3OO9 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURES AND BIOCHEMICAL CHARACTERIZATION OF THE BACTERIAL SOLUTE RECEPTOR ACBH REVEAL AN UNPRECEDENTED EXCLUSIVE SUBSTRATE PREFERENCE FOR B-D-GALACTOPYRANOSE

Authors :   A. Vahedi-Faridi, H. Bulut, A. Licht

Date :   30 Aug 10 (Deposition) - 29 Dec 10 (Release) - 26 Mar 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.76

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

Keywords :   Class 2 Sbp Fold, Abc Transporter Extracellular Solute Binding Protein, D-Galactose Binding, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Licht, H. Bulut, F. Scheffel, O. Daumke, U. F. Wehmeier, W. Saenger, E. Schneider, A. Vahedi-Faridi
Crystal Structures Of The Bacterial Solute Receptor Acbh Displaying An Exclusive Substrate Preference For Beta-D-Galactopyranose
J. Mol. Biol. V. 406 92 2011
PubMed-ID: 21168419 | Reference-DOI: 10.1016/J.JMB.2010.11.048

Molecule 1 - ABC TRANSPORTER BINDING PROTEIN ACBH
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PAL55, PET15B
	Expression System Strain	:	ROSETTA2
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUE IN UNP 39-433
	Gene	:	ACBH
	Mutation	:	YES
	Organism Scientific	:	ACTINOPLANES
	Organism Taxid	:	134676
	Strain	:	SE50/110

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 25)

No.	Name	Count	Type	Full Name
1	GOL	8	Ligand/Ion	GLYCEROL
2	SO4	17	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 11)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	SO4	9	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 14)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL
2	SO4	8	Ligand/Ion	SULFATE ION

Asymmetric Unit (25, 25)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:227 , GLY A:228 , HOH A:500 , HOH A:555 , HOH A:560 , HOH A:727 , HOH A:768 , HOH A:802 , LYS B:227 , GLY B:228	BINDING SITE FOR RESIDUE SO4 A 405
02	AC2	SOFTWARE	GLN A:226 , ARG A:232 , HOH A:661 , HOH A:786 , HOH A:844	BINDING SITE FOR RESIDUE SO4 A 406
03	AC3	SOFTWARE	LYS A:31 , HOH A:486 , HOH A:580 , HOH A:818	BINDING SITE FOR RESIDUE SO4 A 407
04	AC4	SOFTWARE	THR A:93 , LYS A:296 , ALA A:301 , HOH A:748 , HOH A:810	BINDING SITE FOR RESIDUE SO4 A 408
05	AC5	SOFTWARE	HIS A:325 , TRP A:326 , HOH A:718 , HOH A:820	BINDING SITE FOR RESIDUE SO4 A 409
06	AC6	SOFTWARE	TRP A:234 , GLN A:235 , HOH A:492	BINDING SITE FOR RESIDUE SO4 A 410
07	AC7	SOFTWARE	ASN A:57 , ASN A:61 , ASP A:269 , LYS A:345 , HOH A:481 , HOH A:845 , HOH A:996	BINDING SITE FOR RESIDUE SO4 A 411
08	AC8	SOFTWARE	ARG A:159 , HOH B:791 , HOH B:966	BINDING SITE FOR RESIDUE SO4 A 412
09	AC9	SOFTWARE	SER A:261 , ALA A:262 , HOH A:473	BINDING SITE FOR RESIDUE SO4 A 413
10	BC1	SOFTWARE	TYR A:129 , TRP A:131 , TRP A:177 , GLN A:255 , PHE A:359 , HOH A:791	BINDING SITE FOR RESIDUE GOL A 414
11	BC2	SOFTWARE	ASP A:27 , GLU A:28 , HOH A:654 , HOH A:676	BINDING SITE FOR RESIDUE GOL A 415
12	BC3	SOFTWARE	LYS B:115 , TYR B:121	BINDING SITE FOR RESIDUE SO4 B 405
13	BC4	SOFTWARE	HIS B:56 , GLN B:60 , LYS B:362	BINDING SITE FOR RESIDUE SO4 B 406
14	BC5	SOFTWARE	ARG A:219 , ARG B:232 , HOH B:786 , HOH B:959	BINDING SITE FOR RESIDUE SO4 B 407
15	BC6	SOFTWARE	LYS B:299 , ASN B:300 , HOH B:962	BINDING SITE FOR RESIDUE SO4 B 408
16	BC7	SOFTWARE	ARG B:159	BINDING SITE FOR RESIDUE SO4 B 409
17	BC8	SOFTWARE	SER B:261 , ALA B:262 , HOH B:429 , HOH B:535	BINDING SITE FOR RESIDUE SO4 B 410
18	BC9	SOFTWARE	ASN B:57 , ASN B:61 , ASP B:269 , LYS B:345 , HOH B:667 , HOH B:816 , HOH B:874 , HOH B:997	BINDING SITE FOR RESIDUE SO4 B 411
19	CC1	SOFTWARE	LYS B:31 , HOH B:484	BINDING SITE FOR RESIDUE SO4 B 412
20	CC2	SOFTWARE	GLN B:84 , ALA B:88 , GLY B:116 , LEU B:117 , ASP B:118 , HOH B:654	BINDING SITE FOR RESIDUE GOL B 413
21	CC3	SOFTWARE	GLN A:162 , VAL A:167 , GLN B:162 , TYR B:224	BINDING SITE FOR RESIDUE GOL B 414
22	CC4	SOFTWARE	TYR B:193 , ASP B:194 , TYR B:280 , TYR B:284 , HOH B:510 , HOH B:950	BINDING SITE FOR RESIDUE GOL B 415
23	CC5	SOFTWARE	LYS B:160 , GLN B:377 , ASP B:381 , HOH B:588 , HOH B:778	BINDING SITE FOR RESIDUE GOL B 416
24	CC6	SOFTWARE	TRP B:177 , GOL B:418 , HOH B:986	BINDING SITE FOR RESIDUE GOL B 417
25	CC7	SOFTWARE	TYR B:129 , TRP B:131 , TRP B:177 , GLN B:255 , PHE B:359 , ASP B:361 , GOL B:417	BINDING SITE FOR RESIDUE GOL B 418

