A:205 , ILE A:206	BINDING SITE FOR RESIDUE NA A 781

(no "SS Bond" information available for 2DIE)

(no "Cis Peptide Bond" information available for 2DIE)

(no "SAP(SNP)/Variant" information available for 2DIE)

(no "PROSITE Motif" information available for 2DIE)

(no "Exon" information available for 2DIE)

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:481
 aligned with O82839_BACSP | O82839 from UniProtKB/TrEMBL  Length:516

    Alignment length:481
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515 
         O82839_BACSP    36 TNGTMMQYFEWHLPNDGNHWNRLRDDAANLKSKGITAVWIPPAWKGTSQNDVGYGAYDLYDLGEFNQKGTVRTKYGTRSQLQGAVTSLKNNGIQVYGDVVMNHKGGADGTEMVNAVEVNRSNRNQEISGEYTIEAWTKFDFPGRGNTHSNFKWRWYHFDGTDWDQSRQLQNKIYKFRGTGKAWDWEVDIENGNYDYLMYADIDMDHPEVINELRNWGVWYTNTLNLDGFRIDAVKHIKYSYTRDWLTHVRNTTGKPMFAVAEFWKNDLAAIENYLNKTSWNHSVFDVPLHYNLYNASNSGGYFDMRNILNGSVVQKHPIHAVTFVDNHDSQPGEALESFVQSWFKPLAYALILTREQGYPSVFYGDYYGIPTHGVPSMKSKIDPLLQARQTYAYGTQHDYFDHHDIIGWTREGDSSHPNSGLATIMSDGPGGNKWMYVGKHKAGQVWRDITGNRSGTVTINADGWGNFTVNGGAVSVWVKQ 516
               SCOP domains d2diea1 A:5-395 automated matches                                                                                                                                                                                                                                                                                                                                                                      d2diea2 A:396-485 automated matches                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..........hhhhhhhhhhhhhhhhh..eeee....................................hhhhhhhhhhhhhhh..eeeeee...ee....eeeeeeeeeee..eeeee....eeeeeeee...............hhh.eeee............eee.......................eee...hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh....eeehhhhhhhhhhhhhh....hhhhh...hhhhhh...eeee...................hhhhhhhhhhh....eeeeehhhhh.hhhhh...hhhhhhhhhhhhhhh....eeee.....eeeeee..........eeeeee....eeeeee.hhhhh..eeee.......eee.....eeeeee...eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2die A   5 TNGTMMQYFEWHLPNDGNHWNRLRDDAANLKSKGITAVWIPPAWKGTSQNDVGYGAYDLYDLGEFNQKGTVRTKYGTRSQLQGAVTSLKNNGIQVYGDVVMNHKGGADGTEMVNAVEVNRSNRNQEISGEYTIEAWTKFDFPGRGNTHSNFKWRWYHFDGTDWDQSRQLQNKIYKFRGTGKAWDWEVDIENGNYDYLMYADIDMDHPEVINELRNWGVWYTNTLNLDGFRIDAVKHIKYSYTRDWLTHVRNTTGKPMFAVAEFWKNDLAAIENYLNKTSWNHSVFDVPLHYNLYNASNSGGYFDMRNILNGSVVQKHPIHAVTFVDNHDSQPGEALESFVQSWFKPLAYALILTREQGYPSVFYGDYYGIPTHGVPSMKSKIDPLLQARQTYAYGTQHDYFDHHDIIGWTREGDSSHPNSGLATIMSDGPGGNKWMYVGKHKAGQVWRDITGNRSGTVTINADGWGNFTVNGGAVSVWVKQ 485
                                    14        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

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Glycosyl hydrolase domain (397)

Superfamily: Glycosyl hydrolase domain (397)

Family: automated matches (85)

Protein domain: automated matches (85)

Bacillus sp. (1)

d2diea2

A:396-485

Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: (Trans)glycosidases (1191)

Family: Amylase, catalytic domain (385)

Protein domain: automated matches (71)

Bacillus sp. (1)

d2diea1

A:5-395

(no "CATH Domain" information available for 2DIE)

(no "Pfam Domain" information available for 2DIE)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (O82839_BACSP | O82839)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	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: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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2die)

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Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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