1K1Y - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THERMOCOCCUS LITORALIS 4-ALPHA-GLUCANOTRANSFERASE COMPLEXED WITH ACARBOSE

Authors :   H. Imamura, S. Fushinobu, T. Kumasaka, M. Yamamoto, B. S. Jeon, T. Wakag H. Matsuzawa

Date :   26 Sep 01 (Deposition) - 17 Jun 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   4-Alpha-Glucanotransferase Complexed With Acarbose, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Imamura, S. Fushinobu, M. Yamamoto, T. Kumasaka, B. S. Jeon, T. Wakagi, H. Matsuzawa
Crystal Structures Of 4-Alpha-Glucanotransferase From Thermococcus Litoralis And Its Complex With An Inhibitor
J. Biol. Chem. V. 278 19378 2003
PubMed-ID: 12618437 | Reference-DOI: 10.1074/JBC.M213134200

Molecule 1 - 4-ALPHA-GLUCANOTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.4.1.25
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PUT7
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMOCOCCUS LITORALIS
	Organism Taxid	:	2265

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 6)

No.	Name	Count	Type	Full Name
1	ACR	1	Ligand/Ion	ALPHA-ACARBOSE
2	CA	3	Ligand/Ion	CALCIUM ION
3	MAL	1	Ligand/Ion	MALTOSE
4	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	ACR	1	Ligand/Ion	ALPHA-ACARBOSE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	MAL	-1	Ligand/Ion	MALTOSE
4	TRS	-1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	ACR	-1	Ligand/Ion	ALPHA-ACARBOSE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	MAL	1	Ligand/Ion	MALTOSE
4	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 3 (3, 3)

No.	Name	Count	Type	Full Name
1	ACR	1	Ligand/Ion	ALPHA-ACARBOSE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	MAL	1	Ligand/Ion	MALTOSE
4	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:11 , HIS A:13 , GLU A:123 , ARG A:124 , ARG A:182 , TYR A:183 , PHE A:187 , ASP A:213 , ASP A:214 , LYS A:217 , TRP A:221 , TYR A:272 , GLU A:274 , ASP A:354 , HOH A:1612 , HOH A:1637 , HOH A:1654 , HOH A:1660 , HOH A:1683 , HOH A:1752 , HOH A:1787	BINDING SITE FOR RESIDUE ACR A 660
2	AC2	SOFTWARE	PRO B:367 , HIS B:368 , ARG B:371 , HIS B:581 , SER B:582 , HOH B:1640 , HOH B:1794	BINDING SITE FOR RESIDUE MAL B 660
3	AC3	SOFTWARE	ASP A:392 , ASP A:394 , ASP A:396 , ARG A:398 , GLU A:400	BINDING SITE FOR RESIDUE CA A 1601
4	AC4	SOFTWARE	ASP B:392 , ASP B:394 , ASP B:396 , ARG B:398 , GLU B:400	BINDING SITE FOR RESIDUE CA B 1602
5	AC5	SOFTWARE	ASN A:248 , HOH A:1629 , HOH A:1686 , GLU B:60	BINDING SITE FOR RESIDUE CA B 1603
6	AC6	SOFTWARE	HIS B:11 , GLU B:123 , ASP B:214 , HOH B:1690 , HOH B:1717 , HOH B:1738	BINDING SITE FOR RESIDUE TRS B 1604

(no "SS Bond" information available for 1K1Y)

Asymmetric Unit

No.	Residues
1	Ile A:185	-	Pro A:186
2	Ile B:185	-	Pro B:186

(no "SAP(SNP)/Variant" information available for 1K1Y)

(no "PROSITE Motif" information available for 1K1Y)

(no "Exon" information available for 1K1Y)

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:636
 aligned with MALQ_THELN | O32462 from UniProtKB/Swiss-Prot  Length:659

