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(-) Description

Title :  GALACTOSIDASE DOMAIN OF ALPHA-GALACTOSIDASE-SUCROSE KINASE, AGASK, IN COMPLEX WITH GALACTOSE
 
Authors :  G. Sulzenbacher, L. Bruel, M. Tison-Cervera, A. Pujol, C. Nicoletti, J A. Galinier, D. Ropartz, M. Fons, F. Pompeo, T. Giardina
Date :  07 Apr 11  (Deposition) - 28 Sep 11  (Release) - 07 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Bruel, G. Sulzenbacher, M. Tison-Cervera, A. Pujol, C. Nicoletti, J. Perrier, A. Galinier, D. Ropartz, M. Fons, F. Pompeo, T. Giardina
Agask, A Bifunctional Enzyme From The Human Microbiome Coupling Galactosidase And Kinase Activities
J. Biol. Chem. V. 286 40814 2011
PubMed-ID: 21931163  |  Reference-DOI: 10.1074/JBC.M111.286039

(-) Compounds

Molecule 1 - ALPHA-GALACTOSIDASE-SUCROSE KINASE AGASK
    Chains: A
    EC Number: 3.2.1.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: POPIN E
    Organism Scientific: RUMINOCOCCUS GNAVUS E1
    Organism Taxid: 935582

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 35)

Asymmetric Unit (6, 35)
No.NameCountTypeFull Name
1GAL1Ligand/IonBETA-D-GALACTOSE
2GLA1Ligand/IonALPHA D-GALACTOSE
3GOL1Ligand/IonGLYCEROL
4NA27Ligand/IonSODIUM ION
5PGE4Ligand/IonTRIETHYLENE GLYCOL
6PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (5, 32)
No.NameCountTypeFull Name
1GAL4Ligand/IonBETA-D-GALACTOSE
2GLA4Ligand/IonALPHA D-GALACTOSE
3GOL4Ligand/IonGLYCEROL
4NA-1Ligand/IonSODIUM ION
5PGE16Ligand/IonTRIETHYLENE GLYCOL
6PO44Ligand/IonPHOSPHATE ION

(-) Sites  (35, 35)

