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(-) Description

Title :  CRYSTAL STRUCTURE OF THE R3 FORM OF PECTATE LYASE A, ERWINIA CHRYSANTHEMI
 
Authors :  L. M. Thomas, C. Doan, R. L. Oliver, M. D. Yoder
Date :  13 Aug 01  (Deposition) - 19 Jun 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Parallel Beta Helix Beta Elimination, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. M. Thomas, C. N. Doan, R. L. Oliver, M. D. Yoder
Structure Of Pectate Lyase A: Comparison To Other Isoforms.
Acta Crystallogr. , Sect. D V. 58 1008 2002
PubMed-ID: 12037303  |  Reference-DOI: 10.1107/S0907444902005851
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PECTATE LYASE
    Chains: A, B
    EC Number: 4.2.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPEL812
    Expression System Strain: DH5ALPHA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PECTATE LYASE
    Gene: PELA
    Organism Scientific: ERWINIA CHRYSANTHEMI
    Organism Taxid: 556
    Strain: EC16

 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  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:244 , ARG A:246 , GLY A:275 , THR A:276 , PHE A:304 , ASN A:305BINDING SITE FOR RESIDUE SO4 A 1001
2AC2SOFTWAREARG B:244 , ARG B:246 , GLY B:275 , THR B:276 , PHE B:304 , ASN B:305BINDING SITE FOR RESIDUE SO4 B 1002
3AC3SOFTWAREGLU A:240 , ARG A:241 , ARG A:244 , TYR A:270 , PHE A:304BINDING SITE FOR RESIDUE SO4 A 1003
4AC4SOFTWAREGLU B:240 , ARG B:241 , ARG B:244 , TYR B:270BINDING SITE FOR RESIDUE SO4 B 1004

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:298 -A:326
2B:298 -B:326

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:242 -Pro A:243
2Ala B:242 -Pro B:243

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1JRG)

(-) 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:354
 aligned with PLYA_DICCH | P0C1A2 from UniProtKB/Swiss-Prot  Length:393

    Alignment length:361
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392 
           PLYA_DICCH    33 AELVSDKALESAPTVGWASQNGFTTGGAAATSDNIYIVTNISEFTSALSAGAEAKIIQIKGTIDISGGTPYTDFADQKARSQINIPANTTVIGLGTDAKFINGSLIIDGTDGTNNVIIRNVYIQTPIDVEPHYEKGDGWNAEWDAMNITNGAHHVWIDHVTISDGNFTDDMYTTKDGETYVQHDGALDIKRGSDYVTISNSLIDQHDKTMLIGHNDTNSAQDKGKLHVTLFNNVFNRVTERAPRVRYGSIHSFNNVFKGDAKDPVYRYQYSFGIGTSGSVLSEGNSFTIANLSASKACKVVKKFNGSIFSDNGSVLNGSAVDLSGCGFSAYTSKIPYIYDVQPMTTELAQSITDNAGSGKL 393
               SCOP domains d1jrga_ A: Pectate lyase                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1jrgA00 A:1-361 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhh..........hhh.eeee.hhhhhhhhhh.....eeeee..eee........hhhhhhhhheee....eeeee.....eee..eeeee.hhh.eeeeee..eee.......ee.....ee.....eeee...eeeeee..eee....hhhhh.ee..ee.......eee....eeeeee..eeeeeee.eee..-------.....eeeee..eeeeeee...ee..eeeeee..eeeee...........eee...eeeeee..eeeee..hhhhhhh.eee....eeeee..ee..ee........................hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jrg A   1 AELVSDKALESAPTVGWASQNGFTTGGAAATSDNIYIVTNISEFTSALSAGAEAKIIQIKGTIDISGGTPYTDFADQKARSQINIPANTTVIGLGTDAKFINGSLIIDGTDGTNNVIIRNVYIQTPIDVEPHYEKGDGWNAEWDAMNITNGAHHVWIDHVTISDGNFTDDMYTTKDGETYVQHDGALDIKRGSDYVTISNSLIDQHDKTMLIGH-------DKGKLHVTLFNNVFNRVTERAPRVRYGSIHSFNNVFKGDAKDPVYRYQYSFGIGTSGSVLSEGNSFTIANLSASKACKVVKKFNGSIFSDNGSVLNGSAVDLSGCGFSAYTSKIPYIYDVQPMTTELAQSITDNAGSGKL 361
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   |     - |     230       240       250       260       270       280       290       300       310       320       330       340       350       360 
                                                                                                                                                                                                                                               214     222                                                                                                                                           


