3K8M - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SUSG WITH ACARBOSE

Authors :   N. M. Koropatkin, T. J. Smith

Date :   14 Oct 09 (Deposition) - 02 Mar 10 (Release) - 02 Mar 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Amylase, Alpha8/Beta8 Barrel, Cbm, Beta-Sandwich, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. M. Koropatkin, T. J. Smith
Susg: A Unique Cell-Membrane-Associated Alpha-Amylase From A Prominent Human Gut Symbiont Targets Complex Starch Molecules.
Structure V. 18 200 2010
PubMed-ID: 20159465 | Reference-DOI: 10.1016/J.STR.2009.12.010

Molecule 1 - ALPHA-AMYLASE, SUSG
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-28RTEV
	Expression System Strain	:	ROSETTA(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BT_3698, SUSG
	Organism Scientific	:	BACTEROIDES THETAIOTAOMICRON
	Organism Taxid	:	818
	Strain	:	VPI-5482

		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 (6, 35)

No.	Name	Count	Type	Full Name
1	3SA	2	Ligand/Ion	ACARBOSE DERIVED TRISACCHARIDE
2	ACR	4	Ligand/Ion	ALPHA-ACARBOSE
3	CA	4	Ligand/Ion	CALCIUM ION
4	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
5	MAL	2	Ligand/Ion	MALTOSE
6	MSE	22	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (5, 16)

No.	Name	Count	Type	Full Name
1	3SA	1	Ligand/Ion	ACARBOSE DERIVED TRISACCHARIDE
2	ACR	2	Ligand/Ion	ALPHA-ACARBOSE
3	CA	-1	Ligand/Ion	CALCIUM ION
4	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
5	MAL	1	Ligand/Ion	MALTOSE
6	MSE	11	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (4, 15)

No.	Name	Count	Type	Full Name
1	3SA	1	Ligand/Ion	ACARBOSE DERIVED TRISACCHARIDE
2	ACR	2	Ligand/Ion	ALPHA-ACARBOSE
3	CA	-1	Ligand/Ion	CALCIUM ION
4	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
5	MAL	1	Ligand/Ion	MALTOSE
6	MSE	11	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:112 , TYR A:114 , HIS A:154 , PHE A:345 , ARG A:386 , ASP A:388 , GLU A:431 , HIS A:497 , ASP A:498 , ASP A:545 , ARG A:549 , MAL A:740	BINDING SITE FOR RESIDUE 3SA A 693
02	AC2	SOFTWARE	ASP A:73 , ASP A:75 , ASP A:77 , TYR A:79 , ASP A:81	BINDING SITE FOR RESIDUE CA A 700
03	AC3	SOFTWARE	ASN A:153 , ASP A:352 , HIS A:392 , ILE A:393 , HOH A:805 , HOH A:806 , HOH A:807	BINDING SITE FOR RESIDUE CA A 710
04	AC4	SOFTWARE	TYR A:260 , GLU A:263 , TRP A:287 , LEU A:290 , TRP A:299 , LYS A:304 , ASN A:330 , GLN B:210 , SER B:212 , ASP B:213	BINDING SITE FOR RESIDUE ACR A 720
05	AC5	SOFTWARE	ARG A:457 , TRP A:460 , TYR A:469 , LYS A:472 , ASP A:473	BINDING SITE FOR RESIDUE ACR A 730
06	AC6	SOFTWARE	ALA A:389 , LYS A:391 , HIS A:392 , GLU A:431 , LEU A:433 , ASP A:498 , 3SA A:693	BINDING SITE FOR RESIDUE MAL A 740
07	AC7	SOFTWARE	TYR A:203 , ALA A:205 , TRP A:208 , TYR A:340	BINDING SITE FOR RESIDUE EDO A 750
08	AC8	SOFTWARE	HIS B:112 , TYR B:114 , HIS B:154 , PHE B:345 , ARG B:386 , ASP B:388 , HIS B:497 , ASP B:498 , GLY B:544 , ASP B:545 , ARG B:549 , MAL B:840	BINDING SITE FOR RESIDUE 3SA B 693
09	AC9	SOFTWARE	ASP B:73 , ASP B:75 , ASP B:77 , TYR B:79 , ASP B:81	BINDING SITE FOR RESIDUE CA B 800
10	BC1	SOFTWARE	ASN B:153 , ASP B:352 , HIS B:392 , ILE B:393	BINDING SITE FOR RESIDUE CA B 810
11	BC2	SOFTWARE	GLN A:210 , SER A:212 , ASP A:213 , TYR B:260 , TRP B:287 , LEU B:290 , TRP B:299 , LYS B:304 , ASN B:330 , HOH B:729	BINDING SITE FOR RESIDUE ACR B 820
12	BC3	SOFTWARE	TYR B:456 , ARG B:457 , TRP B:460 , TYR B:469 , LYS B:472 , ASP B:473	BINDING SITE FOR RESIDUE ACR B 830
13	BC4	SOFTWARE	LYS B:391 , HIS B:392 , GLU B:431 , LEU B:433 , ASP B:498 , 3SA B:693	BINDING SITE FOR RESIDUE MAL B 840

