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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE BETA-GALACTOSIDASE FROM BACTEROIDES FRAGILIS
 
Authors :  U. A. Ramagopal, M. Rutter, R. Toro, S. Hu, M. Maletic, T. Gheyi, J. M. Sau S. K. Burley, S. C. Almo, New York Sgx Research Center For Struct Genomics (Nysgxrc)
Date :  21 Mar 08  (Deposition) - 29 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Structural Genomics, Putative Beta-Galactosidase, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. A. Ramagopal, M. Rutter, R. Toro, S. Hu, M. Maletic, T. Gheyi, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Putative Beta-Galactosidase From Bacteroides Fragilis.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE BETA-GALACTOSIDASE
    Atcc: 25285
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: BC-PSGX4(BC)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 38-693
    Gene: BF0328
    Organism Scientific: BACTEROIDES FRAGILIS
    Organism Taxid: 272559
    Strain: NCTC 9343

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 16)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MPD12Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:359 , ASN A:428 , GLU A:429 , ASN A:477 , GLU A:510 , TRP A:562 , HOH A:937 , HOH A:1007 , HOH A:1010BINDING SITE FOR RESIDUE PO4 A 810
2AC2SOFTWARELYS A:392 , GLY A:393 , PHE A:394 , LYS A:431BINDING SITE FOR RESIDUE CL A 820
3AC3SOFTWAREALA A:222 , GLY A:224 , THR A:225 , LYS A:285BINDING SITE FOR RESIDUE MPD A 801
4AC4SOFTWAREPHE A:49 , ARG A:60 , HIS A:66 , HOH A:994 , HOH A:1196 , HOH A:1306BINDING SITE FOR RESIDUE MPD A 802

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Leu A:64 -Pro A:65
2Asn A:110 -Ser A:111
3Met A:161 -Pro A:162
4Ala A:358 -His A:359
5Trp A:562 -Asn A:563

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3CMG)

(-) 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:661
 aligned with Q5LIC7_BACFN | Q5LIC7 from UniProtKB/TrEMBL  Length:695

    Alignment length:661
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             695 
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695 
         Q5LIC7_BACFN    36 AQRQDILLNNNWNFRFSHQVQGDTRRVDLPHTWNAQDALAGKIDYKRGIGNYEKALYIRPEWKGKRLFLRFDGVNSIADVFINRKHIGEHRGGYGAFIFEITDLVKYGEKNSVLVRANNGEQLDIMPLVGDFNFYGGIYRDVHLLITDETCISPLDYASPGVYLVQEVVSPQEAKVCAKVNLSNRAADGTAELQVLVTDGTKVICKESRNVSLKQGADILEQLPLLIQKPRLWNGCEDPFMYQVSISLHKDGKQIDSVTQPLGLRYYHTDPDKGFFLNGKHLPLHGVCRHQDRAEVGNALRPQHHEEDVALMREMGVNAIRLAHYPQATYMYDLMDKHGIVTWAEIPFVGPGGYADKGFVDQASFRENGKQQLIELIRQHYNHPSICFWGLFNELKEVGDNPVEYVKELNALAKQEDPTRPTTSASNQDGNLNFITENIAWNRYDGWYGSTPKTLATFLDRTHKKHPELRIGISEYGAGASIYHQQDSLKQPSASGWWHPENWQTYYHMENWKIIAERPFVWGTFVWNMFDFGAAHRTEGDRPGINDKGLVTFDRKVRKDAFYFYKANWNKQEPMIYLAEKRCRLRYQPEQTFMAFTTAPEAELFVNGVSCGKQKADTYSTVVWKNVKLTSGENIIRVTTPGKKPLTDEVTVEYKEDRPL-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cmgA01 A:36-183 Galactose-binding domain-like                                                                                                      3cmgA02 A:184-301  [code=2.60.40.320, no name defined]                                                                3cmgA03 A:302-609 Glycosidases                                                                                                                                                                                                                                                                                      3cmgA04 A:610-698 E-set domains of sugar-utilizing enzymes; domain 3                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....eeeee........eee.........hhhhh.......eeeeeeeee.hhhhh..eeeeee.....eeeeee..eeeeeee.....eeee.........eeeeeeeee.......................eeeeee..eee.........eeeeeeee...eeeeeeeeeeee....eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeeee.....hhhhh...eeeeeeeee..eeeeeeeeee....eeee...eeee..ee...eeee............hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh.eeeee................hhhhhhhhhhhhhhhhhhhh....eeeeeeee........hhhhhhhhhhhhhhhh....eeeee...hhhhhh...eeee.........hhhhhhhhhhhhhhh....eeeeee.......................hhhhhhhhhhhhhhhhhh......eee.....ee...........ee............hhhhhhhhhhhh.....eee......ee....eeeeeee...eeeeee..eeeeeee.....eeeeeee....eeeeeeee.......eeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cmg A  36 SLRQDILLNNNWNFRFSHQVQGDTRRVDLPHTWNAQDALAGKIDYKRGIGNYEKALYIRPEWKGKRLFLRFDGVNSIADVFINRKHIGEHRGGYGAFIFEITDLVKYGEKNSVLVRANNGEQLDIMPLVGDFNFYGGIYRDVHLLITDETCISPLDYASPGVYLVQEVVSPQEAKVCAKVNLSNRAADGTAELQVLVTDGTKVICKESRNVSLKQGADILEQLPLLIQKPRLWNGCEDPFMYQVSISLHKDGKQIDSVTQPLGLRYYHTDPDKGFFLNGKHLPLHGVCRHQDRAEVGNALRPQHHEEDVALMREMGVNAIRLAHYPQATYMYDLMDKHGIVTWAEIPFVGPGGYADKGFVDQASFRENGKQQLIELIRQHYNHPSICFWGLFNELKEVGDNPVEYVKELNALAKQEDPTRPTTSASNQDGNLNFITENIAWNRYDGWYGSTPKTLATFLDRTHKKHPELRIGISEYGAGASIYHQQDSLKQPSASGWWHPENWQTYYHMENWKIIAERPFVWGTFVWNMFDFGAAHRTEGDRPGINDKGLVTFDRKVRKDAFYFYKANWNKQEPMIYLAEKRCRLRYQPEQTFMAFTTAPEAELFVNGVSCGKQKADTYSTVVWKNVKLTSGENIIRVTTPGKKPLTDEVTVEYKEDRHHH 698
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       697 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           693|  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            696
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3CMG)

(-) CATH Domains  (4, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q5LIC7_BACFN | Q5LIC7)
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:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
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.

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