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(-) Description

Title :  CRYSTAL STRUCTURE OF UNSATURATED RHAMNOGALACTURONYL HYDROLASE IN COMPLEX WITH DGLCA-GALNAC
 
Authors :  T. Itoh, A. Ochiai, B. Mikami, W. Hashimoto, K. Murata
Date :  06 Dec 05  (Deposition) - 14 Nov 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Unsaturated Rhamnogalacturonyl Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Itoh, A. Ochiai, B. Mikami, W. Hashimoto, K. Murata
A Novel Glycoside Hydrolase Family 105: The Structure Of Family 105 Unsaturated Rhamnogalacturonyl Hydrolase Complexed With A Disaccharide In Comparison With Family 88 Enzyme Complexed With The Disaccharide
J. Mol. Biol. V. 360 573 2006
PubMed-ID: 16781735  |  Reference-DOI: 10.1016/J.JMB.2006.04.047
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE GLYCOSYL HYDROLASE YTER
    ChainsA
    EC Number3.2.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET21D
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMIDE
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid1423
    SynonymRHAMNOGALACTURONYL HYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1UCD1Ligand/Ion(4S,5R,6R)-6-((2R,3R,4R,5R,6R)-3-ACETAMIDO-2,5-DIHYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-4-YLOXY)-4,5-DIHYDROXY-5,6-DIHYDRO-4H-PYRAN-2-CARBOXYLIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:40 , TYR A:41 , HIS A:42 , LYS A:133 , TYR A:136 , LYS A:232 , ARG A:298 , GLY A:332 , THR A:333 , SER A:334 , HOH A:2002 , HOH A:2053 , HOH A:2126 , HOH A:2200 , HOH A:2390 , HOH A:2420 , HOH A:2509 , HOH A:2624 , HOH A:2625BINDING SITE FOR RESIDUE UCD A 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D8L)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:34 -Pro A:35

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D8L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2D8L)

(-) Exons   (0, 0)

(no "Exon" information available for 2D8L)

(-) 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:363
 aligned with URHG2_BACSU | O34559 from UniProtKB/Swiss-Prot  Length:373

    Alignment length:363
                                    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   
          URHG2_BACSU    11 KSPLTYAEALANTIMNTYTVEELPPANRWHYHQGVFLCGVLRLWEATGEKRYFEYAKAYADLLIDDNGNLLFRRDELDAIQAGLILFPLYEQTKDERYVKAAKRLRSLYGTLNRTSEGGFWHKDGYPYQMWLDGLYMGGPFALKYANLKQETELFDQVVLQESLMRKHTKDAKTGLFYHAWDEAKKMPWANEETGCSPEFWARSIGWYVMSLADMIEELPKKHPNRHVWKNTLQDMIKSICRYQDKETGLWYQIVDKGDRSDNWLESSGSCLYMYAIAKGINKGYLDRAYETTLLKAYQGLIQHKTETSEDGAFLVKDICVGTSAGFYDYYVSRERSTNDLHGAGAFILAMTELEPLFRSAGK 373
               SCOP domains d2d8la_ A: automated matches                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2d8lA00 A:11-373  [code=1.50.10.10, no name defined]                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh................eeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.........eee..................hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhheee.....eee..ee......hhhhhhh..ee..hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d8l A  11 KSPLTYAEALANTIMNTYTVEELPPANRWHYHQGVFLCGVLRLWEATGEKRYFEYAKAYADLLIDDNGNLLFRRDELDAIQAGLILFPLYEQTKDERYVKAAKRLRSLYGTLNRTSEGGFWHKDGYPYQMWLDGLYMGGPFALKYANLKQETELFDQVVLQESLMRKHTKDAKTGLFYHAWDEAKKMPWANEETGCSPEFWARSIGWYVMSLADMIEELPKKHPNRHVWKNTLQDMIKSICRYQDKETGLWYQIVDKGDRSDNWLESSGSCLYMYAIAKGINKGYLDRAYETTLLKAYQGLIQHKTETSEDGAFLVKDICVGTSAGFYDYYVSRERSTNDLHGAGAFILAMTELEPLFRSAGK 373
                                    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   

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  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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D8L)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (URHG2_BACSU | O34559)
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.
    GO:0102211    unsaturated rhamnogalacturonyl hydrolase activity    Catalysis of the reaction: 2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose(1-) + H2O <=> (4S,5S)-4,5-dihydroxy-2,6-dioxohexanoate + alpha-L-rhamnopyranose
biological process
    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: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
        URHG2_BACSU | O345591nc5 2gh4

(-) Related Entries Specified in the PDB File

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