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(-) Description

Title :  CRYSTAL STRUCTURE OF PECTATE LYASE PELI FROM ERWINIA CHRYSANTHEMI IN COMPLEX WITH TETRAGALACTURONIC ACID
 
Authors :  C. Creze, S. Castang, E. Derivery, R. Haser, V. Shevchik, P. Gouet
Date :  02 Nov 07  (Deposition) - 29 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Pectate Lyase, Pectin, Galacturonic Acid, Erwinia Chrysanthemi, Right-Handed Parallel Beta Helix Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Creze, S. Castang, E. Derivery, R. Haser, N. Hugouvieux-Cotte-Pattat, V. E. Shevchik, P. Gouet
The Crystal Structure Of Pectate Lyase Peli From Soft Rot Pathogen Erwinia Chrysanthemi In Complex With Its Substrate
J. Biol. Chem. V. 283 18260 2008
PubMed-ID: 18430740  |  Reference-DOI: 10.1074/JBC.M709931200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENDO-PECTATE LYASE
    Chains: A, B
    EC Number: 4.2.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PT7-6
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PELI
    Organism Scientific: ERWINIA CHRYSANTHEMI
    Organism Taxid: 556

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1ADA8Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
2CA1Ligand/IonCALCIUM ION
3ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1ADA4Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
2CA-1Ligand/IonCALCIUM ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1ADA4Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
2CA-1Ligand/IonCALCIUM ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:249 , ARG A:252 , THR A:322BINDING SITE FOR RESIDUE ADA A 901
02AC2SOFTWARELYS A:224 , GLN A:227 , ARG A:252 , GLY A:255 , ASP A:256BINDING SITE FOR RESIDUE ADA A 902
03AC3SOFTWAREASP A:195 , GLN A:227 , ASN A:229 , CYS A:254 , ASP A:256 , CYS A:257 , LYS A:317BINDING SITE FOR RESIDUE ADA A 903
04AC4SOFTWARESER A:258 , LYS A:317BINDING SITE FOR RESIDUE ADA A 904
05AC5SOFTWARELYS B:249 , ASP B:278 , LYS B:324BINDING SITE FOR RESIDUE ADA B 911
06AC6SOFTWARELYS B:249 , ARG B:252BINDING SITE FOR RESIDUE ADA B 912
07AC7SOFTWARELYS B:224 , GLN B:227 , GLY B:255 , ASP B:256BINDING SITE FOR RESIDUE ADA B 913
08AC8SOFTWAREGLN B:227 , ASN B:229 , ASP B:256 , CYS B:257 , LYS B:317BINDING SITE FOR RESIDUE ADA B 914
09AC9SOFTWAREASP B:191 , ILE B:192 , ASN B:213BINDING SITE FOR RESIDUE CA B 701
10BC1SOFTWAREASP A:146 , SER A:147 , HIS B:176 , ASP B:178BINDING SITE FOR RESIDUE ZN B 711

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:121 -A:134
2A:143 -A:193
3A:177 -A:182
4A:254 -A:257
5A:309 -A:334
6B:121 -B:134
7B:143 -B:193
8B:177 -B:182
9B:254 -B:257
10B:309 -B:334

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:262 -Pro A:263
2Lys A:305 -Pro A:306
3Gly B:262 -Pro B:263
4Lys B:305 -Pro B:306

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3B8Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3B8Y)

(-) Exons   (0, 0)

(no "Exon" information available for 3B8Y)

(-) Sequences/Alignments

Asymmetric 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:304
 aligned with O50325_DICCH | O50325 from UniProtKB/TrEMBL  Length:344

