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(-) Description

Title :  RHAMNOGALACTURONAN LYASE FROM ASPERGILLUS ACULEATUS MUTANT H210A
 
Authors :  M. H. Jensen, H. Otten, U. Christensen, T. V. Borchert, L. L. H. Christen S. Larsen, L. Lo Leggio
Date :  18 Jun 10  (Deposition) - 06 Oct 10  (Release) - 17 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym./Biol. Unit :  A
Keywords :  Carbohydrate Active Enzyme, Lyase, Pectin Degradation, Polysaccharide Lyase Family 4 (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. H. Jensen, H. Otten, U. Christensen, T. V. Borchert, L. L. Christensen, S. Larsen, L. L. Leggio
Structural And Biochemical Studies Elucidate The Mechanism Of Rhamnogalacturonan Lyase From Aspergillus Aculeatus.
J. Mol. Biol. V. 404 100 2010
PubMed-ID: 20851126  |  Reference-DOI: 10.1016/J.JMB.2010.09.013

(-) Compounds

Molecule 1 - RHAMNOGALACTURONASE B
    ChainsA
    EC Number4.2.2.10
    EngineeredYES
    Expression SystemASPERGILLUS ORYZAE
    Expression System Taxid5062
    FragmentRHAMNOGALACTURONASE B, RESIDUES 20-527
    GeneRHGB
    MutationYES
    Organism ScientificASPERGILLUS ACULEATUS
    Organism Taxid5053
    SynonymRHAMNOGALACTURONAN LYASE, RGASE B, RHG B

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2SO44Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:347 , ASP A:349 , GLN A:351 , ASP A:502 , HOH A:848BINDING SITE FOR RESIDUE CA A 800
2AC2SOFTWAREASN A:19 , ARG A:230 , SER A:231 , GLY A:232 , HOH A:961 , HOH A:962 , HOH A:976 , HOH A:1056BINDING SITE FOR RESIDUE SO4 A 901
3AC3SOFTWARELYS A:395 , SER A:490 , HOH A:778 , HOH A:866BINDING SITE FOR RESIDUE SO4 A 902
4AC4SOFTWAREARG A:429 , SER A:487 , GLY A:488 , HOH A:1022BINDING SITE FOR RESIDUE SO4 A 903
5AC5SOFTWAREGLN A:47 , SER A:53 , ARG A:107 , ARG A:111 , HOH A:637BINDING SITE FOR RESIDUE SO4 A 904

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:30 -A:73
2A:164 -A:173

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Glu A:121 -Pro A:122
2Gly A:222 -Pro A:223
3Gly A:375 -Pro A:376
4Asn A:399 -Pro A:400

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NJX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NJX)

(-) Exons   (0, 0)

(no "Exon" information available for 3NJX)

(-) 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:508
 aligned with RGLA_ASPAC | Q00019 from UniProtKB/Swiss-Prot  Length:527

    Alignment length:508
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519        
           RGLA_ASPAC    20 AFGITTSSSAYVIDTNAPNQLKFTVSRSSCDITSIIHYGTELQYSSQGSHIGSGLGSATVTATQSGDYIKVTCVTDTLTQYMVVHNGDPIIHMATYITAEPSIGELRFIARLNSDLLPNEEPFGDVSTTADGTAIEGSDVFLVGSETRSKFYSSERFIDDQRHCIAGDAHRVCMILNQYESSSGGPFHRDINSNNGGSYNALYWYMNSGHVQTESYRMGLHGPYSMYFSRSGTPSTSIDTSFFADLDIKGYVAASGRGKVAGTASGADSSMDWVVHWYNDAAQYWTYTSSSGSFTSPAMKPGTYTMVYYQGEYAVATSSVTVSAGSTTTKNISGSVKTGTTIFKIGEWDGQPTGFRNAANQLRMHPSDSRMSSWGPLTYTVGSSALTDFPMAVFKSVNNPVTIKFTATSAQTGAATLRIGTTLSFAGGRPQATINSYTGSAPAAPTNLDSRGVTRGAYRGLGEVYDVSIPSGTIVAGTNTITINVISGSSGDTYLSPNFIFDCVELFQ 527
               SCOP domains d3njxa1 A:1-250 Rhamnogalacturonase B, RhgB, N-terminal domain                                                                                                                                                                                            d3njxa2 A:251-337 Rhamnogalacturonase B, RhgB, middle domain                           d3njxa3 A:338-508 Rhamnogalacturonase B, RhgB, C-terminal domain                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeee......eeeeee.....eeeeee..ee........ee.......eeeeeee..eeeeeee...eeeeeeee....eeeeeeee........eeeeeee......eee..hhhhh....eeee...eeee..eeee.hhhh.hhhhh.eeeee....eeeee.................eee....eeeeeeee...........eeeeeeeeeee..........hhhhhhh......hhhhh.eeeeeee.......eeeeee....eeeee.....eee......eeeeeeeee..eeeeeeeeee....eee..ee.......eeeeee..........hhhhhh...............eee....hhhhh..eee......eeeeeeehhhhh..eeeeeeeeeee...eeeeee..ee.........................eeeeee.......eeeeeeeeee.....hhhhh.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3njx A   1 AFGITTSSSAYVIDTNAPNQLKFTVSRSSCDITSIIHYGTELQYSSQGSHIGSGLGSATVTATQSGDYIKVTCVTDTLTQYMVVHNGDPIIHMATYITAEPSIGELRFIARLNSDLLPNEEPFGDVSTTADGTAIEGSDVFLVGSETRSKFYSSERFIDDQRHCIAGDAHRVCMILNQYESSSGGPFHRDINSNNGGSYNALYWYMNSGAVQTESYRMGLHGPYSMYFSRSGTPSTSIDTSFFADLDIKGYVAASGRGKVAGTASGADSSMDWVVHWYNDAAQYWTYTSSSGSFTSPAMKPGTYTMVYYQGEYAVATSSVTVSAGSTTTKNISGSVKTGTTIFKIGEWDGQPTGFRNAANQLRMHPSDSRMSSWGPLTYTVGSSALTDFPMAVFKSVNNPVTIKFTATSAQTGAATLRIGTTLSFAGGRPQATINSYTGSAPAAPTNLDSRGVTRGAYRGLGEVYDVSIPSGTIVAGTNTITINVISGSSGDTYLSPNFIFDCVELFQ 508
                                    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       380       390       400       410       420       430       440       450       460       470       480       490       500        

   Legend:   → Mismatch (orange background)
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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  (3, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NJX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3NJX)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RGLA_ASPAC | Q00019)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0016837    carbon-oxygen lyase activity, acting on polysaccharides    Catalysis of the cleavage of a carbon-oxygen bond by the elimination of an alcohol from a polysaccharide.
    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:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0102210    rhamnogalacturonan endolyase activity    Catalysis of the reaction: H2O + a rhamnogalacturonan type I <=> [rhamnogalacturonan I oligosaccharide]-alpha-L-rhamnose + 4-deoxy-4,5-unsaturated D-galactopyranosyluronate-[rhamnogalacturonan I oligosaccharide]
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:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    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: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
        RGLA_ASPAC | Q000191nkg 2xhn 3njv

(-) Related Entries Specified in the PDB File

1nkg NATIVE RHAMNOGALACTURONAN LYASE
3njv RHAMNOGALACTURONAN LYASE MUTANT K150A SUBSTRATE COMPLEX