(no "SS Bond" information available for 3K8M)

(no "Cis Peptide Bond" information available for 3K8M)

(no "SAP(SNP)/Variant" information available for 3K8M)

(no "PROSITE Motif" information available for 3K8M)

(no "Exon" information available for 3K8M)

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:650
 aligned with SUSG_BACTN | Q8A1G3 from UniProtKB/Swiss-Prot  Length:692

    Alignment length:650
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692
           SUSG_BACTN    43 QWTALTASPDTWDETKRADISYQLLLYSFADSDGDGYGDLNGVTQKLDYLNQLGVKALWLSPIHPCMSYHGYDVTDYTKVNPQLGTESDFDRLVTEAHNRGIKIYLDYVMNHTGTAHPWFTEASSSSESPYRNYYSFSEDPKTDIAAGKIAMITQEGAAGYNAAEWFQVSDETAAVKGLLKFTLDWSNAPSPILVVSTGTKADEDNPDTGTDNAKYLYYGEDICKKFYDKGNNIYELTVDFESTWGLLIRTSNASFWPSGTKYGASSSSEKLALNKDFKLTNAGNPANIMFDSQQITYFHSHFCTDWFADLNYGPVDQAGESPAYQAIADAAKGWIARGVDGLRLDAVKHIYHSETSEENPRFLKMFYEDMNAYYKQKGHTDDFYMIGEVLSEYDKVAPYYKGLPALFEFSFWYRLEWGINNSTGCYFAKDILSYQQKYANYRSDYIEATKLSNHDEDRTSSKLGKSADKCKLAAAVLLTSAGHPYIYYGEELGLYGTKDNGDEYVRSPMLWGDSYTTNYTDKTDATVSKNVKTVADQQADTHSLLNIYFSLTRLRNTYPALAEGNMTKHSVYNESQEKDYKPIAAWYMTKDNEKLLVIHNFGGTAMQLPLTDKIEKVLFVNGETQQNTDSDSYTLKLGGYASVVFKLGN 692
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee................eeee..............hhhhhhhhhhhhhhh...eeee.........................hhhhhhhhhhhhhhh..eeeeee...eee..hhhhhhhh......hhhhh.ee.hhhhhhhh..hhhhh.hhhhhhhhh.eee.......eeeeeeeeee.......eeeeee.................eeee...eeee.ee....eeeeeeeeee...eeee...........ee.......ee.....ee..........ee......eee.......eee....hhhhhhhhhhhhhhhhhhhhhhh....eeee.hhhhh......hhhhhhhhhhhhhhhhhhhh.......eeee....hhhhhhhhhhh..eeehhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.....eee.........hhhhhh..hhhhhhhhhhhhhh.....eee.............hhhhhh..................hhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.eeee....hhhhh.....eeeeeeee..eeeeeeee.....eeeee...eeeeeeee..eeeee....eeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k8m A  43 QWTALTASPDTWDETKRADISYQLLLYSFADSDGDGYGDLNGVTQKLDYLNQLGVKALWLSPIHPCmSYHGYDVTDYTKVNPQLGTESDFDRLVTEAHNRGIKIYLDYVmNHTGTAHPWFTEASSSSESPYRNYYSFSEDPKTDIAAGKIAmITQEGAAGYNAAEWFQVSDETAAVKGLLKFTLDWSNAPSPILVVSTGTKADEDNPDTGTDNAKYLYYGEDICKKFYDKGNNIYELTVDFESTWGLLIRTSNASFWPSGTKYGASSSSEKLALNKDFKLTNAGNPANImFDSQQITYFHSHFCTDWFADLNYGPVDQAGESPAYQAIADAAKGWIARGVDGLRLDAVKHIYHSETSEENPRFLKmFYEDmNAYYKQKGHTDDFYmIGEVLSEYDKVAPYYKGLPALFEFSFWYRLEWGINNSTGCYFAKDILSYQQKYANYRSDYIEATKLSNHDEDRTSSKLGKSADKCKLAAAVLLTSAGHPYIYYGEELGLYGTKDNGDEYVRSPmLWGDSYTTNYTDKTDATVSKNVKTVADQQADTHSLLNIYFSLTRLRNTYPALAEGNmTKHSVYNESQEKDYKPIAAWYmTKDNEKLLVIHNFGGTAmQLPLTDKIEKVLFVNGETQQNTDSDSYTLKLGGYASVVFKLGN 692
                                    52        62        72        82        92       102      |112       122       132       142       152       162       172       182       192 |     202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402     | 412|      422     | 432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602      |612       622       632       642      |652       662       672       682       692
                                                                                            109-MSE                                    152-MSE                                   194-MSE                                                                                                                                   332-MSE                                                                     408-MSE|            428-MSE                                                                                                                     552-MSE                                                  609-MSE               631-MSE           649-MSE                                       
                                                                                                                                                                                                                                                                                                                                                                                                            413-MSE