    Alignment length:325
                                    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     
         O50325_DICCH    20 AQTTLMLSQKSDVNYLGWSTDESKVARQEVYRGTTSNPDLRERIAVLDAETRTFKDADTNSGLNYWYWVDVVSENQAQVVSNAVTTAPNAGPLRAAKASSECKPGATFENRTVDCGGVTIGTSCPNDSDKQKPLIILKNATVKNLRISASGRADGIHCDSGNCTIENVIWEDICEDAATNNGKTMTIVGGIAHNAKDGYGGKPDKVLQHNSKNSTTVVKGNFTLTGEHGKLWRSCGDCSNNGGPRFLTVTSATVNGTIDSIAGVNRNYGDVATISGLKIKNYKEGKPPVCEEFKGVVKGQGSTEKYGEKWDTTNCKVSRSGVSKL 344
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3b8yA01 A:20-118 Immunoglobulins                                                                   3b8yA02 A:119-344 Single-stra   nded right-handed beta-helix, Pectin lyase-like                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..eeeeeeee....eeeeeeeee...hhhhheeeeee.....eeee.........eeeeeeee....eee...ee..-----------.......eeee..eeeeeeeee........---...eeee..eeeeeee........eeeee.eeeeeeeee.....eeeee...eeeee..eeee..-------.eeeee....eeeeee..eeeeeeeeeeeee..........eeeee..eeeeeeeeeeeeee.....eeee..eee..........eeee...........eeee......ee.hhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b8y A  20 AQTTLMLSQKSDVNYLGWSTDESKVARQEVYRGTTSNPDLRERIAVLDAETRTFKDADTNSGLNYWYWVDVVSENQAQVVSNAVTTA-----------SSECKPGATFENRTVDCGGVTIGTSCPNDS---KPLIILKNATVKNLRISASGGADGIHCDSGNCTIENVIWEDICEDAATNNGKTMTIVGGIAHNAK-------DKVLQHNSKNSTTVVKGNFTLTGEHGKLWRSCGDCSNNGGPRFLTVTSATVNGTIDSIAGVNRNYGDVATISGLKIKNYKEGKPPVCEEFKGVVKGQGSTEKYGEKWDTTNCKVSRSGVSKL 344
                                    29        39        49        59        69        79        89        99      |  -       119       129       139       | - |     159       169       179       189       199       209     |   -   |   229       239       249       259       269       279       289       299       309       319       329       339     
                                                                                                                106         118                          147 151                                                             215     223                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:294
 aligned with O50325_DICCH | O50325 from UniProtKB/TrEMBL  Length:344

    Alignment length:325
                                    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     
         O50325_DICCH    20 AQTTLMLSQKSDVNYLGWSTDESKVARQEVYRGTTSNPDLRERIAVLDAETRTFKDADTNSGLNYWYWVDVVSENQAQVVSNAVTTAPNAGPLRAAKASSECKPGATFENRTVDCGGVTIGTSCPNDSDKQKPLIILKNATVKNLRISASGRADGIHCDSGNCTIENVIWEDICEDAATNNGKTMTIVGGIAHNAKDGYGGKPDKVLQHNSKNSTTVVKGNFTLTGEHGKLWRSCGDCSNNGGPRFLTVTSATVNGTIDSIAGVNRNYGDVATISGLKIKNYKEGKPPVCEEFKGVVKGQGSTEKYGEKWDTTNCKVSRSGVSKL 344
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3b8yB01 B:20-106 Immunoglobulins                                                                   3b8yB02 B:119-344 Single-s      tranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....eeeeeee....eeeeeeeee........eeeeee.....eeee.-----...eeeeeeee....eee...ee..------------......eeee..eeeeeeeee.....------...eeee..eeeeeee........eeeee.eeeeeeeee.....eeeee...eeeee..eeee.--------.eeeee....eeeeee..eeeeeeeeeeeee..........eeeee..eeeeeeeeeeeeee.hhh.eeee..eeee.........eeeee.........eeeee......ee.hhh.eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b8y B  20 AQTTLMLSQKSDVNYLGWSTDESKVARQEVYRGTTSNPDLRERIAVLDAETRTFKDA-----LNYWYWVDVVSENQAQVVSNAVTTA------------SECKPGATFENRTVDCGGVTIGTSCP------KPLIILKNATVKNLRISASGGADGIHCDSGNCTIENVIWEDICEDAATNNGKTMTIVGGIAHNA--------DKVLQHNSKNSTTVVKGNFTLTGEHGKLWRSCGDCSNNGGPRFLTVTSATVNGTIDSIAGVNRNYGDVATISGLKIKNYKEGKPPVCEEFKGVVKGQGSTEKYGEKWDTTNCKVSRSGVSKL 344
                                    29        39        49        59        69      |  -  |     89        99      |  -       119       129       139    |    - |     159       169       179       189       199       209    |    -   |   229       239       249       259       269       279       289       299       309       319       329       339     
                                                                                   76    82                     106          119                      144    151                                                            214      223
   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  (0, 0)

(no "SCOP Domain" information available for 3B8Y)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3B8Y)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (O50325_DICCH | O50325)
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.
    GO:0030570    pectate lyase activity    Catalysis of the reaction: a pectate = a pectate + a pectate oligosaccharide with 4-(4-deoxy-alpha-D-galact-4-enuronosyl)-D-galacturonate end. This reaction is the eliminative cleavage of pectate to give oligosaccharides with 4-deoxy-alpha-D-gluc-4-enuronosyl groups at their non-reducing ends.
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/TrEMBL
        O50325_DICCH | O50325: 3b4n 3b90

(-) Related Entries Specified in the PDB File

3b4n THE UNLIGANDED STRUCTURE OF PECTATE LYASE PELI.
3b90