Asymmetric Unit (35, 35)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:81 , THR A:82 , GLY A:83 , ASP A:84 , TYR A:85 , ARG A:220 , ALA A:484 , ASP A:485 , VAL A:486 , HOH A:2178 , HOH A:2201 , HOH A:3056BINDING SITE FOR RESIDUE GOL A1722
02AC2SOFTWARETYR A:50 , ASP A:65 , THR A:67 , TYR A:68BINDING SITE FOR RESIDUE PGE A1723
03AC3SOFTWAREPRO A:27 , ASP A:65 , HOH A:2138 , HOH A:3057 , HOH A:3058BINDING SITE FOR RESIDUE PGE A1724
04AC4SOFTWAREALA A:395 , GLU A:396 , THR A:399 , HOH A:2218 , HOH A:3059 , HOH A:3060 , HOH A:3061BINDING SITE FOR RESIDUE PGE A1725
05AC5SOFTWAREARG A:456 , ASP A:501 , HOH A:3062 , HOH A:3063 , HOH A:3064 , HOH A:3065BINDING SITE FOR RESIDUE PGE A1726
06AC6SOFTWAREARG A:111 , TYR A:115 , ARG A:116 , ARG A:164 , HOH A:3067 , HOH A:3069BINDING SITE FOR RESIDUE PO4 A1727
07AC7SOFTWAREGLN A:187 , GLY A:188 , LYS A:263 , ASN A:267 , GLN A:268 , THR A:269BINDING SITE FOR RESIDUE NA A1728
08AC8SOFTWAREGLN A:75 , PRO A:78 , SER A:79 , THR A:82 , ASP A:84BINDING SITE FOR RESIDUE NA A1729
09AC9SOFTWARETYR A:253 , TYR A:493 , VAL A:496 , LEU A:497BINDING SITE FOR RESIDUE NA A1730
10BC1SOFTWAREPHE A:195 , TYR A:196 , GLY A:197 , ARG A:203 , HIS A:226 , NA A:1750BINDING SITE FOR RESIDUE NA A1731
11BC2SOFTWARESER A:519 , GLY A:521 , GLY A:522 , GLY A:523 , ARG A:524 , PHE A:525 , ILE A:536 , NA A:1751BINDING SITE FOR RESIDUE NA A1732
12BC3SOFTWAREALA A:72 , LEU A:73 , PRO A:74 , ARG A:86 , GLN A:268 , HOH A:2367BINDING SITE FOR RESIDUE NA A1733
13BC4SOFTWAREGLY A:57 , GLY A:83 , TYR A:85 , NA A:1752BINDING SITE FOR RESIDUE NA A1734
14BC5SOFTWAREHIS A:33 , GLN A:75 , CYS A:182 , LEU A:183 , ASP A:184BINDING SITE FOR RESIDUE NA A1735
15BC6SOFTWAREARG A:194 , GLY A:211 , HIS A:212 , GLY A:213 , THR A:214 , HOH A:2387BINDING SITE FOR RESIDUE NA A1736
16BC7SOFTWAREGLY A:218 , SER A:219 , SER A:225 , GLN A:227 , TYR A:228 , HOH A:2437BINDING SITE FOR RESIDUE NA A1737
17BC8SOFTWAREASP A:71 , ARG A:86 , ASP A:264 , GLN A:265 , HOH A:2165BINDING SITE FOR RESIDUE NA A1738
18BC9SOFTWAREHIS A:212 , TYR A:228 , LYS A:263 , ASP A:264 , GLN A:265 , HOH A:2445BINDING SITE FOR RESIDUE NA A1739
19CC1SOFTWAREPHE A:55 , THR A:223 , SER A:482 , HOH A:2444 , HOH A:2816BINDING SITE FOR RESIDUE NA A1740
20CC2SOFTWARETHR A:49 , ALA A:72 , LEU A:73 , HOH A:2125 , HOH A:2154 , HOH A:2166BINDING SITE FOR RESIDUE NA A1741
21CC3SOFTWAREARG A:547 , GLN A:551 , ALA A:565 , ALA A:588 , HOH A:2840 , HOH A:2870BINDING SITE FOR RESIDUE NA A1742
22CC4SOFTWAREGLU A:176 , GLU A:277 , PHE A:280 , HOH A:2520 , HOH A:2521BINDING SITE FOR RESIDUE NA A1743
23CC5SOFTWARESER A:224 , SER A:225 , ASN A:229 , GLY A:523 , ARG A:524 , PHE A:525 , NA A:1750BINDING SITE FOR RESIDUE NA A1744
24CC6SOFTWARELEU A:31 , GLN A:75 , GLU A:76 , TYR A:77 , HOH A:2171BINDING SITE FOR RESIDUE NA A1745
25CC7SOFTWARETYR A:552 , ARG A:631 , SER A:633 , ALA A:642 , HOH A:2934 , HOH A:2952BINDING SITE FOR RESIDUE NA A1746
26CC8SOFTWAREVAL A:586 , MET A:589 , SER A:656 , GLN A:714 , HOH A:2872BINDING SITE FOR RESIDUE NA A1747
27CC9SOFTWARETYR A:85 , SER A:219 , ARG A:220 , HOH A:2437BINDING SITE FOR RESIDUE NA A1748
28DC1SOFTWARESER A:258 , GLU A:260 , LEU A:272 , HOH A:2514BINDING SITE FOR RESIDUE NA A1749
29DC2SOFTWAREARG A:203 , SER A:225 , ASN A:229 , NA A:1731 , NA A:1744BINDING SITE FOR RESIDUE NA A1750
30DC3SOFTWAREGLY A:517 , CYS A:518 , ARG A:524 , ILE A:536 , NA A:1732 , HOH A:2815BINDING SITE FOR RESIDUE NA A1751
31DC4SOFTWARETYR A:85 , VAL A:440 , ARG A:481 , SER A:482 , NA A:1734 , HOH A:2733BINDING SITE FOR RESIDUE NA A1752
32DC5SOFTWAREHIS A:199 , ALA A:200 , GLU A:202 , GLY A:520 , SER A:539 , ASP A:540BINDING SITE FOR RESIDUE NA A1753
33DC6SOFTWARELEU A:250 , PHE A:251 , ASP A:526 , ALA A:527 , TYR A:558BINDING SITE FOR RESIDUE NA A1754
34DC7SOFTWARETRP A:336 , ASP A:366 , ASP A:367 , TRP A:411 , ARG A:443 , LYS A:476 , ASP A:478 , ASN A:480 , CYS A:518 , GLY A:520 , GLY A:521 , TRP A:537 , ASP A:540 , HOH A:3070 , HOH A:3071BINDING SITE FOR RESIDUE GLA A1755
35DC8SOFTWARETRP A:336 , ASP A:366 , ASP A:367 , TRP A:411 , ARG A:443 , LYS A:476 , ASP A:478 , ASN A:480 , CYS A:518 , GLY A:520 , GLY A:521 , TRP A:537 , ASP A:540 , HOH A:3070BINDING SITE FOR RESIDUE GAL A1756

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Val A:570 -Pro A:571

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALPHA_GALACTOSIDASEPS00512 Alpha-galactosidase signature.AGASK_RUMGN359-374  1A:359-374
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALPHA_GALACTOSIDASEPS00512 Alpha-galactosidase signature.AGASK_RUMGN359-374  4A:359-374

(-) Exons   (0, 0)

(no "Exon" information available for 2YFO)

(-) 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:719
 aligned with AGASK_RUMGN | G4T4R7 from UniProtKB/Swiss-Prot  Length:935