Chain A from PDB  Type:PROTEIN  Length:354
 aligned with PLYA_DICD3 | P0C1A3 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:361
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391 
           PLYA_DICD3    32 AELVNSKALESAPAAGWASQNGSTTGGAAATSDNIYVVTNISEFTSALSAGAVAKIIQITGTVDISGGTPYKDFADQKARSQINIPANTTVIGIGTDAKFINGSLIIDGTDGTNNVIIRNVYIQTPIDVEPHYEKGDGWNAEWDGMNITNGAHHVWVDHVTISDGSFTDDMYTTKDGETYVQHDGALDIKRGSDYVTISNSLFDQHDKTMLIGHSDTNSAQDKGKLHVTLFNNVFNRVTERAPRVRYGSIHSFNNVFNGDVKDPVYRYLYSFGIGTSGSVLSEGNSFTIANLSASKACKVVKKFNGSIFSDNGSVLNGSAADLSGCGFSAYTSAIPYVYAVQPMTTELAQSITDHAGSGKL 392
               SCOP domains d1jrga_ A: Pectate lyase                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1jrgA00 A:1-361 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhh..........hhh.eeee.hhhhhhhhhh.....eeeee..eee........hhhhhhhhheee....eeeee.....eee..eeeee.hhh.eeeeee..eee.......ee.....ee.....eeee...eeeeee..eee....hhhhh.ee..ee.......eee....eeeeee..eeeeeee.eee..-------.....eeeee..eeeeeee...ee..eeeeee..eeeee...........eee...eeeeee..eeeee..hhhhhhh.eee....eeeee..ee..ee........................hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jrg A   1 AELVSDKALESAPTVGWASQNGFTTGGAAATSDNIYIVTNISEFTSALSAGAEAKIIQIKGTIDISGGTPYTDFADQKARSQINIPANTTVIGLGTDAKFINGSLIIDGTDGTNNVIIRNVYIQTPIDVEPHYEKGDGWNAEWDAMNITNGAHHVWIDHVTISDGNFTDDMYTTKDGETYVQHDGALDIKRGSDYVTISNSLIDQHDKTMLIGH-------DKGKLHVTLFNNVFNRVTERAPRVRYGSIHSFNNVFKGDAKDPVYRYQYSFGIGTSGSVLSEGNSFTIANLSASKACKVVKKFNGSIFSDNGSVLNGSAVDLSGCGFSAYTSKIPYIYDVQPMTTELAQSITDNAGSGKL 361
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   |     - |     230       240       250       260       270       280       290       300       310       320       330       340       350       360 
                                                                                                                                                                                                                                               214     222                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:350
 aligned with PLYA_DICCH | P0C1A2 from UniProtKB/Swiss-Prot  Length:393

