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(-) Description

Title :  THE 1.5A CRYSTAL STRUCTURE OF ALPHA-D-GLUCURONIDASE FROM BACILLUS STEAROTHERMOPHILUS T-1, COMPLEXED WITH 4-O-METHYL-GLUCURONIC ACID AND XYLOTRIOSE
 
Authors :  G. Golan, D. Shallom, A. Teplitsky, G. Zaide, S. Shulami, T. Baasov, V. S A. Thompson, Y. Shoham, G. Shoham
Date :  21 Mar 02  (Deposition) - 21 Mar 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Golan, D. Shallom, A. Teplitsky, G. Zaide, S. Shulami, T. Baasov, V. Stojanoff, A. Thompson, Y. Shoham, G. Shoham
Crystal Structures Of Geobacillus Stearothermophilus {Alpha}-Glucuronidase Complexed With Its Substrate And Products: Mechanistic Implications.
J. Biol. Chem. V. 279 3014 2004
PubMed-ID: 14573597  |  Reference-DOI: 10.1074/JBC.M310098200

(-) Compounds

Molecule 1 - ALPHA-D-GLUCURONIDASE
    Chains: A
    EC Number: 3.2.1.139
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET9D
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: AGUA
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric Unit (3, 17)
No.NameCountTypeFull Name
1GCW1Ligand/Ion4-O-METHYL-BETA-D-GLUCURONIC ACID
2GOL14Ligand/IonGLYCEROL
3XYP2Ligand/IonBETA-D-XYLOPYRANOSE
Biological Unit 1 (3, 34)
No.NameCountTypeFull Name
1GCW2Ligand/Ion4-O-METHYL-BETA-D-GLUCURONIC ACID
2GOL28Ligand/IonGLYCEROL
3XYP4Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:150 , GLU A:158 , ARG A:159 , VAL A:200 , ASN A:201 , LYS A:281 , GLU A:285 , ARG A:318 , PHE A:320 , LYS A:359 , ASP A:364 , GLU A:392 , XYP A:702BINDING SITE FOR RESIDUE GCW A 701
02AC2SOFTWAREGLU A:285 , PHE A:320 , TYR A:322 , ARG A:335 , ASP A:364 , TRP A:520 , HIS A:527 , TYR A:535 , TRP A:540 , GCW A:701 , XYP A:703 , HOH A:1198BINDING SITE FOR RESIDUE XYP A 702
03AC3SOFTWAREARG A:159 , GLY A:525 , HIS A:527 , TRP A:540 , XYP A:702 , GOL A:763 , HOH A:1370BINDING SITE FOR RESIDUE XYP A 703
04AC4SOFTWARELYS A:630 , TYR A:638 , HIS A:639 , LEU A:642 , HOH A:1404BINDING SITE FOR RESIDUE GOL A 750
05AC5SOFTWAREARG A:368 , GLU A:369 , VAL A:371 , GLU A:409 , PHE A:413 , LEU A:585 , HOH A:817 , HOH A:853 , HOH A:859 , HOH A:1077BINDING SITE FOR RESIDUE GOL A 751
06AC6SOFTWAREGLY A:519 , TRP A:520 , MET A:521 , VAL A:532 , ASP A:533 , GLY A:534 , TYR A:535 , GLU A:536 , THR A:542 , TYR A:543 , HIS A:544 , HOH A:815 , HOH A:998BINDING SITE FOR RESIDUE GOL A 752
07AC7SOFTWARETYR A:91 , TYR A:116 , HIS A:120 , ARG A:123 , SER A:189 , VAL A:190 , GLY A:191 , TRP A:470 , HOH A:807 , HOH A:918BINDING SITE FOR RESIDUE GOL A 753
08AC8SOFTWAREASN A:451 , GLY A:454 , HIS A:455 , THR A:456 , ASP A:640 , VAL A:641 , ARG A:644BINDING SITE FOR RESIDUE GOL A 754
09AC9SOFTWARETRP A:259 , GLY A:674 , ARG A:675 , LYS A:676 , HOH A:883 , HOH A:917 , HOH A:1126 , HOH A:1180 , HOH A:1201 , HOH A:1335BINDING SITE FOR RESIDUE GOL A 755
10BC1SOFTWAREARG A:22 , GLU A:602 , ASN A:610 , THR A:611 , GLU A:614 , GLN A:618 , HOH A:891 , HOH A:1047 , HOH A:1052 , HOH A:1084 , HOH A:1379BINDING SITE FOR RESIDUE GOL A 756
11BC2SOFTWARELYS A:620 , LYS A:653 , ARG A:656 , HOH A:1018 , HOH A:1320BINDING SITE FOR RESIDUE GOL A 757
12BC3SOFTWARESER A:19 , GLU A:129 , HOH A:850 , HOH A:893 , HOH A:1093 , HOH A:1176BINDING SITE FOR RESIDUE GOL A 758
13BC4SOFTWARETRP A:68 , GLU A:75 , GLU A:76 , PHE A:77 , ARG A:94 , TYR A:105 , HOH A:1293 , HOH A:1317 , HOH A:1328 , HOH A:1348BINDING SITE FOR RESIDUE GOL A 759
14BC5SOFTWAREARG A:11 , TYR A:12 , LYS A:44 , SER A:48 , HOH A:1051BINDING SITE FOR RESIDUE GOL A 760
15BC6SOFTWAREARG A:331 , TYR A:664 , ARG A:665 , TYR A:678 , HOH A:874 , HOH A:964 , HOH A:1351 , HOH A:1365BINDING SITE FOR RESIDUE GOL A 761
16BC7SOFTWARESER A:448 , HOH A:1120 , HOH A:1401 , HOH A:1411BINDING SITE FOR RESIDUE GOL A 762
17BC8SOFTWAREGLU A:285 , ARG A:335 , ASP A:364 , TRP A:520 , HIS A:527 , TYR A:535 , TRP A:540 , XYP A:703 , HOH A:1198BINDING SITE FOR RESIDUE GOL A 763