(no "SS Bond" information available for 3OO9)

(no "Cis Peptide Bond" information available for 3OO9)

(no "SAP(SNP)/Variant" information available for 3OO9)

(no "PROSITE Motif" information available for 3OO9)

(no "Exon" information available for 3OO9)

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:395
 aligned with Q27GR2_ACTS5 | Q27GR2 from UniProtKB/TrEMBL  Length:433

    Alignment length:395
                                    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     
         Q27GR2_ACTS5    39 TSVSDGNGPITFGSNYSDEAPKAAFASLMQQATTSTTVPVTVNTTDHNTFQNNISNYLQGTPDSLATWFAGYRLQFFAAQGLLTPIDDVWDKIGGTFNDAAKSLSKGLDGHYYLVPLYNYPWVVFYNKSVFQSKGYEVPASWEAFIALARKMQSDGLVPLAFADKDGWPALGTFDILNLRINGYDYHIKLMKHEVPWTDPGVTKVFDQWRELAAYQQKGANGRTWQDAAKALENKQAGMMFQGSNQVAANYSAKNLPDLDFFVFPAINPQYGTDYMDAPTDGFILPKKGKNAAAAKKVLQYIGTAEAEAAFLKTDHWDVGLANGLIAPTYNDIQKKSVAEIGKCKSVSQFMDRDTVPDMANAMIKLIQQFIDQPTPETIATVQKSAEDQAKTIFR 433
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...eeeee...hhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh........eeeeee..eeeeeehhhhhhhh.....hhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..eeeeeeehhhhhhhh...hhh.eeee............eee...eeee......hhhhhhhhhhhhhhhhhhhhhhhhh...ee..........hhhhhhhhhhhhhh.eee.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oo9 A  10 MSVSDGNGPITFGSNYSDEAPKAAFASLMQQATTSTTVPVTVNTTDHNTFQNNISNYLQGTPDSLATWFAGYRLQFFAAQGLLTPIDDVWDKIGGTFNDAAKSLSKGLDGHYYLVPLYNYPWVVFYNKSVFQSKGYEVPASWEAFIALARKMQSDGLVPLAFADKDGWPALGTFDILNLRINGYDYHIKLMKHEVPWTDPGVTKVFDQWRELAAYQQKGANGRTWQDAAKALENKQAGMMFQGSNQVAANYSAKNLPDLDFFVFPAINPQYGTDYMDAPTDGFILPKKGKNAAAAKKVLQYIGTAEAEAAFLKTDHWDVGLANGLIAPTYNDIQKKSVAEIGKCKSVSQFMDKDTVPDMANAMIKLIQQFIDQPTPETIATVQKSAEDQAKTIFR 404
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399

