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(-) Description

Title :  GLYCOSIDE HYDROLASE FAMILY 76 (MANNOSIDASE) BT3792 FROM BACTEROIDES THETAIOTAOMICRON VPI-5482
 
Authors :  F. Cuskin, E. C. Lowe, Y. Zhu, M. Temple, A. J. Thompson, A. Cartmell, K. P D. Bracke, W. Vervecken, J. L. Munoz-Munoz, M. D. L. Suits, A. B. Borast S. J. Williams, G. J. Davies, W. D. Abbott, E. C. Martens, H. J. Gilbert
Date :  13 Aug 13  (Deposition) - 13 Nov 13  (Release) - 04 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Gut Microbiota (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Cuskin, E. C. Lowe, M. J. Temple, Y. Zhu, E. A. Cameron, N. A. Pudlo, N. T. Porter, K. Urs, A. J. Thompson, A. Cartmell, A. Rogowski, B. S. Hamilton, R. Chen, T. J. Tolbert, K. Piens, D. Bracke, W. Vervecken, Z. Hakki, G. Speciale, J. L. Munoz-Munoz, A. Day, M. J. Pena, R. Mclean, M. D. Suits, A. B. Boraston, T. Atherly, C. J. Ziemer, S. J. Williams, G. J. Davies, D. W. Abbott, E. C. Martens, H. J. Gilbert
Human Gut Bacteroidetes Can Utilize Yeast Mannan Through A Selfish Mechanism.
Nature V. 517 165 2015
PubMed-ID: 25567280  |  Reference-DOI: 10.1038/NATURE13995

(-) Compounds

Molecule 1 - GLYCOSIDE HYDROLASE FAMILY 76 MANNOSIDASE
    Chains: A, B
    EC Number: 3.2.1.101
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28A
    Expression System Vector Type: PLASMID
    Fragment: ENZYMATIC FRAGMENT, RESIDUES 155-525
    Gene: BT3792
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON VPI-5482
    Organism Taxid: 226186
    Other Details: BT3792 GENE FRAGMENT ENCODING RESIDUES 155- 514

 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, 15)

Asymmetric Unit (2, 15)
No.NameCountTypeFull Name
1EDO13Ligand/Ion1,2-ETHANEDIOL
2GOL2Ligand/IonGLYCEROL
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1EDO9Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:439 , GLY A:441 , ALA A:443 , ASN A:446 , ASP A:490 , ASP A:491 , HOH A:2127 , HOH A:2130BINDING SITE FOR RESIDUE EDO A1526
02AC2SOFTWAREALA B:439 , GLY B:441 , ALA B:443 , ASN B:446 , ASP B:490 , ASP B:491 , HOH B:2112 , HOH B:2116BINDING SITE FOR RESIDUE EDO B1526
03AC3SOFTWAREPHE A:169 , SER A:175 , CYS A:176 , TRP A:177 , GLN A:198 , MET A:227 , MET A:228 , GLY A:231 , ILE A:232 , HOH A:2005BINDING SITE FOR RESIDUE EDO A1527
04AC4SOFTWARECYS B:176 , TRP B:177 , GLN B:198 , LEU B:202 , MET B:228 , GLY B:231 , ILE B:232 , HOH B:2006BINDING SITE FOR RESIDUE EDO B1527
05AC5SOFTWAREGLY A:197 , LEU A:505 , HOH A:2007 , HOH A:2013BINDING SITE FOR RESIDUE EDO A1528
06AC6SOFTWAREGLY A:300 , TYR A:349 , ASP A:352 , VAL A:353 , HOH A:2082BINDING SITE FOR RESIDUE EDO A1529
07AC7SOFTWAREARG A:516 , VAL A:519 , LEU A:520 , HOH A:2133BINDING SITE FOR RESIDUE EDO A1530
08AC8SOFTWARETRP A:305 , HIS A:316 , CYS A:318 , ASP A:364 , HOH A:2094BINDING SITE FOR RESIDUE EDO A1531
09AC9SOFTWAREMET A:277 , THR A:281 , HOH A:2036 , HOH A:2148 , THR B:281BINDING SITE FOR RESIDUE EDO A1532
10BC1SOFTWARELYS B:329 , GLN B:393 , ARG B:451 , GLU B:455 , ARG B:516 , HOH B:2040BINDING SITE FOR RESIDUE EDO B1528
11BC2SOFTWARELYS A:421BINDING SITE FOR RESIDUE EDO A1533
12BC3SOFTWAREASP A:269 , LYS A:329 , GLN A:393 , ARG A:451 , GLU A:455 , ARG A:516BINDING SITE FOR RESIDUE EDO A1534
13BC4SOFTWARETRP B:305 , HIS B:316 , CYS B:318 , ASP B:364 , HOH B:2058 , HOH B:2080BINDING SITE FOR RESIDUE EDO B1529
14BC5SOFTWAREPHE A:256 , ASP A:258 , ASP A:259 , TRP A:305BINDING SITE FOR RESIDUE GOL A1535
15BC6SOFTWAREASP B:258 , ASP B:259 , TRP B:305 , HOH B:2011BINDING SITE FOR RESIDUE GOL B1530

