1UD8 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF AMYK38 WITH LITHIUM ION

Authors :   T. Nonaka, M. Fujihashi, A. Kita, H. Hagihara, K. Ozaki, S. Ito, K. Miki

Date :   28 Apr 03 (Deposition) - 22 Jul 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.88

Chains :   Asym./Biol. Unit : A

Keywords :   Calcium-Free, Alkaline, Alpha-Amylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Nonaka, M. Fujihashi, A. Kita, H. Hagihara, K. Ozaki, S. Ito, K. Miki
Crystal Structure Of Calcium-Free Alpha-Amylase From Bacillus Sp. Strain Ksm-K38 (Amyk38) And Its Sodium Ion Binding Sites
J. Biol. Chem. V. 278 24818 2003
PubMed-ID: 12719434 | Reference-DOI: 10.1074/JBC.M212763200
(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 Taxid	:	1423
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-480
	Organism Scientific	:	BACILLUS SP. KSM-K38
	Organism Taxid	:	129736
	Synonym	:	ALPHA-AMYLASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 3)

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

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:104 , ASP A:194 , ASN A:200 , HIS A:235	BINDING SITE FOR RESIDUE NA A 1001
2	AC2	SOFTWARE	GLY A:300 , TYR A:302 , TRP A:403 , ASP A:404 , ASN A:427 , HOH A:2018	BINDING SITE FOR RESIDUE NA A 1002
3	AC3	SOFTWARE	ASN A:289 , VAL A:324 , ASP A:325 , SER A:337 , VAL A:339	BINDING SITE FOR RESIDUE NA A 1003

(no "SS Bond" information available for 1UD8)

Asymmetric/Biological Unit

No.	Residues
1	Trp A:184	-	Arg A:185

(no "SAP(SNP)/Variant" information available for 1UD8)

(no "PROSITE Motif" information available for 1UD8)

(no "Exon" information available for 1UD8)

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:480
 aligned with Q93I48_9BACI | Q93I48 from UniProtKB/TrEMBL  Length:501

    Alignment length:480
                                    31        41        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       431       441       451       461       471       481       491       501
         Q93I48_9BACI    22 DGLNGTMMQYYEWHLENDGQHWNRLHDDAAALSDAGITAIWIPPAYKGNSQADVGYGAYDLYDLGEFNQKGTVRTKYGTKAQLERAIGSLKSNDINVYGDVVMNHKMGADFTEAVQAVQVNPTNRWQDISGAYTIDAWTGFDFSGRNNAYSDFKWRWFHFNGVDWDQRYQENHIFRFANTNWNWRVDEENGNYDYLLGSNIDFSHPEVQDELKDWGSWFTDELDLDGYRLDAIKHIPFWYTSDWVRHQRNEADQDLFVVGEYWKDDVGALEFYLDEMNWEMSLFDVPLNYNFYRASQQGGSYDMRNILRGSLVEAHPMHAVTFVDNHDTQPGESLESWVADWFKPLAYATILTREGGYPNVFYGDYYGIPNDNISAKKDMIDELLDARQNYAYGTQHDYFDHWDVVGWTREGSSSRPNSGLATIMSNGPGGSKWMYVGRQNAGQTWTDLTGNNGASVTINGDGWGEFFTNGGSVSVYVNQ 501
               SCOP domains d1ud8a2 A:1-390 Bacterial alpha-amylase                                                                                                                                                                                                                                                                                                                                                               d1ud8a1 A:391-480 Bacterial alpha-Amylase                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---------------------Alpha-amylase-1ud8A01 A:22-380                                                                                                                                                                                                                                                                                                                                         ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..........hhhhhhhhhhhhhhhhh..eeee....ee.........eee..................hhhhhhhhhhhhhhh..eeeeee...ee....eeeeeeeeeee..eeeee....eeeeeeee..hhhhh........hhh.eeeeeee....eeeeeee.....................eee...hhhhhhhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhh...eeehhhhhhhhhhhhhhh...hhhhh...hhhhhh...ee.....................hhhhhhhhhhhh.....eeehhhhh.hhhhh...hhhhhhhhhhhhhhh....eeee.....eeeeee..........eeeeee....eeeeee.hhhhh..eeee.......eee.....eeeeee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ud8 A   1 DGLNGTMMQYYEWHLENDGQHWNRLHDDAAALSDAGITAIWIPPAYKGNSQADVGYGAYDLYDLGEFNQKGTVRTKYGTKAQLERAIGSLKSNDINVYGDVVMNHKMGADFTEAVQAVQVNPTNRWQDISGAYTIDAWTGFDFSGRNNAYSDFKWRWFHFNGVDWDQRYQENHIFRFANTNWNWRVDEENGNYDYLLGSNIDFSHPEVQDELKDWGSWFTDELDLDGYRLDAIKHIPFWYTSDWVRHQRNEADQDLFVVGEYWKDDVGALEFYLDEMNWEMSLFDVPLNYNFYRASQQGGSYDMRNILRGSLVEAHPMHAVTFVDNHDTQPGESLESWVADWFKPLAYATILTREGGYPNVFYGDYYGIPNDNISAKKDMIDELLDARQNYAYGTQHDYFDHWDVVGWTREGSSSRPNSGLATIMSNGPGGSKWMYVGRQNAGQTWTDLTGNNGASVTINGDGWGEFFTNGGSVSVYVNQ 480
                                    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

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 "CATH Domain" information available for 1UD8)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Glyco_hydro_tim (488)

Family: Alpha-amylase (138)

Bacillus sp. KSM-K38 (6)

Alpha-amylase-1ud8A01

A:22-380

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q93I48_9BACI | Q93I48)

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.
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
		Trp A:184 - Arg A:185	[ RasMol ]

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	Q93I48_9BACI \| Q93I48	:	1ud2 1ud3 1ud4 1ud5 1ud6

1ud2	THE STRUCTURE WHICH SODIUM IONS, INSTEAD OF CALCIUM IONS, ARE USED TO RETAIN THE STRUCTURE AND FUNCTION OF AMYK38.
1ud3	THE STRUCTURE OF THE N289H MUTANT OF AMYK38.
1ud4	THE STRUCTURE OF THE CALCIUM-FREE ALPHA-AMYLASE, AMYK38, FROM THE CRYSTAL GROWN IN THE CACL2 CONTAINING SOLUTION.
1ud5	THIS STRUCTURE WAS DETERMINED FROM THE DATASET OF THE CRYSTAL SOAKED INTO RB+ ION CONTAINING SOLUTION.
1ud6	THIS STRUCTURE WAS DETERMINED FROM THE DATASET OF THE CRYSTAL SOAKED INTO K+ ION CONTAINING SOLUTION.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 2)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (4, 4)

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