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(-) Description

Title :  B. THETAIOTAOMICRON SUSD WITH MALTOTRIOSE
 
Authors :  N. M. Koropatkin, E. C. Martens, J. I. Gordon, T. J. Smith
Date :  14 Mar 08  (Deposition) - 01 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Tpr Repeat, Carbohydrate Binding, Starch Binding, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. M. Koropatkin, E. C. Martens, J. I. Gordon, T. J. Smith
Starch Catabolism By A Prominent Human Gut Symbiont Is Directed By The Recognition Of Amylose Helices.
Structure V. 16 1105 2008
PubMed-ID: 18611383  |  Reference-DOI: 10.1016/J.STR.2008.03.017

(-) Compounds

Molecule 1 - SUSD
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-28A
    Expression System StrainROSETTA(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 26-551
    GeneSUSD
    Organism ScientificBACTEROIDES THETAIOTAOMICRON
    Organism Taxid226186
    StrainVPI-5482

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2MLR2Ligand/IonMALTOTRIOSE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MLR1Ligand/IonMALTOTRIOSE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MLR1Ligand/IonMALTOTRIOSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:273 , GLN A:288 , ASP A:430 , ASP A:432BINDING SITE FOR RESIDUE CA A 600
2AC2SOFTWAREASP B:273 , GLN B:288 , ASP B:430 , ASP B:432BINDING SITE FOR RESIDUE CA B 700
3AC3SOFTWAREASP A:73 , GLU A:74 , TRP A:96 , TRP A:98 , ASN A:101 , ASN A:295 , TRP A:320 , CYS A:322BINDING SITE FOR RESIDUE MLR A 903
4AC4SOFTWAREGLN A:240 , ASP B:73 , GLU B:74 , TRP B:98 , ASN B:101 , ASN B:318 , TRP B:320 , CYS B:322BINDING SITE FOR RESIDUE MLR B 904

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3CKB)

(-) Sequences/Alignments

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:504
 aligned with SUSD_BACTN | Q8A1G2 from UniProtKB/Swiss-Prot  Length:551

    Alignment length:511
                                    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 
           SUSD_BACTN    41 SFDQQGVFVKGYAMLGVTGQKGIDGSPDLDGQDEGESGFYRTTFNCNELPTDECLWAWQENQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWSCIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK 551
               SCOP domains d3ckba_ A: Starch u       tilization system protein SusD                                                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------3ckbA02 A:210-307,A:412-490  [code=1.25.40.10, no name defined]                                   3ckbA03 A:308-411 SusD-like                                                                             3ckbA02 A:210-307,A:412-490  [code=1.25.40.10, no name defined]                ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.....-------...........hhhhhhhhhhhh....eee......hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhheeee.........eeeehhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh......hhhhhhh.....hhhhhh.eeeee..hhhhhh..hhhhhhhhh.................eeehhhhhh....hhhhh...............hhhhhhhhhhhh..hhhhhhhhhh.....ee................hhhhh.ee......................eeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhh.........hhhhhhhhhhhhhh...hhhhhhhhh...........hhhhh......hhhhhh...hhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ckb A  41 SFDQQGVFVKGYAMLGVTG-------PDLDGQDEGESGFYRTTFNCNELPTDECLWAWQKNQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWSCIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK 551
                                    50        |-      | 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 
                                             59      67                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:501
 aligned with SUSD_BACTN | Q8A1G2 from UniProtKB/Swiss-Prot  Length:551

    Alignment length:511
                                    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 
           SUSD_BACTN    41 SFDQQGVFVKGYAMLGVTGQKGIDGSPDLDGQDEGESGFYRTTFNCNELPTDECLWAWQENQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWSCIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK 551
               SCOP domains d3ckbb_ B: Starch u          tilization system protein SusD                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------3ckbB02 B:210-307,B:412-490  [code=1.25.40.10, no name defined]                                   3ckbB03 B:308-411 SusD-like                                                                             3ckbB02 B:210-307,B:412-490  [code=1.25.40.10, no name defined]                ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh..----------........hhhhhhhhhhhh....eee......hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhheeee.........eeeehhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhh.....hhhhhh.eeeee..........hhhhhhhhh.................eeehhhhhh....hhhhh...............hhhhhhhhhhhh..hhhhhhhhhh.....ee................hhhhh.ee......................eeeeehhhhhhhhhhhhhhh...hhhhhhhhhhhh.........hhhhhhhhhhhhhh...hhhhhhhhh...........hhhhh......hhhhhh...hhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ckb B  41 SFDQQGVFVKGYAMLGVTG----------DGQDEGESGFYRTTFNCNELPTDECLWAWQKNQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWSCIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK 551
                                    50        |-        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 
                                             59         70                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit

(-) CATH Domains  (2, 4)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SUSD_BACTN | Q8A1G2)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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:0005983    starch catabolic process    The chemical reactions and pathways resulting in the breakdown of starch, the most important reserve polysaccharide in plants.
    GO:0005982    starch metabolic process    The chemical reactions and pathways involving starch, the most important reserve polysaccharide in plants. It is a glucan consisting of two components, amylose and amylopectin, which are both glucose homopolymers. Starch is synthesized as a temporary storage form of carbon and can be catabolized to produce sucrose.
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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SUSD_BACTN | Q8A1G23ck7 3ck8 3ck9 3ckc

(-) Related Entries Specified in the PDB File

3ck7 B. THETAIOTAOMICRON SUSD WITH ALPHA-CYCLODEXTRIN
3ck8 B. THETAIOTAOMICRON SUSD WITH BETA-CYCLODEXTRIN
3ck9 B. THETAIOTAOMICRON SUSD WITH MALTOHEPTAOSE
3ckc B. THETAIOTAOMICRON SUSD