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(-) Description

Title :  CRYSTAL STRUCTURE OF THE E263A NUCLEOPHILE MUTANT OF BACILLUS LICHENIFORMIS ENDO-BETA-1,4-GALACTANASE IN COMPLEX WITH GALACTOTRIOSE
 
Authors :  D Welner, J. Le Nours, L. De Maria, C. T. Jorgensen, L. L. H. Christensen, S. Larsen, L. Lo Leggio
Date :  23 Mar 06  (Deposition) - 13 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta-Alpha-8-Barrel, Protein-Oligosaccharide Complex, Nucleophile Inactive Mutant, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Le Nours, L. De Maria, D. Welner, C. T. Jorgensen, L. L. H. Christensen, S. Larsen, L. Lo Leggio
Oligosaccharide Binding Of Bacillus Licheniformis Endo-Beta-1, 4-Galactanase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCCOSYL HYDROLASE FAMILY 53
    Chains: A, B
    EC Number: 3.2.1.89
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Taxid: 1423
    Mutation: YES
    Organism Scientific: BACILLUS LICHENIFORMIS
    Organism Taxid: 1402

 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, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2GAL6Ligand/IonBETA-D-GALACTOSE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GAL3Ligand/IonBETA-D-GALACTOSE
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GAL3Ligand/IonBETA-D-GALACTOSE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:117 , LYS B:120 , TRP B:320 , GAL B:702 , HOH B:943 , HOH B:990BINDING SITE FOR RESIDUE GAL B 703
2AC2SOFTWARELYS B:120 , HIS B:276 , TRP B:347 , ASP B:359 , GAL B:701 , GAL B:703BINDING SITE FOR RESIDUE GAL B 702
3AC3SOFTWAREGLY B:277 , LYS B:282 , GAL B:702 , HOH B:976BINDING SITE FOR RESIDUE GAL B 701
4AC4SOFTWAREASP A:117 , LYS A:120 , TRP A:320 , TRP A:347 , GAL A:802 , HOH A:916 , HOH A:1031BINDING SITE FOR RESIDUE GAL A 803
5AC5SOFTWAREHIS A:276 , TRP A:347 , ASP A:359 , TRP A:363 , ALA A:368 , GAL A:801 , GAL A:803BINDING SITE FOR RESIDUE GAL A 802
6AC6SOFTWAREHIS A:276 , GLY A:277 , LYS A:282 , TRP A:363 , GAL A:802BINDING SITE FOR RESIDUE GAL A 801
7AC7SOFTWAREASP A:272 , ASP A:274 , HIS A:276 , ASN A:278 , SER A:367 , ASP A:370BINDING SITE FOR RESIDUE CA A 901
8AC8SOFTWAREASP B:272 , ASP B:274 , HIS B:276 , ASN B:278 , SER B:367 , ASP B:370BINDING SITE FOR RESIDUE CA B 902

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GFT)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:280 -Pro A:281
2Ala B:280 -Pro B:281

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GFT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GFT)

(-) Exons   (0, 0)

(no "Exon" information available for 2GFT)

(-) 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:386
 aligned with GANA_BACLD | Q65CX5 from UniProtKB/Swiss-Prot  Length:424

    Alignment length:386
                                    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      
           GANA_BACLD    36 GLYVEKVSGLRKDFIKGVDVSSIIALEESGVAFYNESGKKQDIFKTLKEAGVNYVRVRIWNDPYDANGNGYGGGNNDLEKAIQIGKRATANGMKLLADFHYSDFWADPAKQKAPKAWANLNFEDKKTALYQYTKQSLKAMKAAGIDIGMVQVGNETNGGLAGETDWAKMSQLFNAGSQAVRETDSNILVALHFTNPETSGRYAWIAETLHRHHVDYDVFASSYYPFWHGTLKNLTSVLTSVADTYGKKVMVAETSYTYTAEDGDGHGNTAPKNGQTLNNPVTVQGQANAVRDVIQAVSDVGEAGIGVFYWEPAWIPVGPAHRLEKNKALWETYGSGWATSYAAEYDPEDAGKWFGGSAVDNQALFDFKGRPLPSLHVFQYVDTGTP 421
               SCOP domains d2gfta_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2gftA00 A:11-396 Glycosidases                                                                                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeee..hhhhhhhh............hhhhhhhhh...eeeeee.................hhhhhhhhhhhhhhh..eeeeee..............hhhhh..hhhhhhhhhhhhhhhhhhhhhhh...eeeeee............hhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhh.....eeeeee......hhhhhhhhhhhhhhhhh.eeeeeee...........................hhhhhhhhhhhhhhhhhh....eeeeeee........hhhhhhhhhhhhhhhh....hhhhhh....hhhhhh....hhhhh........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gft A  11 GLYVEKVSGLRKDFIKGVDVSSIIALEESGVAFYNESGKKQDIFKTLKEAGVNYVRVRIWNDPYDANGNGYGGGNNDLEKAIQIGKRATANGMKLLADFHYSDFWADPAKQKAPKAWANLNFEDKKTALYQYTKQSLKAMKAAGIDIGMVQVGNETNGGLAGETDWAKMSQLFNAGSQAVRETDSNILVALHFTNPETSGRYAWIAETLHRHHVDYDVFASSYYPFWHGTLKNLTSVLTSVADTYGKKVMVAATSYTYTAEDGDGHGNTAPKNGQTLNNPVTVQGQANAVRDVIQAVSDVGEAGIGVFYWEPAWIPVGPAHRLEKNKALWETYGSGWATSYAAEYDPEDAGKWFGGSAVDNQALFDFKGRPLPSLHVFQYVDTGTP 396
                                    20        30        40        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      