Chain B from PDB  Type:PROTEIN  Length:395
 aligned with Q27GR2_ACTS5 | Q27GR2 from UniProtKB/TrEMBL  Length:433

    Alignment length:395
                                    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     
         Q27GR2_ACTS5    39 TSVSDGNGPITFGSNYSDEAPKAAFASLMQQATTSTTVPVTVNTTDHNTFQNNISNYLQGTPDSLATWFAGYRLQFFAAQGLLTPIDDVWDKIGGTFNDAAKSLSKGLDGHYYLVPLYNYPWVVFYNKSVFQSKGYEVPASWEAFIALARKMQSDGLVPLAFADKDGWPALGTFDILNLRINGYDYHIKLMKHEVPWTDPGVTKVFDQWRELAAYQQKGANGRTWQDAAKALENKQAGMMFQGSNQVAANYSAKNLPDLDFFVFPAINPQYGTDYMDAPTDGFILPKKGKNAAAAKKVLQYIGTAEAEAAFLKTDHWDVGLANGLIAPTYNDIQKKSVAEIGKCKSVSQFMDRDTVPDMANAMIKLIQQFIDQPTPETIATVQKSAEDQAKTIFR 433
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------SBP_bac_1-3oo9B01 B:23-318                                                                                                                                                                                                                                                                              -------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------SBP_bac_1-3oo9B02 B:23-318                                                                                                                                                                                                                                                                              -------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhh...eeeee...hhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh........eeeeee..eeeeeehhhhhhhh.....hhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..eeeeeeehhhhhhhh...hhh.eeee............eee..eeeee......hhhhhhhhhhhhhhhhhhhhhhh.....ee..........hhhhhhhhhhhhhh.eee.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oo9 B  10 MSVSDGNGPITFGSNYSDEAPKAAFASLMQQATTSTTVPVTVNTTDHNTFQNNISNYLQGTPDSLATWFAGYRLQFFAAQGLLTPIDDVWDKIGGTFNDAAKSLSKGLDGHYYLVPLYNYPWVVFYNKSVFQSKGYEVPASWEAFIALARKMQSDGLVPLAFADKDGWPALGTFDILNLRINGYDYHIKLMKHEVPWTDPGVTKVFDQWRELAAYQQKGANGRTWQDAAKALENKQAGMMFQGSNQVAANYSAKNLPDLDFFVFPAINPQYGTDYMDAPTDGFILPKKGKNAAAAKKVLQYIGTAEAEAAFLKTDHWDVGLANGLIAPTYNDIQKKSVAEIGKCKSVSQFMDKDTVPDMANAMIKLIQQFIDQPTPETIATVQKSAEDQAKTIFR 404
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399

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 3OO9)

(no "CATH Domain" information available for 3OO9)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PBP (391)

Family: SBP_bac_1 (83)

Actinoplanes sp. (strain 50/110) (5)

1a	SBP_bac_1-3oo9B01	B:23-318
1b	SBP_bac_1-3oo9B02	B:23-318

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q27GR2_ACTS5 | Q27GR2)

molecular function
	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: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: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.
	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.
	GO:0045493	xylan catabolic process	The chemical reactions and pathways resulting in the breakdown of xylan, a polymer containing a beta-1,4-linked D-xylose backbone.

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Description

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Ligands, Modified Residues, Ions (2, 25)

Sites (25, 25)

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