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(-) Description

Title :  STRUCTURE OF BETA-1,4-GALACTANASE
 
Authors :  J. Le Nours, L. De Maria, D. Welner, C. T. Jorgensen, L. L. H. Christensen, S. Larsen, L. Lo Leggio
Date :  06 Oct 06  (Deposition) - 18 Dec 07  (Release) - 24 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Glycoside Hydrolase Family 53, Hydrolase, Gh-A, Beta-1, Galactan, 4-Galactanase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Le Nours, L. De Maria, D. Welner, C. T. Jorgensen, L. L. H. Christensen, T. V. Borchert, S. Larsen, L. Lo Leggio
Investigating The Binding Of Beta-1, 4-Galactan To Bacillus Licheniformis Beta-1, 4-Galactanase By Crystallography And Computational Modeling.
Proteins V. 75 977 2009
PubMed-ID: 19089956  |  Reference-DOI: 10.1002/PROT.22310

(-) Compounds

Molecule 1 - YVFO
    Atcc: 14580
    Chains: A, B
    EC Number: 3.2.1.89
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Strain: PL2306
    Expression System Taxid: 1423
    Expression System Vector: PMOL944
    Fragment: RESIDUES 28-424
    Organism Scientific: BACILLUS LICHENIFORMIS
    Organism Taxid: 1402
    Synonym: BETA-1,4-GALACTANASE

 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  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1B2G2Ligand/IonGALACTOBIOSE
2B4G2Ligand/IonGALACTOTRIOSE
3CA2Ligand/IonCALCIUM ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1B2G1Ligand/IonGALACTOBIOSE
2B4G1Ligand/IonGALACTOTRIOSE
3CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1B2G1Ligand/IonGALACTOBIOSE
2B4G1Ligand/IonGALACTOTRIOSE
3CA-1Ligand/IonCALCIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:272 , ASP A:274 , HIS A:276 , ASN A:278 , SER A:367 , ASP A:370BINDING SITE FOR RESIDUE CA A 901
2AC2SOFTWAREASP B:272 , ASP B:274 , HIS B:276 , ASN B:278 , SER B:367 , ASP B:370BINDING SITE FOR RESIDUE CA B 902
3AC3SOFTWAREASP B:117 , LYS B:120 , HIS B:276 , GLY B:277 , LYS B:282 , TRP B:320 , TRP B:347 , ASP B:359 , TRP B:363 , ALA B:368 , B2G B:1399 , HOH B:2042 , HOH B:2045BINDING SITE FOR RESIDUE B4G B1398
4AC4SOFTWAREASP A:117 , LYS A:120 , HIS A:276 , GLY A:277 , ASN A:278 , LYS A:282 , TRP A:320 , TRP A:347 , ASP A:359 , TRP A:363 , ALA A:368 , B2G A:1398BINDING SITE FOR RESIDUE B4G A1397
5AC5SOFTWAREPRO B:118 , ALA B:119 , GLU B:165 , THR B:204 , ASN B:205 , HIS B:238 , B4G B:1398BINDING SITE FOR RESIDUE B2G B1399
6AC6SOFTWAREPRO A:118 , ALA A:119 , GLU A:165 , THR A:204 , ASN A:205 , SER A:232 , HIS A:238 , B4G A:1397BINDING SITE FOR RESIDUE B2G A1398

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J74)

(-) 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 2J74)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2J74)

(-) Exons   (0, 0)

(no "Exon" information available for 2J74)

