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(-) Description

Title :  STRUCTURE OF THE THERMOSTABLE PECTATE LYASE PL 47
 
Authors :  T. Nakaniwa, T. Tada, A. Yamaguchi, T. Kitatani, M. Takao, T. Sakai, K. N
Date :  27 Feb 04  (Deposition) - 19 Apr 05  (Release) - 23 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym./Biol. Unit :  A
Keywords :  Pectate Lyase, Pl 47, Thermostable, Bacillus Subtilis, Pectin, Calcium Ion, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Nakaniwa, T. Tada, A. Yamaguchi, T. Kitatani, M. Takao, T. Sakai, K. Nishimura
Structural Basis For Thermostability Of Pectate Lyase From Bacillus Sp. Ts 47
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PECTATE LYASE 47
    Chains: A
    EC Number: 4.2.2.2
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Plasmid: PUB110
    Expression System Taxid: 1423
    Expression System Vector Type: PLASMID
    Organism Scientific: BACILLUS SP. TS-47
    Organism Taxid: 132676

 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
1CA1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:190 , ASP A:229 , ASP A:233 , HOH A:482 , HOH A:770 , HOH A:771BINDING SITE FOR RESIDUE CA A 417

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:286 -Pro A:287

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VBL)

(-) 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:416
 aligned with Q9AJM4_9BACI | Q9AJM4 from UniProtKB/TrEMBL  Length:441

    Alignment length:416
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435      
         Q9AJM4_9BACI    26 KELGHEVLKPYDGWAAYGEGTTGGAMASPQNVFVVTNRTELIQALGGNNHTNQYNSVPKIIYVKGTIDLNVDDNNQPVGPDFYKDPHFDFEAYLREYDPATWGKKEVEGPLEEARVRSQKKQKDRIMVYVGSNTSIIGVGKDAKIKGGGFLIKNVDNVIIRNIEFEAPLDYFPEWDPTDGTLGEWNSEYDSISIEGSSHIWIDHNTFTDGDHPDRSLGTYFGRPFQQHDGALDIKNSSDFITISYNVFTNHDKVTLIGASDSRMADSGHLRVTLHHNYYKNVTQRLPRVRFGQVHIYNNYYEFSNLADYDFQYAWGVGVFSQIYAQNNYFSFDWDIDPSLIIKVWSKNEESMYETGTIVDLPNGRRYIDLVASYNESNTLQLKKEVTWKPMFYHVIHPTPSVPALVKAKAGAGNLH 441
               SCOP domains d1vbla_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1vblA00 A:1-416 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------Pec_lyase_C-1vblA01 A:111-330                                                                                                                                                                                               -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh......hhhhh..........hhh.eeee.hhhhhhhhh....hhhhhh...eeeee..eee..........hhhhhh....hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhheee....eeeee.....eee..eeeee..eeeeee..eee.......eee.......eee.....eeee..eeeeee..eee....hhhhh.ee..ee.......eeee...eeeeee..eeeeeee..ee.....hhhhh....eeee..eeeeeee...ee...eeeee..eeee...........eeee...eeeee..eeee....hhhh.eeee.....eeeee..eeee..eeee.hhhhhhhhhh....ee.............hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vbl A   1 KELGHEVLKPYDGWAAYGEGTTGGAMASPQNVFVVTNRTELIQALGGNNHTNQYNSVPKIIYVKGTIDLNVDDNNQPVGPDFYKDPHFDFEAYLREYDPATWGKKEVEGPLEEARVRSQKKQKDRIMVYVGSNTSIIGVGKDAKIKGGGFLIKNVDNVIIRNIEFEAPLDYFPEWDPTDGTLGEWNSEYDSISIEGSSHIWIDHNTFTDGDHPDRSLGTYFGRPFQQHDGALDIKNSSDFITISYNVFTNHDKVTLIGASDSRMADSGHLRVTLHHNYYKNVTQRLPRVRFGQVHIYNNYYEFSNLADYDFQYAWGVGVFSQIYAQNNYFSFDWDIDPSLIIKVWSKNEESMYETGTIVDLPNGRRYIDLVASYNESNTLQLKKEVTWKPMFYHVIHPTPSVPALVKAKAGAGNLH 416
                                    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
   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  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9AJM4_9BACI | Q9AJM4)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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: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

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