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(-) Description

Title :  CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS A4 BETA-GALACTOSIDASE IN COMPLEX WITH GALACTOSE
 
Authors :  M. Hidaka, S. Fushinobu, N. Ohtsu, H. Motoshima, H. Matsuzawa, H. Shoun
Date :  29 Jan 02  (Deposition) - 02 Oct 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Tim Barrel, Glycoside Hydrolase Family 42, Trimer, Galactose Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Hidaka, S. Fushinobu, N. Ohtsu, H. Motoshima, H. Matsuzawa, H. Shoun, T. Wakagi
Trimeric Crystal Structure Of The Glycoside Hydrolase Famil 42 Beta-Galactosidase From Thermus Thermophilus A4 And The Structure Of Its Complex With Galactose.
J. Mol. Biol. V. 322 79 2002
PubMed-ID: 12215416  |  Reference-DOI: 10.1016/S0022-2836(02)00746-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-GALACTOSIDASE
    Chains: A
    EC Number: 3.2.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEXM9
    Expression System Strain: JM105
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Strain: A4

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric Unit (5, 7)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL1Ligand/IonCHLORIDE ION
3GAL1Ligand/IonBETA-D-GALACTOSE
4MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5ZN1Ligand/IonZINC ION
Biological Unit 1 (3, 15)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3GAL3Ligand/IonBETA-D-GALACTOSE
4MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:36 , ARG A:102 , ASN A:140 , GLU A:141 , ASP A:264 , TYR A:266 , GLU A:312 , TRP A:320 , PHE A:350 , GLU A:360 , HIS A:363 , HOH A:808 , HOH A:869BINDING SITE FOR RESIDUE GAL A 701
2AC2SOFTWARETYR A:7 , TRP A:11 , ARG A:351 , ARG A:353BINDING SITE FOR RESIDUE CL A 801
3AC3SOFTWAREHOH A:818 , HOH A:891BINDING SITE FOR RESIDUE ACT A 804
4AC4SOFTWAREARG A:560BINDING SITE FOR RESIDUE ACT A 805
5AC5SOFTWARECYS A:106 , CYS A:150 , CYS A:152BINDING SITE FOR RESIDUE ZN A 806
6AC6SOFTWARELEU A:424 , TYR A:428BINDING SITE FOR RESIDUE MPD A 802
7AC7SOFTWAREALA A:433 , ARG A:436 , PRO A:573 , HOH A:865BINDING SITE FOR RESIDUE MPD A 803

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KWK)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Phe A:350 -Arg A:351
2Pro A:499 -Pro A:500
3Gly A:613 -Pro A:614

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KWK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KWK)

(-) Exons   (0, 0)

(no "Exon" information available for 1KWK)

(-) 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:644
 aligned with BGAL_THETH | O69315 from UniProtKB/Swiss-Prot  Length:645