    Alignment length:659
                                    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       590       600       610       620       630       640       650         
           MALQ_THELN     1 MERINFIFGIHNHQPLGNFGWVFEEAYNRSYRPFMEILEEFPEMKVNVHFSGPLLEWIEENKPDYLDLLRSLIKRGQLEIVVAGFYEPVLAAIPKEDRLVQIEMLKDYARKLGYDAKGVWLTERVWQPELVKSLREAGIEYVVVDDYHFMSAGLSKEELFWPYYTEDGGEVITVFPIDEKLRYLIPFRPVKKTIEYLESLTSDDPSKVAVFHDDGEKFGVWPGTYEWVYEKGWLREFFDAITSNEKINLMTYSEYLSKFTPRGLVYLPIASYFEMSEWSLPAKQAKLFVEFVEQLKEEGKFEKYRVFVRGGIWKNFFFKYPESNFMHKRMLMVSKAVRDNPEARKYILKAQCNDAYWHGVFGGIYLPHLRRTVWENIIKAQRYLKPENKILDVDFDGRAEIMVENDGFIATIKPHYGGSIFELSSKRKAVNYNDVLPRRWEHYHEVPEATKPEKESEEGIASIHELGKQIPEEIRRELAYDWQLRAILQDHFIKPEETLDNYRLVKYHELGDFVNQPYEYEMIENGVKLWREGGVYAEEKIPARVEKKIELTEDGFIAKYRVLLEKPYKALFGVEINLAVHSVMEKPEEFEAKEFEVNDPYGIGKVRIELDKAAKVWKFPIKTLSQSEAGWDFIQQGVSYTMLFPIEKELEFTVRFREL 659
               SCOP domains d1k1ya3 A:1-310 4-alpha-glucanotransferase, N-terminal domain                                                                                                                                                                                                                                                         d1k1ya1 A:311-384 4-alpha-glucanotransferase, domain 2                    d1k1ya2 A:385-659 4-alpha-glucanotransferase, C-terminal doma                       in                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee......hhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhhhhhhhhh.....eee.hhhh...hhhhhhhhh...eeeeehhhhhhhh.hhhhh...eeeee..eeeeeeeehhhhhhhh...hhhhhhhhhhhhh......eeeeeee.hhh....hhhhhhh..hhhhhhhhhhhh...eee.hhhhhhhhh..............hhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh......eee........eeeee...eeeeee.....eeeeeee....ee..............-----------------------..hhhhhh..........eeeeeee....hhhhhhh..............eeeee..eeeeeeeeeee...eeeeeeeeeeeee..eeeeeeeeee.....eeeeeeeee.........eeeeeeeeeeee....eeeeeeeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k1y A   1 MERINFIFGIHNHQPLGNFGWVFEEAYNRSYRPFMEILEEFPEMKVNVHFSGPLLEWIEENKPDYLDLLRSLIKRGQLEIVVAGFYEPVLAAIPKEDRLVQIEMLKDYARKLGYDAKGVWLTERVWQPELVKSLREAGIEYVVVDDYHFMSAGLSKEELFWPYYTEDGGEVITVFPIDEKLRYLIPFRPVKKTIEYLESLTSDDPSKVAVFHDDGEKFGVWPGTYEWVYEKGWLREFFDAITSNEKINLMTYSEYLSKFTPRGLVYLPIASYFEMSEWSLPAKQAKLFVEFVEQLKEEGKFEKYRVFVRGGIWKNFFFKYPESNFMHKRMLMVSKAVRDNPEARKYILKAQCNDAYWHGVFGGIYLPHLRRTVWENIIKAQRYLKPENKILDVDFDGRAEIMVENDGFIATIKPHYGGSIFELSSKRKAVNYNDVLPRRWEHYHE-----------------------QIPEEIRRELAYDWQLRAILQDHFIKPEETLDNYRLVKYHELGDFVNQPYEYEMIENGVKLWREGGVYAEEKIPARVEKKIELTEDGFIAKYRVLLEKPYKALFGVEINLAVHSVMEKPEEFEAKEFEVNDPYGIGKVRIELDKAAKVWKFPIKTLSQSEAGWDFIQQGVSYTMLFPIEKELEFTVRFREL 659
                                    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    |    -         -       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      445                     469

Chain B from PDB  Type:PROTEIN  Length:636
 aligned with MALQ_THELN | O32462 from UniProtKB/Swiss-Prot  Length:659

