Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  THE CRYSTAL STRUCTURE OF ALPHA-D-GLUCURONIDASE (E386Q) FROM BACILLUS STEAROTHERMOPHILUS T-6
 
Authors :  G. Golan, D. Shallom, A. Teplitsky, G. Zaide, S. Shulami, T. Baasov, V. S A. Thompson, Y. Shoham, G. Shoham
Date :  17 Sep 02  (Deposition) - 17 Sep 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
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
    Mutation: YES
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Strain: T-6

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1GOL10Ligand/IonGLYCEROL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:91 , TYR A:116 , HIS A:120 , ARG A:123 , SER A:189 , VAL A:190 , GLY A:191 , ARG A:467 , TRP A:470 , HOH A:857 , HOH A:864BINDING SITE FOR RESIDUE GOL A 701
2AC2SOFTWAREARG A:368 , GLU A:369 , VAL A:371 , GLU A:409 , LEU A:585 , HOH A:831 , HOH A:901 , HOH A:1123 , HOH A:1132BINDING SITE FOR RESIDUE GOL A 703
3AC3SOFTWARESER A:19 , GLU A:129 , ILE A:131 , HOH A:977 , HOH A:1087 , HOH A:1236BINDING SITE FOR RESIDUE GOL A 704
4AC4SOFTWARETYR A:340 , LYS A:344 , ALA A:377 , ALA A:565 , GLN A:566 , TYR A:567 , PHE A:568 , HOH A:1115BINDING SITE FOR RESIDUE GOL A 705
5AC5SOFTWARELYS A:620 , LYS A:653 , ARG A:656BINDING SITE FOR RESIDUE GOL A 706

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1MQR)

(-) 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:674
 aligned with AGUA_GEOSE | Q09LY5 from UniProtKB/Swiss-Prot  Length:679

    Alignment length:677
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       
           AGUA_GEOSE     3 AGYEPCWLRYERKDQYSRLRFEEIVAKRTSPIFQAVVEELQKGLRSMMEIEPQVVQEVNETANSIWLGTLEDEEFERPLEGTLVHPEGYVIRSDVDDGPFRIYIIGKTDAGVLYGVFHFLRLLQMGENIAQLSIIEQPKNRLRMINHWDNMDGSIERGYAGRSIFFVDDQFVKQNQRIKDYARLLASVGINAISINNVNVHKTETKLITDHFLPDVAEVADIFRTYGIKTFLSINYASPIEIGGLPTADPLDPEVRRWWKETAKRIYQYIPDFGGFVVKADSEFRPGPFTYGRDHAEGANMLAEALAPFGGLVIWRCFVYNCQQDWRDRTTDRAKAAYDHFKPLDGQFRENVILQIKNGPMDFQVREPVSPLFGAMPKTNQMMEVQITQEYTGQQKHLCFLIPQWKEVLDFDTYAKGKGSEVKKVIDGSLFDYRYSGIAGVSNIGSDPNWTGHTLAQANLYGFGRLAWNPDLSAEEIANEWVVQTFGDDSQVVETISWMLLSSWRIYENYTSPLGVGWMVNPGHHYGPNVDGYEYSHWGTYHYADRDGIGVDRTVATGTGYTAQYFPENAAMYESLDTCPDELLLFFHHVPYTHRLHSGETVIQHIYNTHFEGVEQAKQLRKRWEQLKGKIDEKRYHDVLERLTIQVEHAKEWRDVINTYFYRKSGIDDQYGRKIYR 679
               SCOP domains d1mqra2 A:3-142 alpha-D-glucuronidase, N-terminal domain                                                                                    d1mqra1 A:143-679 alpha-D-glucuro nidase catalytic domain                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------1mqrA01 A:16-140 Chitobiase, domain 2                                                                                        1mqrA02 A:141-473 Glycosidases                                                                                                                                                                                                                                                                                                               1mqrA03 A:474-679 Alpha-d-glucuronidase, C-terminal Domain                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................eeee...hhhhhhhhhhhhhhhhhhhh...eee........eeeeee.hhh...hhhhhh......eeeee.......eeeeee.hhhhhhhhhhhhhhhhhh.......eeee.....eeeee...................ee..ee..-hhhhhhhhhhhhhh...eee......hhhhhhhhh..hhhhhhhhhhhhhhh..eeeeee..hhhhhh.........hhhhhhhhhhhhhhhhhhh....eeee........hhhhhh.hhhhhhhhhhhhhhhhh.eeeee...--..........hhhhhhhhhhhhhh......eeeeee.......................eeeeee..............hhhhhhhhhh..........hhhhhhh.........eeeee...........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.....................................ee..........hhhhhhhhhhhhhhhh....hhhhhhhhh.ee.........hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mqr A   3 AGYEPCWLRYERKDQYSRLRFEEIVAKRTSPIFQAVVEELQKGLRSMMEIEPQVVQEVNETANSIWLGTLEDEEFERPLEGTLVHPEGYVIRSDVDDGPFRIYIIGKTDAGVLYGVFHFLRLLQMGENIAQLSIIEQPKNRLRMINHWDNMDGSIERGYAGRSIFFVDDQFVK-NQRIKDYARLLASVGINAISINNVNVHKTETKLITDHFLPDVAEVADIFRTYGIKTFLSINYASPIEIGGLPTADPLDPEVRRWWKETAKRIYQYIPDFGGFVVKADSEFRPGPFTYGRDHAEGANMLAEALAPFGGLVIWRCFV--CQQDWRDRTTDRAKAAYDHFKPLDGQFRENVILQIKNGPMDFQVREPVSPLFGAMPKTNQMMQVQITQEYTGQQKHLCFLIPQWKEVLDFDTYAKGKGSEVKKVIDGSLFDYRYSGIAGVSNIGSDPNWTGHTLAQANLYGFGRLAWNPDLSAEEIANEWVVQTFGDDSQVVETISWMLLSSWRIYENYTSPLGVGWMVNPGHHYGPNVDGYEYSHWGTYHYADRDGIGVDRTVATGTGYTAQYFPENAAMYESLDTCPDELLLFFHHVPYTHRLHSGETVIQHIYNTHFEGVEQAKQLRKRWEQLKGKIDEKRYHDVLERLTIQVEHAKEWRDVINTYFYRKSGIDDQYGRKIYR 679
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172  | |  182       192       202       212       222       232       242       252       262       272       282       292       302       312        |- |     332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       
                                                                                                                                                                                                      175 |                                                                                                                                             321  |                                                                                                                                                                                                                                                                                                                                                                   
                                                                                                                                                                                                        177                                                                                                                                                324
   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  (0, 0)