(-) 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: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 d2j74a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2j74A00 A:11-397 Glycosidases                                                                                                                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeee..hhhhhhhh............hhhhhhhhh...eeeeee.................hhhhhhhhhhhhhhh..eeeeee.....................hhhhhhhhhhhhhhhhhhhhhhh...eeeeee............hhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhh.....eeeee.......hhhhhhhhhhhhhhhhh.eeeeee............................hhhhhhhhhhhhhhhhhh....eeeeeee........hhhhhhhhhhhhhhhh....hhhhhhh...hhhhh.....hhhhh........hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j74 A  11 GLYVEKVSGLRKDFIKGVDVSSIIALEESGVAFYNESGKKQDIFKTLKEAGVNYVRVRIWNDPYDANGNGYGGGNNDLEKAIQIGKRATANGMKLLADFHYSDFWADPAKQKAPKAWANLNFEDKKTALYQYTKQSLKAMKAAGIDIGMVQVGNETNGGLAGETDWAKMSQLFNAGSQAVRETDSNILVALHFTNPETSGRYAWIAETLHRHHVDYDVFASSYYPFWHGTLKNLTSVLTSVADTYGKKVMVAETSYTYTAEDGDGHGNTAPKNGQTLNNPVTVQGQANAVRDVIQAVSDVGEAGIGVFYWEPAWIPVGPAHRLEKNKALWETYGSGWATSYAAEYDPEDAGKWFGGSAVDNQALFDFKGRPLPSLHVFQYVDTGTPF 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       


Chain B from PDB  Type:PROTEIN  Length:388
 aligned with GANA_BACLD | Q65CX5 from UniProtKB/Swiss-Prot  Length:424

    Alignment length:388
                                    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 GLYVEKVSGLRKDFIKGVDVSSIIALEESGVAFYNESGKKQDIFKTLKEAGVNYVRVRIWNDPYDANGNGYGGGNNDLEKAIQIGKRATANGMKLLADFHYSDFWADPAKQKAPKAWANLNFEDKKTALYQYTKQSLKAMKAAGIDIGMVQVGNETNGGLAGETDWAKMSQLFNAGSQAVRETDSNILVALHFTNPETSGRYAWIAETLHRHHVDYDVFASSYYPFWHGTLKNLTSVLTSVADTYGKKVMVAETSYTYTAEDGDGHGNTAPKNGQTLNNPVTVQGQANAVRDVIQAVSDVGEAGIGVFYWEPAWIPVGPAHRLEKNKALWETYGSGWATSYAAEYDPEDAGKWFGGSAVDNQALFDFKGRPLPSLHVFQYVDTGTPFK 423
               SCOP domains d2j74b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2j74B00 B:11-398 Glycosidases                                                                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeee..hhhhhhhh............hhhhhhhhh...eeeeee.................hhhhhhhhhhhhhhh..eeeeee.....................hhhhhhhhhhhhhhhhhhhhhhh...eeeeee............hhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhh.....eeeee.......hhhhhhhhhhhhhhhhh.eeeeee............................hhhhhhhhhhhhhhhhhh....eeeeeee........hhhhhhhhhhhhhhhh....hhhhhhh...hhhhh.....hhhhh........hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j74 B  11 GLYVEKVSGLRKDFIKGVDVSSIIALEESGVAFYNESGKKQDIFKTLKEAGVNYVRVRIWNDPYDANGNGYGGGNNDLEKAIQIGKRATANGMKLLADFHYSDFWADPAKQKAPKAWANLNFEDKKTALYQYTKQSLKAMKAAGIDIGMVQVGNETNGGLAGETDWAKMSQLFNAGSQAVRETDSNILVALHFTNPETSGRYAWIAETLHRHHVDYDVFASSYYPFWHGTLKNLTSVLTSVADTYGKKVMVAETSYTYTAEDGDGHGNTAPKNGQTLNNPVTVQGQANAVRDVIQAVSDVGEAGIGVFYWEPAWIPVGPAHRLEKNKALWETYGSGWATSYAAEYDPEDAGKWFGGSAVDNQALFDFKGRPLPSLHVFQYVDTGTPFK 398
                                    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 2J74)

(-) 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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  2j74
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  3.2.1.89
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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 2gft

(-) Related Entries Specified in the PDB File

1ur0 THE STRUCTURE OF ENDO-BETA-1,4-GALACTANASE FROM BACILLUS LICHENIFORMIS IN COMPLEX WITH TWO OLIGOSACCHARIDE PRODUCTS.
1ur4 THE STRUCTURE OF ENDO-BETA-1,4-GALACTANASE FROM BACILLUS LICHENIFORMIS IN COMPLEX WITH TWO OLIGOSACCHARIDE PRODUCTS.
2ccr STRUCTURE OF BETA-1,4-GALACTANASE