    Alignment length:658
                                    11        21        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       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651        
           MALQ_THELN     2 ERINFIFGIHNHQPLGNFGWVFEEAYNRSYRPFMEILEEFPEMKVNVHFSGPLLEWIEENKPDYLDLLRSLIKRGQLEIVVAGFYEPVLAAIPKEDRLVQIEMLKDYARKLGYDAKGVWLTERVWQPELVKSLREAGIEYVVVDDYHFMSAGLSKEELFWPYYTEDGGEVITVFPIDEKLRYLIPFRPVKKTIEYLESLTSDDPSKVAVFHDDGEKFGVWPGTYEWVYEKGWLREFFDAITSNEKINLMTYSEYLSKFTPRGLVYLPIASYFEMSEWSLPAKQAKLFVEFVEQLKEEGKFEKYRVFVRGGIWKNFFFKYPESNFMHKRMLMVSKAVRDNPEARKYILKAQCNDAYWHGVFGGIYLPHLRRTVWENIIKAQRYLKPENKILDVDFDGRAEIMVENDGFIATIKPHYGGSIFELSSKRKAVNYNDVLPRRWEHYHEVPEATKPEKESEEGIASIHELGKQIPEEIRRELAYDWQLRAILQDHFIKPEETLDNYRLVKYHELGDFVNQPYEYEMIENGVKLWREGGVYAEEKIPARVEKKIELTEDGFIAKYRVLLEKPYKALFGVEINLAVHSVMEKPEEFEAKEFEVNDPYGIGKVRIELDKAAKVWKFPIKTLSQSEAGWDFIQQGVSYTMLFPIEKELEFTVRFREL 659
               SCOP domains d1k1yb3 B:2-310 4-alpha-glucanotransferase, N-terminal domain                                                                                                                                                                                                                                                        d1k1yb1 B:311-384 4-alpha-glucanotransferase, domain 2                    d1k1yb2 B:385-659 4-alpha-glucanotransferase, C-terminal domai                      n                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhhhhhhhhh.....eee.hhhh...hhhhhhhhh...eeeeehhhhhhhh.hhhhh...eeeee..eeeeeeeehhhhhhhh...hhhhhhhhhhhh.......eeeeeee.hhh....hhhhhhh..hhhhhhhhhhhh...eee.hhhhhhhhh............hhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh......eee........eeeee...eeeee.......eeeeee....ee.........hhhhh.----------------------.....hhhhh........eeeeeee....hhhhhhh..............eeee...eeeeee...ee...ee.eeeeeeeeee..eeeeeeeeee.....eeeeeeeee.........eeeeeeeeeeee....eeeeeeeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k1y B   2 ERINFIFGIHNHQPLGNFGWVFEEAYNRSYRPFMEILEEFPEMKVNVHFSGPLLEWIEENKPDYLDLLRSLIKRGQLEIVVAGFYEPVLAAIPKEDRLVQIEMLKDYARKLGYDAKGVWLTERVWQPELVKSLREAGIEYVVVDDYHFMSAGLSKEELFWPYYTEDGGEVITVFPIDEKLRYLIPFRPVKKTIEYLESLTSDDPSKVAVFHDDGEKFGVWPGTYEWVYEKGWLREFFDAITSNEKINLMTYSEYLSKFTPRGLVYLPIASYFEMSEWSLPAKQAKLFVEFVEQLKEEGKFEKYRVFVRGGIWKNFFFKYPESNFMHKRMLMVSKAVRDNPEARKYILKAQCNDAYWHGVFGGIYLPHLRRTVWENIIKAQRYLKPENKILDVDFDGRAEIMVENDGFIATIKPHYGGSIFELSSKRKAVNYNDVLPRRWEHYHEV----------------------QIPEEIRRELAYDWQLRAILQDHFIKPEETLDNYRLVKYHELGDFVNQPYEYEMIENGVKLWREGGVYAEEKIPARVEKKIELTEDGFIAKYRVLLEKPYKALFGVEINLAVHSVMEKPEEFEAKEFEVNDPYGIGKVRIELDKAAKVWKFPIKTLSQSEAGWDFIQQGVSYTMLFPIEKELEFTVRFREL 659
                                    11        21        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    |    -         -       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      446                    469

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 1K1Y)

(no "Pfam Domain" information available for 1K1Y)

Asymmetric Unit(hide GO term definitions)

Chain A,B (MALQ_THELN | O32462)

molecular function
	GO:0004134	4-alpha-glucanotransferase activity	Catalysis of the transfer of a segment of a (1->4)-alpha-D-glucan to a new 4-position in an acceptor, which may be glucose or (1->4)-alpha-D-glucan.
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	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:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0016757	transferase activity, transferring glycosyl groups	Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
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:0005977	glycogen metabolic process	The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages.

Asymmetric Unit
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	Cis Peptide Bonds
		Ile A:185 - Pro A:186	[ RasMol ]
		Ile B:185 - Pro B:186	[ RasMol ]

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	1k1y
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	MALQ_THELN \| O32462
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	2.4.1.25
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	MALQ_THELN \| O32462	:	1k1w 1k1x

1k1w	1K1W CONTAINS THE SAME PROTEIN WITH GLUCOSE
1k1x	1K1X CONTAINS THE SAME PROTEIN WITH 2-AMINO-2-HYDROXYMETHYL -PROPANE-1,3-DIOL

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (3, 6)

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Gene Ontology (7, 7)

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