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1L8N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1L8N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1L8N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1L8N)

(-) Exons   (0, 0)

(no "Exon" information available for 1L8N)

(-) 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:671
 aligned with Q8VVD2_GEOSE | Q8VVD2 from UniProtKB/TrEMBL  Length:679

    Alignment length:675
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673     
         Q8VVD2_GEOSE     4 GYEPCWLRYERKDQYSRLRFEEIVAKRTSPIFQAAVEELQKGLRSMMEIEPQVVQEVNETANSIWLGTLEDEEFERPLEGTLVHPEGYVIRSDVDDGPFRIYIIGKTDAGVLYGVFHFLRLLQMGENIAQLSIIEQPKNRLRMINHWDNMDGSIERGYAGRSIFFVDDQFVKQNQRIKDYARLLASVGINAISINNVNVHKTETKLITDHFLPDVAEVADIFRTYGIKTFLSINYASPIEIGGLPTADPLDPEVRWWWKETAKRIYQYIPDFGGFVVKADSEFRPGPFTYGRDHAEGANMLAEALAPFGGLVIWRCFVYNCQQDWRDRTTDRAKAAYDHFKPLDGQFRENVILQIKNGPMDFQVREPVSPLFGAMPKTNQMMEVQITQEYTGQQKHLCFLIPQWKEVLDFDTYAKGKGSEVKKVIDGSLFDYRYSGIAGVSNIGSDPNWTGHTLAQANLYGFGRLAWNPDLSAEEIANEWVVQTFGDDSQVVETISWMLLSSWRIYENYTSPLGVGWMVNPGHHYGPNVDGYEYSHWGTYHYADRDGIGVDRTVATGTGYTAQYFPENAAMYESLDTCPDELLLFFHHVPYTHRLHSGETVIQHIYNTHFEGVEQAKQLRKRWEQLKGKIDEKRYHDVLERLTIQVEHAKEWRDVINTYFYRKSGIDDQYGRKIY 678
               SCOP domains d1l8na2 A:4-142 alpha-D-glucuronidase, N-terminal domain                                                                                   d1l8na1 A:143-678 alpha-D-glucur  onidase catalytic domain                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------1l8nA01 A:16-140 Chitobiase, domain 2                                                                                        1l8nA02 A:141-473 Glycosidases                                                                                                                                                                                                                                                                                                               1l8nA03 A:474-678 Alpha-d-glucuronidase, C-terminal Domain                                                                                                                                                    CATH domains
               Pfam domains ----Glyco_hydro_67N-1l8nA03 A:8-121                                                                                   Glyco_hydro_67M-1l8nA02 A:122-452                                                                                                                                                                                                                                                                                                          Glyco_hydro_67C-1l8nA01 A:453-678                                                                                                                                                                                                  Pfam domains
