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(-) Description

Title :  CRYSTAL STRUCTURE OF UNSATURATED GLUCURONYL HYDROLASE, RESPONSIBLE FOR THE DEGRADATION OF GLYCOSAMINOGLYCAN, FROM BACILLUS SP. GL1 AT 1.8 A RESOLUTION
 
Authors :  T. Itoh, S. Akao, W. Hashimoto, B. Mikami, K. Murata
Date :  18 Mar 04  (Deposition) - 13 Jul 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Alpha-Barrel, Unsaturated Glucuronyl Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Itoh, S. Akao, W. Hashimoto, B. Mikami, K. Murata
Crystal Structure Of Unsaturated Glucuronyl Hydrolase, Responsible For The Degradation Of Glycosaminoglycan, From Bacillus Sp. Gl1 At 1. 8 A Resolution
J. Biol. Chem. V. 279 31804 2004
PubMed-ID: 15148314  |  Reference-DOI: 10.1074/JBC.M403288200

(-) Compounds

Molecule 1 - UNSATURATED GLUCURONYL HYDROLASE
    Chains: A
    EC Number: 3.2.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: BACILLUS SP.
    Organism Taxid: 84635
    Strain: GL1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1DTT2Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
2GLY4Mod. Amino AcidGLYCINE
3MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:42 , ASP A:149 , GLN A:211 , TRP A:219 , ARG A:221 , TRP A:225 , TYR A:338 , DTT A:501 , HOH A:1443BINDING SITE FOR RESIDUE GLY A 401
2AC2SOFTWAREGLY A:320 , ARG A:334 , ARG A:335 , HOH A:1193 , HOH A:1237 , HOH A:1325BINDING SITE FOR RESIDUE GLY A 402
3AC3SOFTWAREASP A:60 , GLN A:62 , TYR A:63 , HOH A:1312BINDING SITE FOR RESIDUE GLY A 403
4AC4SOFTWARELEU A:290BINDING SITE FOR RESIDUE GLY A 404
5AC5SOFTWARETRP A:134 , HIS A:210 , GLN A:211 , TYR A:338 , GLY A:401 , DTT A:502 , HOH A:1020 , HOH A:1031BINDING SITE FOR RESIDUE DTT A 501
6AC6SOFTWARETRP A:134 , HIS A:210 , DTT A:501 , HOH A:1451BINDING SITE FOR RESIDUE DTT A 502
7AC7SOFTWARETYR A:55 , GLY A:59 , HOH A:1247BINDING SITE FOR RESIDUE MPD A 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VD5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VD5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VD5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VD5)

(-) Exons   (0, 0)

(no "Exon" information available for 1VD5)

(-) Sequences/Alignments

Asymmetric/Biological 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:381
 aligned with UGL_BACGL | Q9RC92 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:381
                                                                                                                                                                                                                                                                                                                                                                                                                  377    
                                    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      |  - 
            UGL_BACGL     1 MWQQAIGDALGITARNLKKFGDRFPHVSDGSNKYVLNDNTDWTDGFWSGILWLCYEYTGDEQYREGAVRTVASFRERLDRFENLDHHDIGFLYSLSAKAQWIVEKDESARKLALDAADVLMRRWRADAGIIQAWGPKGDPENGGRIIIDCLLNLPLLLWAGEQTGDPEYRRVAEAHALKSRRFLVRGDDSSYHTFYFDPENGNAIRGGTHQGNTDGSTWTRGQAWGIYGFALNSRYLGNADLLETAKRMARHFLARVPEDGVVYWDFEVPQEPSSYRDSSASAITACGLLEIASQLDESDPERQRFIDAAKTTVTALRDGYAERDDGEAEGFIRRGSYHVRGGISPDDYTIWGDYYYLEALLRLERGVTGYWYERGR----   -
               SCOP domains d1vd5a_ A: Unsaturated glucuronyl hydrolase                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1vd5A00 A:1-377  [code=1.50.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                      ---- CATH domains
               Pfam domains --------------------------Glyco_hydro_88-1vd5A01 A:27-367                                                                                                                                                                                                                                                                                                                      -------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh..eeeee.....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................eee.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.........eeee......eeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh............................hhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vd5 A   1 MWQQAIGDALGITARNLKKFGDRFPHVSDGSNKYVLNDNTDWTDGFWSGILWLCYEYTGDEQYREGAVRTVASFRERLDRFENLDHHDIGFLYSLSAKAQWIVEKDESARKLALDAADVLMRRWRADAGIIQAWGPKGDPENGGRIIIDCLLNLPLLLWAGEQTGDPEYRRVAEAHALKSRRFLVRGDDSSYHTFYFDPENGNAIRGGTHQGNTDGSTWTRGQAWGIYGFALNSRYLGNADLLETAKRMARHFLARVPEDGVVYWDFEVPQEPSSYRDSSASAITACGLLEIASQLDESDPERQRFIDAAKTTVTALRDGYAERDDGEAEGFIRRGSYHVRGGISPDDYTIWGDYYYLEALLRLERGVTGYWYERGRGGGG 404
                                    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      |403 
                                                                                                                                                                                                                                                                                                                                                                                                                  377|   
                                                                                                                                                                                                                                                                                                                                                                                                                   401
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: 6_Hairpin (120)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (UGL_BACGL | Q9RC92)
molecular function
    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: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.
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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        UGL_BACGL | Q9RC92: 2ahf 2ahg 2d5j 2fuz 2fv0 2fv1

(-) Related Entries Specified in the PDB File

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