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C1S)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:181 -Pro A:182
2Leu A:308 -Asn A:309
3Tyr B:181 -Pro B:182
4Leu B:308 -Asn B:309

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C1S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C1S)

(-) Exons   (0, 0)

(no "Exon" information available for 4C1S)

(-) 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:375
 aligned with Q8A174_BACTN | Q8A174 from UniProtKB/TrEMBL  Length:525

    Alignment length:375
                                   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     
         Q8A174_BACTN   151 PEMLDRAHSYMTSVIGYYFGKSSRSCWRSNYPYDGKGYWDGDALVWGQGGGLSAFVAMRDATKESEVENLYGAMDDMMFKGIQYFCQLDRGILAYSCYPAAGNERFYDDNVWIGLDMVDWYTETKEMRYLTQAKVVWRYLIDHGWDETCGGGVHWRELNEHTTSKHSCSTGPTAVMGCKMYLATQEQEYLDWAIKCYDYMLDVLQDKSDHLFYDNVRPNKDDPNLPGDLEKNKYSYNSGQPLQAACLLYKITGEQKYLDEAYAIAESCHKKWFMPYRSKELNLTFNILAPGHAWFNTIMCRGFFELYSIDNDRKYIDDIEKSMIHAWSSSCHQGNNLLNDDDLRGGTTKTGWEILHQGALVELYARLAVLERENR 525
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh..........ee.....hhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.eeee..eeee.........eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh....eee......eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeee.......eeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeee....eeeeee...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......................eehhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c1s A 151 SHMADRAHSYMTSVIGYYFGKSSRSCWRSNYPYDGKGYWDGDALVWGQGGGLSAFVAMRDATKESEVENLYGAMDDMMFKGIQYFCQLDRGILAYSCYPAAGNERFYDDNVWIGLDMVDWYTETKEMRYLTQAKVVWRYLIDHGWDETCGGGVHWRELNEHTTSKHSCSTGPTAVMGCKMYLATQEQEYLDWAIKCYDYMLDVLQDKSDHLFYDNVRPNKDDPNLPGDLEKNKYSYNSGQPLQAACLLYKITGEQKYLDEAYAIAESCHKKWFMPYRSKELNLTFNILAPGHAWFNTIMCRGFFELYSIDNDRKYIDDIEKSMIHAWSSSCHQGNNLLNDDDLRGGTTKTGWEILHQGALVELYARLAVLERENR 525
                                   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     


Chain B from PDB  Type:PROTEIN  Length:375
 aligned with Q8A174_BACTN | Q8A174 from UniProtKB/TrEMBL  Length:525

    Alignment length:375
                                   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     
         Q8A174_BACTN   151 PEMLDRAHSYMTSVIGYYFGKSSRSCWRSNYPYDGKGYWDGDALVWGQGGGLSAFVAMRDATKESEVENLYGAMDDMMFKGIQYFCQLDRGILAYSCYPAAGNERFYDDNVWIGLDMVDWYTETKEMRYLTQAKVVWRYLIDHGWDETCGGGVHWRELNEHTTSKHSCSTGPTAVMGCKMYLATQEQEYLDWAIKCYDYMLDVLQDKSDHLFYDNVRPNKDDPNLPGDLEKNKYSYNSGQPLQAACLLYKITGEQKYLDEAYAIAESCHKKWFMPYRSKELNLTFNILAPGHAWFNTIMCRGFFELYSIDNDRKYIDDIEKSMIHAWSSSCHQGNNLLNDDDLRGGTTKTGWEILHQGALVELYARLAVLERENR 525
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh..........ee.....hhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.eeee..eeee.........eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh....eee......eehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..........eeee.......eeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeee....eeeeee...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.......................eehhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c1s B 151 SHMADRAHSYMTSVIGYYFGKSSRSCWRSNYPYDGKGYWDGDALVWGQGGGLSAFVAMRDATKESEVENLYGAMDDMMFKGIQYFCQLDRGILAYSCYPAAGNERFYDDNVWIGLDMVDWYTETKEMRYLTQAKVVWRYLIDHGWDETCGGGVHWRELNEHTTSKHSCSTGPTAVMGCKMYLATQEQEYLDWAIKCYDYMLDVLQDKSDHLFYDNVRPNKDDPNLPGDLEKNKYSYNSGQPLQAACLLYKITGEQKYLDEAYAIAESCHKKWFMPYRSKELNLTFNILAPGHAWFNTIMCRGFFELYSIDNDRKYIDDIEKSMIHAWSSSCHQGNNLLNDDDLRGGTTKTGWEILHQGALVELYARLAVLERENR 525
                                   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
   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  (0, 0)

(no "SCOP Domain" information available for 4C1S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C1S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C1S)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8A174_BACTN | Q8A174)
molecular function
    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.

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 Related Entries

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(-) Related Entries Specified in the PDB File

4c1r BACTEROIDES THETAIOTAOMICRON VPI-5482 MANNOSYL-6- PHOSPHATASE BT3783