         Sec.struct. author .....................eeee...hhhhhhhhhhhhhhhhhhhh...eee........eeeeee.hhh...hhhhhh......eeeee...--..eeeeee.hhhhhhhhhhhhhhhhhh.......eeee.....eeeee...................ee..ee.--hhhhhhhhhhhhhh...eee........hhhhhhh..hhhhhhhhhhhhhhh..eeeeee..hhhhhh.........hhhhhhhhhhhhhhhhhhh....eeee........hhhhhh.hhhhhhhhhhhhhhhhh.eeeee...............hhhhhhhhhhhhhh......eeeeee.......................eeeeee..............hhhhhhhhhh..........hhhhhhh.........eeeee...........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh....................................ee..........hhhhhhhhhhhhhhhh....hhhhhhhhh.ee.........hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l8n A   4 GYEPCWLRYERKDQYSRLRFEEIVAKRTSPIFQAAVEELQKGLRSMMEIEPQVVQEVNETANSIWLGTLEDEEFERPLEGTLVHPEGYVIRSDVD--PFRIYIIGKTDAGVLYGVFHFLRLLQMGENIAQLSIIEQPKNRLRMINHWDNMDGSIERGYAGRSIFFVDDQFV--NQRIKDYARLLASVGINAISINNVNVHKTETKLITDHFLPDVAEVADIFRTYGIKTFLSINYASPIEIGGLPTADPLDPEVRWWWKETAKRIYQYIPDFGGFVVKADSEFRPGPFTYGRDHAEGANMLAEALAPFGGLVIWRCFVYNCQQDWRDRTTDRAKAAYDHFKPLDGQFRENVILQIKNGPMDFQVREPVSPLFGAMPKTNQMMEVQITQEYTGQQKHLCFLIPQWKEVLDFDTYAKGKGSEVKKVIDGSLFDYRYSGIAGVSNIGSDPNWTGHTLAQANLYGFGRLAWNPDLSAEEIANEWVVQTFGDDSQVVETISWMLLSSWRIYENYTSPLGVGWMVNPGHHYGPNVDGYEYSHWGTYHYADRDGIGVDRTVATGTGYTAQYFPENAAMYESLDTCPDELLLFFHHVPYTHRLHSGETVIQHIYNTHFEGVEQAKQLRKRWEQLKGKIDEKRYHDVLERLTIQVEHAKEWRDVINTYFYRKSGIDDQYGRKIY 678
                                    13        23        33        43        53        63        73        83        93    |  103       113       123       133       143       153       163       173|  |   183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673     
                                                                                                                         98  |                                                                      174  |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
                                                                                                                           101                                                                         177
   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  (2, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (3, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: Glyco_hydro_67C] (5)
(-)
Clan: no clan defined [family: Glyco_hydro_67M] (5)
(-)
Clan: no clan defined [family: Glyco_hydro_67N] (5)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q8VVD2_GEOSE | Q8VVD2)
molecular function
    GO:0046559    alpha-glucuronidase activity    Catalysis of the reaction: an alpha-D-glucuronoside + H2O = an alcohol + D-glucuronate.
    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:0033939    xylan alpha-1,2-glucuronosidase activity    Catalysis of the hydrolysis of alpha-D-(1->2)-(4-O-methyl)glucuronosyl links in the main chain of hardwood xylans.
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:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
    GO:0045493    xylan catabolic process    The chemical reactions and pathways resulting in the breakdown of xylan, a polymer containing a beta-1,4-linked D-xylose backbone.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q8VVD2_GEOSE | Q8VVD2: 1k9e 1mqp
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        Q8VVD2_GEOSE | Q8VVD2: 1k9d 1mqq

(-) Related Entries Specified in the PDB File

1k9d 1k9e 1k9f