    Alignment length:719
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711         
          AGASK_RUMGN     2 AIIYNPNKKIFTLHTAHTTYQMQVDPLGYLLHLYYGEKTNSSMDYVLTYADRGFSGNPYAAGMDRTYSLDALPQEYPSLGTGDYRNIALNIKNEKGVESADLLFKSYEIRNGKYRLQGLPAVWADEKEAQTLEIVLADENAQVEVHLLYGVLEENDVITRSVRIKNTGTGQITIEKAAAACLDFVQGEFDVLRFYGKHAMERNLERTPLGHGTIAFGSRRGTSSHQYNPAVILAEKGTTETAGSCYGMLFVYSGNFSCEAEKDQFNQTRLLLGLNEELFSYPLASGETFTVPEVILSYSAEGLSALSQQYHNCIRNHVCRSKYVHMQRPVLINSWEAAYFDFTGDTIVDLAKEAASLGIDMVVMDDGWFGKRNDDNSSLGDWQVNETKLGGSLAELITRVHEQGMKFGIWIEPEMINEDSDLYRAHPDWAIRIQGKKPVRSRNQLLLDFSRKEVRDCVFDQICVVLDQGKIDYVKWDMNRSMADVYAGNLSYDYVLGVYDFMERLCSRYPDLLLEGCSGGGGRFDAGMLYYSPQIWCSDNTDAINRTRIQYGTSFFYPVSAMGAHVSAVPNHQTGRVTSFHTRGVTAMAGTFGYELNPALLSDEEKQQIREQIKTYKKYETLINEGTYWRLSDPFTDEIAAWMSVSEEQDHALVSVVRLMAEANQATVYVRLRGLKPDAVYLEEQSGRQYSGAALMHAGIPLPPFTEEYEAYQFAFTEL 720
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....eeeee...eeeeeee.....eeeeeeee.....hhhhh...........hhh...........................eeee..........eeeeeeeee.................eeeeeeeeee....eeeeeeeeee....eeeeeeeeee.....eeeeee..eeeee....eeeeeeeee..eeeeeeeee...eeeeeee...........eeeeee.........eeeeee.....eeeeeee.....eeeeee.......eee....eeeeeeeeeeee...hhhhhhhhhhhhhhh....hhhhh...eeeeehhh.....hhhhhhhhhhhhhh....eeeee....................hhhh...hhhhhhhhhhh..eeeeeee........hhhhh.hhh......................hhhhhhhhhhhhhhhh.....eeeeee..........hhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhh..eee......hhhhhhhhhhhh....hhheeeeee............hhhhhhhhhh.eeeee..hhhh.hhhhhhhhhhhhhhhhh.hhhhhheeee........eeeeeee.....eeeeeeee.........eeee........eeee.....eeehhhhhhheeee.......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALPHA_GALACTOSID---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yfo A   2 AIIYNPNKKIFTLHTAHTTYQMQVDPLGYLLHLYYGEKTNSSMDYVLTYADRGFSGNPYAAGMDRTYSLDALPQEYPSLGTGDYRNIALNIKNEKGVESADLLFKSYEIRNGKYRLQGLPAVWADEKEAQTLEIVLADENAQVEVHLLYGVLEENDVITRSVRIKNTGTGQITIEKAAAACLDFVQGEFDVLRFYGKHAMERNLERTPLGHGTIAFGSRRGTSSHQYNPAVILAEKGTTETAGSCYGMLFVYSGNFSCEAEKDQFNQTRLLLGLNEELFSYPLASGETFTVPEVILSYSAEGLSALSQQYHNCIRNHVCRSKYVHMQRPVLINSWEAAYFDFTGDTIVDLAKEAASLGIDMVVMDDGWFGKRNDDNSSLGDWQVNETKLGGSLAELITRVHEQGMKFGIWIEPEMINEDSDLYRAHPDWAIRIQGKKPVRSRNQLLLDFSRKEVRDCVFDQICVVLDQGKIDYVKWDMNRSMADVYAGNLSYDYVLGVYDFMERLCSRYPDLLLEGCSGGGGRFDAGMLYYSPQIWCSDNTDAINRTRIQYGTSFFYPVSAMGAHVSAVPNHQTGRVTSFHTRGVTAMAGTFGYELNPALLSDEEKQQIREQIKTYKKYETLINEGTYWRLSDPFTDEIAAWMSVSEEQDHALVSVVRLMAEANQATVYVRLRGLKPDAVYLEEQSGRQYSGAALMHAGIPLPPFTEEYEAYQFAFTEL 720
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711
   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 2YFO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YFO)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 16)

Asymmetric Unit(hide GO term definitions)
Chain A   (AGASK_RUMGN | G4T4R7)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004557    alpha-galactosidase activity    Catalysis of the hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactohydrolase.
    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.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
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.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.

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  2yfo
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  AGASK_RUMGN | G4T4R7
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 Related Entries

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UniProtKB/Swiss-Prot
        AGASK_RUMGN | G4T4R7: 2yfn

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