1Y3P - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE OF ALGQ1, ALGINATE-BINDING PROTEIN, COMPLEXED WITH AN ALGINATE TETRASACCHARIDE

Authors :   K. Momma, Y. Mishima, W. Hashimoto, B. Mikami, K. Murata

Date :   26 Nov 04 (Deposition) - 12 Apr 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   Sugar Binding Protein, Alginate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Momma, Y. Mishima, W. Hashimoto, B. Mikami, K. Murata
Direct Evidence For Sphingomonas Sp. A1 Periplasmic Protein As Macromolecule-Binding Proteins Associated With The Abc Transporter: Molecular Insights Into Alginate Transport In The Periplasm(, )
Biochemistry V. 44 5053 2005
PubMed-ID: 15794643 | Reference-DOI: 10.1021/BI047781R

Molecule 1 - ALGQ1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-490
	Organism Scientific	:	SPHINGOMONAS SP.
	Organism Taxid	:	90322
	Strain	:	A1
	Synonym	:	ALGINATE-BINDING PROTEIN

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 5)

No.	Name	Count	Type	Full Name
1	BEM	1	Ligand/Ion	BETA-D-MANNURONIC ACID
2	CA	1	Ligand/Ion	CALCIUM ION
3	LGU	1	Ligand/Ion	ALPHA-L-GULURONATE
4	MAV	2	Ligand/Ion	ALPHA-D-MANNOPYRANURONIC ACID

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:186 , TRP A:270 , ALA A:272 , SER A:273 , ASN A:375 , TYR A:379 , GLN A:391 , TYR A:395 , GLU A:396 , MAV A:495 , HOH A:567 , HOH A:581	BINDING SITE FOR RESIDUE BEM A 494
2	AC2	SOFTWARE	ARG A:20 , TYR A:129 , ARG A:137 , ARG A:186 , TRP A:270 , TYR A:379 , BEM A:494 , LGU A:496 , HOH A:538 , HOH A:567 , HOH A:594 , HOH A:652	BINDING SITE FOR RESIDUE MAV A 495
3	AC3	SOFTWARE	ASP A:74 , ASN A:75 , ASP A:187 , ARG A:313 , MAV A:495 , MAV A:497 , HOH A:852	BINDING SITE FOR RESIDUE LGU A 496
4	AC4	SOFTWARE	ARG A:20 , ASP A:21 , GLN A:55 , ASP A:74 , ASN A:75 , GLU A:189 , TRP A:208 , LGU A:496 , HOH A:505 , HOH A:576	BINDING SITE FOR RESIDUE MAV A 497
5	AC5	SOFTWARE	ASP A:171 , ASN A:173 , ASN A:175 , LYS A:177 , ASP A:179 , GLU A:180	BINDING SITE FOR RESIDUE CA A 493

(no "SS Bond" information available for 1Y3P)

Asymmetric/Biological Unit

No.	Residues
1	Ile A:311	-	Pro A:312

(no "SAP(SNP)/Variant" information available for 1Y3P)

(no "PROSITE Motif" information available for 1Y3P)

(no "Exon" information available for 1Y3P)

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:490
 aligned with Q9KWT6_SPHSX | Q9KWT6 from UniProtKB/TrEMBL  Length:526