    Alignment length:644
                                    10        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       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640    
           BGAL_THETH     1 MLGVCYYPEHWPKERWKEDARRMREAGLSHVRIGEFAWALLEPEPGRLEWGWLDEAIATLAAEGLKVVLGTPTATPPKWLVDRYPEILPVDREGRRRRFGGRRHYCFSSPVYREEARRIVTLLAERYGGLEAVAGFQTDNEYGCHDTVRCYCPRCQEAFRGWLEARYGTIEALNEAWGTAFWSQRYRSFAEVELPHLTVAEPNPSHLLDYYRFASDQVRAFNRLQVEILRAHAPGKFVTHNFMGFFTDLDAFALAQDLDFASWDSYPLGFTDLMPLPPEEKLRYARTGHPDVAAFHHDLYRGVGRGRFWVMEQQPGPVNWAPHNPSPAPGMVRLWTWEALAHGAEVVSYFRWRQAPFAQEQMHAGLHRPDSAPDQGFFEAKRVAEELAALALPPVAQAPVALVFDYEAAWIYEVQPQGAEWSYLGLVYLFYSALRRLGLDVDVVPPGASLRGYAFAVVPSLPIVREEALEAFREAEGPVLFGPRSGSKTETFQIPKELPPGPLQALLPLKVVRVESLPPGLLEVAEGALGRFPLGLWREWVEAPLKPLLTFQDGKGALYREGRYLYLAAWPSPELAGRLLSALAAEAGLKVLSLPEGLRLRRRGTWVFAFNYGPEAVEAPASEGARFLLGSRRVGPYDLAVWEE 644
               SCOP domains d1kwka2 A:1-393 A4 beta-galactosidase                                                                                                                                                                                                                                                                                                                                                                    d1kwka3 A:394-590 A4 beta-galactosidase middle domain                                                                                                                                                d1kwka1 A:591-644 A4 beta-galactosidase                SCOP domains
               CATH domains 1kwkA01 A:1-394 Glycosidases                                                                                                                                                                                                                                                                                                                                                                              1kwkA02 A:395-594  [code=3.40.50.880, no name defined]                                                                                                                                                  1kwkA03 A:595-644 Golgi alpha-mannosidase II       CATH domains
               Pfam domains ----Glyco_hydro_42-1kwkA03 A:5-390                                                                                                                                                                                                                                                                                                                                                                    -------Glyco_hydro_42M-1kwkA02 A:398-590                                                                                                                                                                ------Glyco_hydro_42C-1kwkA01 A:597-644                Pfam domains
         Sec.struct. author .eeee.hhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhh.......hhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhh....eeeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.ee.......hhhhhhhhh..eeeeehhhhhhhhh..hhhhhhhh......hhhhhhhhhhhhhh...eeeeee................hhhhhhhhhhhhh....eee........................hhhhhhhhhhhhhhhh..........eeee.hhhhhhhhhhh......hhhhhhhhhhhhhhh....eeee..........eeee......hhhhhhhhhh....eee..................hhhhhhh...eeeeeee......eeeee..eeeee..eeeeee......eee....eeeeee..eeee....hhhhhhhhhhhhhhhh..........eeeeee..eeeeee.....ee.......eeee...ee...eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kwk A   1 MLGVCYYPEHWPKERWKEDARRMREAGLSHVRIGEFAWALLEPEPGRLEWGWLDEAIATLAAEGLKVVLGTPTATPPKWLVDRYPEILPVDREGRRRRFGGRRHYCFSSPVYREEARRIVTLLAERYGGLEAVAGFQTDNEYGCHDTVRCYCPRCQEAFRGWLEARYGTIEALNEAWGTAFWSQRYRSFAEVELPHLTVAEPNPSHLLDYYRFASDQVRAFNRLQVEILRAHAPGKFVTHNFMGFFTDLDAFALAQDLDFASWDSYPLGFTDLMPLPPEEKLRYARTGHPDVAAFHHDLYRGVGRGRFWVMEQQPGPVNWAPHNPSPAPGMVRLWTWEALAHGAEVVSYFRWRQAPFAQEQMHAGLHRPDSAPDQGFFEAKRVAEELAALALPPVAQAPVALVFDYEAAWIYEVQPQGAEWSYLGLVYLFYSALRRLGLDVDVVPPGASLRGYAFAVVPSLPIVREEALEAFREAEGPVLFGPRSGSKTETFQIPKELPPGPLQALLPLKVVRVESLPPGLLEVAEGALGRFPLGLWREWVEAPLKPLLTFQDGKGALYREGRYLYLAAWPSPELAGRLLSALAAEAGLKVLSLPEGLRLRRRGTWVFAFNYGPEAVEAPASEGARFLLGSRRVGPYDLAVWEE 644
                                    10        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       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640
   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  (3, 3)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (3, 3)

Asymmetric Unit
(-)
Clan: GHD (106)
(-)
Clan: Glutaminase_I (73)
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (BGAL_THETH | O69315)
molecular function
    GO:0004565    beta-galactosidase activity    Catalysis of the hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-D-galactosides.
    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:0006012    galactose metabolic process    The chemical reactions and pathways involving galactose, the aldohexose galacto-hexose. D-galactose is widely distributed in combined form in plants, animals and microorganisms as a constituent of oligo- and polysaccharides; it also occurs in galactolipids and as its glucoside in lactose and melibiose.
    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.
cellular component
    GO:0009341    beta-galactosidase complex    A protein complex that possesses beta-galactosidase activity, i.e. catalyzes the hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides. In E. coli, the complex is a homotetramer; dimeric and hexameric beta-galactosidase complexes have been observed in other species.

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  1kwk
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 Related Entries

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

UniProtKB/Swiss-Prot
        BGAL_THETH | O69315: 1kwg

(-) Related Entries Specified in the PDB File

1kwg 1KWG CONTAINS THE SAME PROTEIN WITHOUT GALACTOSE.