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(-) Description

Title :  PECTIN LYASE B
 
Authors :  J. Vitali, F. Jurnak
Date :  13 May 99  (Deposition) - 19 May 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Pectin Lyase, Beta-Helix Protein, Pectin, Plant Cell Wall (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Vitali, B. Schick, H. C. Kester, J. Visser, F. Jurnak
The Tree-Dimensional Structure Of Aspergillus Niger Pectin Lyase B At 1. 7-A Resolution.
Plant Physiol. V. 116 69 1998
PubMed-ID: 9449837  |  Reference-DOI: 10.1104/PP.116.1.69
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PECTIN LYASE B
    Chains: A
    EC Number: 4.2.2.10
    Organism Scientific: ASPERGILLUS NIGER
    Organism Taxid: 5061

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1QCX)

(-) Sites  (0, 0)

(no "Site" information available for 1QCX)

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:63 -A:82
2A:72 -A:206
3A:303 -A:311

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:182 -Thr A:183
2Met A:237 -Pro A:238
3Thr A:285 -Pro A:286

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1QCX)

(-) 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:359
 aligned with PELB_ASPNG | Q00205 from UniProtKB/Swiss-Prot  Length:378

    Alignment length:359
                                                                                                                          116                                                                                                                                                                                                                                                                      
                                                                                                                        115 |                                                                                                                                                                                                                                                                      
                                    30        40        50        60        70        80        90       100       110    | |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         
           PELB_ASPNG    21 AGVVGAAEGFAHGVTGGGSASPVYPTTTDELVSYLGDNEPRVIILDRTFDFTGTEGTETTTGCAPWGTASQCQVAINLHSWCDNYQASAPKVSVT-DKAGILPITVNSNKSIVGQGTKGVIKGKGLRVVSGAKNVIIQNIAVTDINPKYVWGGDAITVDDSDLVWIDHVTTARIGRQHIVLGTSADNRVTISYSLIDGRSDYSATCNGHHYWGVYLDGSNDMVTLKGNYFYNLSGRMPKVQGNTLLHAVNNLFHNFDGHAFEIGTGGYVLAEGNVFQDVNIVVETPISGQLFSSPDANTNQQCASVFGRSCQLNAFGNSGSMSGSDTSIISKFAGKTIAAAHPPGNIAQWTMKNAGQGK 378
               SCOP domains d1qcxa_ A: Pectin lyase                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1qcxA00 A:1-359 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------Pec_lyase_C-1qcxA01 A:76-276                                                                                                                                                                             ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........................hhhhhhhhh....eeeee..eee......eeeeeee..........eee....hhhh......eeeeee.hhhh..eeee..eeeee.....eee...eee......eeee..eee.....ee.....eee...........ee.......eee.......eeee..eee................eee....eeeeee..eee.......ee...eeeeee..eee.......ee...eeeeee..eee............eee.....hhhhhhhhhh.......eee.........hhhhhhh..........hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qcx A   1 AGVVGAAEGFAHGVTGGGSASPVYPTTTDELVSYLGDNEPRVIILDQTFDFTGTEGTETTTGCAPWGTASQCQVAINLHSWCDNYQASAPKVSVTYDKAGILPITVNSNKSIVGQGTKGVIKGKGLRVVSGAKNVIIQNIAVTDINPKYVWGGDAITVDDSDLVWIDHVTTARIGRQHIVLGTSADNRVTISYSLIDGRSDYSATCNGHHYWGVYLDGSNDMVTLKGNYFYNLSGRMPKVQGNTLLHAVNNLFHNFDGHAFEIGTGGYVLAEGNVFQDVNVVVETPISGQLFSSPDANTNQQCASVFGRSCQLNAFGNSGSMSGSDTSIISKFAGKTIAAAHPPGAIAQWTMKNAGQGK 359
                                    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
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Pec_lyase (42)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PELB_ASPNG | Q00205)
molecular function
    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:0047490    pectin lyase activity    Catalysis of the reaction: a pectin = an oligosaccharide with 4-deoxy-6-O-methyl-alpha-D-galact-4-enuronate end + a pectin. This reaction is the eliminative cleavage of (1->4)-alpha-D-galacturonan methyl ester to give oligosaccharides with 4-deoxy-6-O-methyl-alpha-D-galact-4-enuronosyl groups at their nonreducing ends.
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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  Cis Peptide Bonds
    Gly A:182 - Thr A:183   [ RasMol ]  
    Met A:237 - Pro A:238   [ RasMol ]  
    Thr A:285 - Pro A:286   [ RasMol ]  
 

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