    Alignment length:490
                                    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
         Q9KWT6_SPHSX    25 REATWVTEKPLTLKIHMHFRDKWVWDENWPVAREVARLTNVKLVGVANRAATNSQEQFNLMMASGQLPDIVGGDNLKDKFIRYGMEGAFIPLNKLIDQNAPNLKAFFKTHPEVQRAITAPDGNIYYLPYVPDGLVSRGYFIRQDWLDKLHLKTPQTVDELYTVLKAFKEKDPNGNGKADEIPFINRDPEEVFRLVNFWGARSTGSNTWMDFYVENGKIKHPFAEVAFKDGIKHVAQWYKEGLIDPEIFTRKARSREQTFGNNIGGMTHDWFASTALFNDALSKNIPGFKLVPMAPPINSKGQRWEEDARQIPRPDGWAITATNKNPVETIKLFDFYFGPKGRELSNFGVPGLTYDIKNGKPVYKDTVLKAAQPVNNQMYDIGAQIPIGFWQDYEYERQWTNDVALQGIDMYIKNKYVLPQFTGVNLTVEEREIYDKYWPDVKTYMFEMGQSWVMGTKDPEKTWNDYQQQLKNRGFYQVMIVMQKAYDRQY 514
               SCOP domains d1y3pa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1y3pA01 A:1-132,A:311-399 Periplasmic binding protein-like II                                                                       1y3pA02 A:133-310,A:400-490 Periplasmic binding protein-like II                                                                                                                   1y3pA01 A:1-132,A:311-399 Periplasmic binding protein-like II                            1y3pA02 A:133-310,A:400-490 Periplasmic binding protein-like II                             CATH domains
               Pfam domains --------------------------------SBP_bac_1-1y3pA01 A:33-343                                                                                                                                                                                                                                                                                             --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee...ee....hhhhhhhhhhhheeeee.......hhhhhhhhhhh......eeee..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh........eee.......eeeeeehhhhhhh......hhhhhhhhhhhhhhh..........eee.....hhhhhhhhhhh............eee..eeehhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhh....eeeeeeehhhhhhhhhhhh.......eeee...................eeeeeee.....hhhhhhhhhhhh.hhhhhhhhhhh.....eeee..eeeehhhhhh...hhhhhhhhh..........hhhhhhh..hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y3p A   1 REATWVTEKPLTLKIHMHFRDKWVWDENWPVAREVARLTNVKLVGVANRAATNSQEQFNLMMASGQLPDIVGGDNLKDKFIRYGMEGAFIPLNKLIDQNAPNLKAFFKTHPEVQRAITAPDGNIYYLPYVPDGLVSRGYFIRQDWLDKLHLKTPQTVDELYTVLKAFKEKDPNGNGKADEIPFINRDPEEVFRLVNFWGARSTGSNTWMDFYVENGKIKHPFAEVAFKDGIKHVAQWYKEGLIDPEIFTRKARSREQTFGNNIGGMTHDWFASTALFNDALSKNIPGFKLVPMAPPINSKGQRWEEDARQIPRPDGWAITATNKNPVETIKLFDFYFGPKGRELSNFGVPGLTYDIKNGKPVYKDTVLKAAQPVNNQMYDIGAQIPIGFWQDYEYERQWTNDVALQGIDMYIKNKYVLPQFTGVNLTVEEREIYDKYWPDVKTYMFEMGQSWVMGTKDPEKTWNDYQQQLKNRGFYQVMIVMQKAYDRQY 490
                                    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

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

Fold: Periplasmic binding protein-like II (813)

Superfamily: Periplasmic binding protein-like II (813)

Family: Phosphate binding protein-like (463)

Protein domain: automated matches (76)

Sphingomonas sp. [TaxId: 90322] (5)

d1y3pa_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: D-Maltodextrin-Binding Protein; domain 2 (600)

Homologous Superfamily: Periplasmic binding protein-like II (486)

A1 (Sphingomonas sp) (5)

1a	1y3pA01	A:1-132,A:311-399
1b	1y3pA02	A:133-310,A:400-490

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PBP (391)

Family: SBP_bac_1 (83)

Sphingomonas sp (2)

SBP_bac_1-1y3pA01

A:33-343

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q9KWT6_SPHSX | Q9KWT6)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005215	transporter activity	Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ile A:311 - Pro A:312	[ RasMol ]

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UniProtKB/TrEMBL
	Q9KWT6_SPHSX \| Q9KWT6	:	1y3n 1y3q 3a09 3vlu 3vlv 3vlw

1j1n	ALGINATE-BINDING PROTEIN ALGQ2 COMPLEXED WITH AN ALGINATE TETRASACCHARIDE
1kwh	ALGINATE-BINDING PROTEIN ALGQ2
1y3n	THE SAME PROTEIN COMPLEXED WITH AN ALGINATE DISACCHARIDE
1y3q	THE SAME PROTEIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 1)

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