Chain B from PDB  Type:PROTEIN  Length:387
 aligned with GANA_BACLD | Q65CX5 from UniProtKB/Swiss-Prot  Length:424

    Alignment length:387
                                    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       
           GANA_BACLD    36 GLYVEKVSGLRKDFIKGVDVSSIIALEESGVAFYNESGKKQDIFKTLKEAGVNYVRVRIWNDPYDANGNGYGGGNNDLEKAIQIGKRATANGMKLLADFHYSDFWADPAKQKAPKAWANLNFEDKKTALYQYTKQSLKAMKAAGIDIGMVQVGNETNGGLAGETDWAKMSQLFNAGSQAVRETDSNILVALHFTNPETSGRYAWIAETLHRHHVDYDVFASSYYPFWHGTLKNLTSVLTSVADTYGKKVMVAETSYTYTAEDGDGHGNTAPKNGQTLNNPVTVQGQANAVRDVIQAVSDVGEAGIGVFYWEPAWIPVGPAHRLEKNKALWETYGSGWATSYAAEYDPEDAGKWFGGSAVDNQALFDFKGRPLPSLHVFQYVDTGTPF 422
               SCOP domains d2gftb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2gftB00 B:11-397 Glycosidases                                                                                                                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeee..hhhhhhhh............hhhhhhhhh...eeeeee.................hhhhhhhhhhhhhhh..eeeeee..............hhhhh..hhhhhhhhhhhhhhhhhhhhhhh...eeeeee............hhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhh.....eeeeee......hhhhhhhhhhhhhhhhh.eeeeeee...........................hhhhhhhhhhhhhhhhhh....eeeeeee........hhhhhhhhhhhhhhhh....hhhhhh....hhhhhh....hhhhh........hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gft B  11 GLYVEKVSGLRKDFIKGVDVSSIIALEESGVAFYNESGKKQDIFKTLKEAGVNYVRVRIWNDPYDANGNGYGGGNNDLEKAIQIGKRATANGMKLLADFHYSDFWADPAKQKAPKAWANLNFEDKKTALYQYTKQSLKAMKAAGIDIGMVQVGNETNGGLAGETDWAKMSQLFNAGSQAVRETDSNILVALHFTNPETSGRYAWIAETLHRHHVDYDVFASSYYPFWHGTLKNLTSVLTSVADTYGKKVMVAATSYTYTAEDGDGHGNTAPKNGQTLNNPVTVQGQANAVRDVIQAVSDVGEAGIGVFYWEPAWIPVGPAHRLEKNKALWETYGSGWATSYAAEYDPEDAGKWFGGSAVDNQALFDFKGRPLPSLHVFQYVDTGTPF 397
                                    20        30        40        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
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GFT)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GANA_BACLD | Q65CX5)
molecular function
    GO:0031218    arabinogalactan endo-1,4-beta-galactosidase activity    Catalysis of the endohydrolysis of (1->4)-beta-D-galactosidic linkages in arabinogalactans.
    GO:0015926    glucosidase activity    Catalysis of the hydrolysis of glucosyl compounds, substances containing a group derived from a cyclic form of glucose or a glucose derivative.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        GANA_BACLD | Q65CX5: 1r8l 1ur0 1ur4 2ccr 2j74

(-) Related Entries Specified in the PDB File

1r8l 1ur0 1ur4 2ccr