    Alignment length:361
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392 
           PLYA_DICCH    33 AELVSDKALESAPTVGWASQNGFTTGGAAATSDNIYIVTNISEFTSALSAGAEAKIIQIKGTIDISGGTPYTDFADQKARSQINIPANTTVIGLGTDAKFINGSLIIDGTDGTNNVIIRNVYIQTPIDVEPHYEKGDGWNAEWDAMNITNGAHHVWIDHVTISDGNFTDDMYTTKDGETYVQHDGALDIKRGSDYVTISNSLIDQHDKTMLIGHNDTNSAQDKGKLHVTLFNNVFNRVTERAPRVRYGSIHSFNNVFKGDAKDPVYRYQYSFGIGTSGSVLSEGNSFTIANLSASKACKVVKKFNGSIFSDNGSVLNGSAVDLSGCGFSAYTSKIPYIYDVQPMTTELAQSITDNAGSGKL 393
               SCOP domains d1jrgb_ B: Pectate lyase                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1jrgB00 B:1-361 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhh..........hhh.eeee.hhhhhhhhhh.....eeeee..eee........hhhhhhhhheee....eeeee.....eee..eeeee.hhh.eeeeee..eee.....................eeee...eeeeee..eee....hhhhh..............eee....eeeeee..eeeeeee.eee.-----------..eeeee..eeeeeee...ee..eeeeee..eeeee...........eee...eeeeee..eeeee..hhhhhhh.eee....eeeee..ee..ee........................hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jrg B   1 AELVSDKALESAPTVGWASQNGFTTGGAAATSDNIYIVTNISEFTSALSAGAEAKIIQIKGTIDISGGTPYTDFADQKARSQINIPANTTVIGLGTDAKFINGSLIIDGTDGTNNVIIRNVYIQTPIDVEPHYEKGDGWNAEWDAMNITNGAHHVWIDHVTISDGNFTDDMYTTKDGETYVQHDGALDIKRGSDYVTISNSLIDQHDKTMLIG-----------KLHVTLFNNVFNRVTERAPRVRYGSIHSFNNVFKGDAKDPVYRYQYSFGIGTSGSVLSEGNSFTIANLSASKACKVVKKFNGSIFSDNGSVLNGSAVDLSGCGFSAYTSKIPYIYDVQPMTTELAQSITDNAGSGKL 361
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  |      -    |  230       240       250       260       270       280       290       300       310       320       330       340       350       360 
                                                                                                                                                                                                                                              213         225                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:350
 aligned with PLYA_DICD3 | P0C1A3 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:361
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391 
           PLYA_DICD3    32 AELVNSKALESAPAAGWASQNGSTTGGAAATSDNIYVVTNISEFTSALSAGAVAKIIQITGTVDISGGTPYKDFADQKARSQINIPANTTVIGIGTDAKFINGSLIIDGTDGTNNVIIRNVYIQTPIDVEPHYEKGDGWNAEWDGMNITNGAHHVWVDHVTISDGSFTDDMYTTKDGETYVQHDGALDIKRGSDYVTISNSLFDQHDKTMLIGHSDTNSAQDKGKLHVTLFNNVFNRVTERAPRVRYGSIHSFNNVFNGDVKDPVYRYLYSFGIGTSGSVLSEGNSFTIANLSASKACKVVKKFNGSIFSDNGSVLNGSAADLSGCGFSAYTSAIPYVYAVQPMTTELAQSITDHAGSGKL 392
               SCOP domains d1jrgb_ B: Pectate lyase                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1jrgB00 B:1-361 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhh..........hhh.eeee.hhhhhhhhhh.....eeeee..eee........hhhhhhhhheee....eeeee.....eee..eeeee.hhh.eeeeee..eee.....................eeee...eeeeee..eee....hhhhh..............eee....eeeeee..eeeeeee.eee.-----------..eeeee..eeeeeee...ee..eeeeee..eeeee...........eee...eeeeee..eeeee..hhhhhhh.eee....eeeee..ee..ee........................hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jrg B   1 AELVSDKALESAPTVGWASQNGFTTGGAAATSDNIYIVTNISEFTSALSAGAEAKIIQIKGTIDISGGTPYTDFADQKARSQINIPANTTVIGLGTDAKFINGSLIIDGTDGTNNVIIRNVYIQTPIDVEPHYEKGDGWNAEWDAMNITNGAHHVWIDHVTISDGNFTDDMYTTKDGETYVQHDGALDIKRGSDYVTISNSLIDQHDKTMLIG-----------KLHVTLFNNVFNRVTERAPRVRYGSIHSFNNVFKGDAKDPVYRYQYSFGIGTSGSVLSEGNSFTIANLSASKACKVVKKFNGSIFSDNGSVLNGSAVDLSGCGFSAYTSKIPYIYDVQPMTTELAQSITDNAGSGKL 361
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  |      -    |  230       240       250       260       270       280       290       300       310       320       330       340       350       360 
                                                                                                                                                                                                                                              213         225
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1JRG)

(-) Gene Ontology  (5, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PLYA_DICCH | P0C1A2)
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.
biological process
    GO:0045490    pectin catabolic process    The chemical reactions and pathways resulting in the breakdown of pectin, a polymer containing a backbone of alpha-1,4-linked D-galacturonic acid residues.
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.

Chain A,B   (PLYA_DICD3 | P0C1A3)
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.
biological process
    GO:0045490    pectin catabolic process    The chemical reactions and pathways resulting in the breakdown of pectin, a polymer containing a backbone of alpha-1,4-linked D-galacturonic acid residues.
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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  1jrg
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PLYA_DICCH | P0C1A2: 1jta 1ooc 1pe9
        PLYA_DICD3 | P0C1A3: 1jta 1ooc 1pe9

(-) Related Entries Specified in the PDB File

1jta 1JTA CONTAINS THE SAME PROTEIN WITH A DIFFERENT SPACE GROUP (C121)