Chain B from PDB  Type:PROTEIN  Length:646
 aligned with SUSG_BACTN | Q8A1G3 from UniProtKB/Swiss-Prot  Length:692

    Alignment length:650
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692
           SUSG_BACTN    43 QWTALTASPDTWDETKRADISYQLLLYSFADSDGDGYGDLNGVTQKLDYLNQLGVKALWLSPIHPCMSYHGYDVTDYTKVNPQLGTESDFDRLVTEAHNRGIKIYLDYVMNHTGTAHPWFTEASSSSESPYRNYYSFSEDPKTDIAAGKIAMITQEGAAGYNAAEWFQVSDETAAVKGLLKFTLDWSNAPSPILVVSTGTKADEDNPDTGTDNAKYLYYGEDICKKFYDKGNNIYELTVDFESTWGLLIRTSNASFWPSGTKYGASSSSEKLALNKDFKLTNAGNPANIMFDSQQITYFHSHFCTDWFADLNYGPVDQAGESPAYQAIADAAKGWIARGVDGLRLDAVKHIYHSETSEENPRFLKMFYEDMNAYYKQKGHTDDFYMIGEVLSEYDKVAPYYKGLPALFEFSFWYRLEWGINNSTGCYFAKDILSYQQKYANYRSDYIEATKLSNHDEDRTSSKLGKSADKCKLAAAVLLTSAGHPYIYYGEELGLYGTKDNGDEYVRSPMLWGDSYTTNYTDKTDATVSKNVKTVADQQADTHSLLNIYFSLTRLRNTYPALAEGNMTKHSVYNESQEKDYKPIAAWYMTKDNEKLLVIHNFGGTAMQLPLTDKIEKVLFVNGETQQNTDSDSYTLKLGGYASVVFKLGN 692
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee................eeee..............hhhhhhhhhhhhhh....eeee.........................hhhhhhhhhhhhhhh..eeeeee...eee..hhhhhhhh.....hhhhhh.ee.hhhhhhhh..............hhh.eee.......eeeeeeeeee.......eeeeee.................eeee...eeee.ee....eeeeeeeeee...eeee...........ee.......ee.....ee..........ee......eee.......eee....hhhhhhhhhhhhhhhhhhhhhhh....eeee.............hhhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhh..eeeehhhhhhhhhhhhh....hhhhhhhhhhhhhhh.....eeeee.......hhhhhh..hhhhhhhhhhhhhh...eeeee.............hhhhhhh.................hhhhh...hhhhhh....hhhhhhhhhhhhhh.hhhhhh.eeee....hhhhh.....eeeeeeee..eeeeeeee.....eeee....eeeeeeee..eeee.----.eeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k8m B  43 QWTALTASPDTWDETKRADISYQLLLYSFADSDGDGYGDLNGVTQKLDYLNQLGVKALWLSPIHPCmSYHGYDVTDYTKVNPQLGTESDFDRLVTEAHNRGIKIYLDYVmNHTGTAHPWFTEASSSSESPYRNYYSFSEDPKTDIAAGKIAmITQEGAAGYNAAEWFQVSDETAAVKGLLKFTLDWSNAPSPILVVSTGTKADEDNPDTGTDNAKYLYYGEDICKKFYDKGNNIYELTVDFESTWGLLIRTSNASFWPSGTKYGASSSSEKLALNKDFKLTNAGNPANImFDSQQITYFHSHFCTDWFADLNYGPVDQAGESPAYQAIADAAKGWIARGVDGLRLDAVKHIYHSETSEENPRFLKmFYEDmNAYYKQKGHTDDFYmIGEVLSEYDKVAPYYKGLPALFEFSFWYRLEWGINNSTGCYFAKDILSYQQKYANYRSDYIEATKLSNHDEDRTSSKLGKSADKCKLAAAVLLTSAGHPYIYYGEELGLYGTKDNGDEYVRSPmLWGDSYTTNYTDKTDATVSKNVKTVADQQADTHSLLNIYFSLTRLRNTYPALAEGNmTKHSVYNESQEKDYKPIAAWYmTKDNEKLLVIHNFGGTAmQLPLTDKIEKVLFVNGETQQNT----YTLKLGGYASVVFKLGN 692
                                    52        62        72        82        92       102      |112       122       132       142       152       162       172       182       192 |     202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402     | 412|      422     | 432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602      |612       622       632       642      |652       662        |-   |   682       692
                                                                                            109-MSE                                    152-MSE                                   194-MSE                                                                                                                                   332-MSE                                                                     408-MSE|            428-MSE                                                                                                                     552-MSE                                                  609-MSE               631-MSE           649-MSE               671  676                
                                                                                                                                                                                                                                                                                                                                                                                                            413-MSE

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 3K8M)

(no "CATH Domain" information available for 3K8M)

(no "Pfam Domain" information available for 3K8M)

Asymmetric Unit(hide GO term definitions)

Chain A,B (SUSG_BACTN | Q8A1G3)

molecular function
	GO:0004556	alpha-amylase activity	Catalysis of the endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more alpha-(1->4)-linked D-glucose units.
	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: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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:2001070	starch binding	Interacting selectively and non-covalently with starch.
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: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:0000272	polysaccharide catabolic process	The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
	GO:0005983	starch catabolic process	The chemical reactions and pathways resulting in the breakdown of starch, the most important reserve polysaccharide in plants.
cellular component
	GO:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019867	outer membrane	The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.

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	Cis Peptide Bonds
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	3k8m
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	SUSG_BACTN \| Q8A1G3	:	3k8k 3k8l

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 35)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Gene Ontology (15, 15)

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