(no "Pfam Domain" information available for 1MQR)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (AGUA_GEOSE | Q09LY5)
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:2000886    glucuronoxylan catabolic process    The chemical reactions and pathways resulting in the breakdown of a glucuronoxylan.
    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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1mqr)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1mqr
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  AGUA_GEOSE | Q09LY5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.2.1.139
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  AGUA_GEOSE | Q09LY5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        AGUA_GEOSE | Q09LY5: 1k9e 1k9f 1mqp

(-) Related Entries Specified in the PDB File

1k9d THE 1.7 A CRYSTAL STRUCTURE OF ALPHA-D-GLUCURONIDASE, A FAMILY-67 GLYCOSIDE HYDROLASE FROM BACILLUS STEAROTHERMOPHILUS T-1
1k9e CRYSTAL STRUCTURE OF A MUTATED FAMILY-67 ALPHA-D- GLUCURONIDASE (E285N) FROM BACILLUS STEAROTHERMOPHILUS T-6, COMPLEXED WITH 4-O-METHYL-GLUCURONIC ACID
1k9f CRYSTAL STRUCTURE OF A MUTATED FAMILY-67 ALPHA-D- GLUCURONIDASE (E285N) FROM BACILLUS STEAROTHERMOPHILUS T-6, COMPLEXED WITH ALDOTETRAOURONIC ACID
1l8n THE 1.5A CRYSTAL STRUCTURE OF ALPHA-D-GLUCURONIDASE FROM BACILLUS STEAROTHERMOPHILUS T-1, COMPLEXED WITH 4-O-METHYL- GLUCURONIC ACID AND XYLOTRIOSE
1mqp THE CRYSTAL STRUCTURE OF ALPHA-D-GLUCURONIDASE FROM BACILLUS STEAROTHERMOPHILUS T-6
1mqq THE CRYSTAL STRUCTURE OF ALPHA-D-GLUCURONIDASE FROM BACILLUS STEAROTHERMOPHILUS T-1 COMPLEXED WITH GLUCURONIC ACID