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(-) Description

Title :  PECTIN METHYLESTERASE PEMA FROM ERWINIA CHRYSANTHEMI
 
Authors :  J. Jenkins, O. Mayans, D. Smith, K. Worboys, R. Pickersgill
Date :  05 Jul 99  (Deposition) - 14 Jul 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.37
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase (Aspartyl Esterase), Esterase, Pectin Degradation, Right-Handed Parallel Beta Helix (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Jenkins, O. Mayans, D. Smith, K. Worboys, R. Pickersgill
Three-Dimensional Structure Of Erwinia Chrysanthemi Pectin Methylesterase Reveals A Novel Esterase Active Site
J. Mol. Biol. V. 305 951 2001
PubMed-ID: 11162105  |  Reference-DOI: 10.1006/JMBI.2000.4324
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PECTIN METHYLESTERASE
    Cellular LocationEXTRACELLULAR
    ChainsA, B
    EC Number3.1.1.11
    EngineeredYES
    Expression SystemBACILLUS SUBTILIS
    Expression System Cellular LocationSECRETED
    Expression System GeneALPHA AMYLASE PROMOTER
    Expression System PlasmidPKTH1746
    Expression System StrainIHO 6064 (SACA321, METB5)
    Expression System Taxid1423
    FragmentMATURE ENZYME (RESIDUES 25-366)
    GenePEMA
    Organism ScientificERWINIA CHRYSANTHEMI
    Organism Taxid556
    Other DetailsTHE EXPRESSION SYSTEM STRAIN IS FROM THE UK NATIONAL COLLECTION OF PLANT PATHOGENIC BACTERIA (NCPPB)
    StrainB374
    SynonymPECTINESTERASE

 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, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:272BINDING SITE FOR RESIDUE CL A 400
2AC2SOFTWARETHR B:272BINDING SITE FOR RESIDUE CL B 400

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:192 -A:212
2B:192 -B:212

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1QJV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PECTINESTERASE_2PS00503 Pectinesterase signature 2.PMEA_DICCH194-203
 
  2A:194-203
B:194-203
PMEA_DICD3194-203
 
  2A:194-203
B:194-203
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PECTINESTERASE_2PS00503 Pectinesterase signature 2.PMEA_DICCH194-203
 
  1A:194-203
-
PMEA_DICD3194-203
 
  1A:194-203
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PECTINESTERASE_2PS00503 Pectinesterase signature 2.PMEA_DICCH194-203
 
  1-
B:194-203
PMEA_DICD3194-203
 
  1-
B:194-203

(-) Exons   (0, 0)

(no "Exon" information available for 1QJV)

(-) 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:342
 aligned with PMEA_DICCH | P0C1A8 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:342
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364  
           PMEA_DICCH    25 ATTYNAVVSKSSSDGKTFKTIADAIASAPAGSTPFVILIKNGVYNERLTITRNNLLLKGESRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVIRESDSVPAKSYGLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHIYGWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGAAVSKDRRQLTDAQAAEYTQSKVLGDWTPTLP 366
               SCOP domains d1qjva_ A: Pectin methylesterase PemA                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1qjvA00 A:25-366 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eee...........hhhhhhhh.......eeeee..eeee..eee....eeeee.....eeeee.............hhhhhh..eee.....eee.eeeee..hhhhhhh................eee......eeee.eeee.....eee...eeeee..eeee....eee..eeeee..eeee...............eee.........eeee..eeee..................eeee..eeee......eeeee.............eeee.....eeeehhhhheeeee................hhhhhh..hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------PECTINESTE------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qjv A  25 ATTYNAVVSKSSSDGKTFKTIADAIASAPAGSTPFVILIKNGVYNERLTITRNNLHLKGESRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVIRESDSVPAKSYGLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHIYGWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGAAVSKDRRQLTDAQAAEYTQSKVLGDWTPTLP 366
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364  

Chain A from PDB  Type:PROTEIN  Length:342
 aligned with PMEA_DICD3 | P0C1A9 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:342
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364  
           PMEA_DICD3    25 ATTYNAVVSKSSSDGKTFKTIADAIASAPAGSTPFVILIKNGVYNERLTITRNNLHLKGESRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVIRESDSVPAKSYGLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHIYGWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGATVSKDRRQLTDAQAAEYTQSKVLGDWTPTLP 366
               SCOP domains d1qjva_ A: Pectin methylesterase PemA                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1qjvA00 A:25-366 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eee...........hhhhhhhh.......eeeee..eeee..eee....eeeee.....eeeee.............hhhhhh..eee.....eee.eeeee..hhhhhhh................eee......eeee.eeee.....eee...eeeee..eeee....eee..eeeee..eeee...............eee.........eeee..eeee..................eeee..eeee......eeeee.............eeee.....eeeehhhhheeeee................hhhhhh..hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------PECTINESTE------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qjv A  25 ATTYNAVVSKSSSDGKTFKTIADAIASAPAGSTPFVILIKNGVYNERLTITRNNLHLKGESRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVIRESDSVPAKSYGLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHIYGWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGAAVSKDRRQLTDAQAAEYTQSKVLGDWTPTLP 366
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364  

Chain B from PDB  Type:PROTEIN  Length:342
 aligned with PMEA_DICCH | P0C1A8 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:342
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364  
           PMEA_DICCH    25 ATTYNAVVSKSSSDGKTFKTIADAIASAPAGSTPFVILIKNGVYNERLTITRNNLLLKGESRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVIRESDSVPAKSYGLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHIYGWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGAAVSKDRRQLTDAQAAEYTQSKVLGDWTPTLP 366
               SCOP domains d1qjvb_ B: Pectin methylesterase PemA                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1qjvB00 B:25-366 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eee...........hhhhhhhh.......eeeee..eeee..eee....eeeee.....eeeee.............hhhhhh..eee.....eee.eeeee..hhhhhhhh...............eee......eeee.eeee.....eee...eeeee..eeee....eee..eeeee..eeee...............eee.........eeee..eeee..................eeee..eeee......eeeee.............eeee.....eeeehhhhheeeee................hhhhhh..hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------PECTINESTE------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qjv B  25 ATTYNAVVSKSSSDGKTFKTIADAIASAPAGSTPFVILIKNGVYNERLTITRNNLHLKGESRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVIRESDSVPAKSYGLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHIYGWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGAAVSKDRRQLTDAQAAEYTQSKVLGDWTPTLP 366
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364  

Chain B from PDB  Type:PROTEIN  Length:342
 aligned with PMEA_DICD3 | P0C1A9 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:342
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364  
           PMEA_DICD3    25 ATTYNAVVSKSSSDGKTFKTIADAIASAPAGSTPFVILIKNGVYNERLTITRNNLHLKGESRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVIRESDSVPAKSYGLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHIYGWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGATVSKDRRQLTDAQAAEYTQSKVLGDWTPTLP 366
               SCOP domains d1qjvb_ B: Pectin methylesterase PemA                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1qjvB00 B:25-366 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eee...........hhhhhhhh.......eeeee..eeee..eee....eeeee.....eeeee.............hhhhhh..eee.....eee.eeeee..hhhhhhhh...............eee......eeee.eeee.....eee...eeeee..eeee....eee..eeeee..eeee...............eee.........eeee..eeee..................eeee..eeee......eeeee.............eeee.....eeeehhhhheeeee................hhhhhh..hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------PECTINESTE------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qjv B  25 ATTYNAVVSKSSSDGKTFKTIADAIASAPAGSTPFVILIKNGVYNERLTITRNNLHLKGESRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVIRESDSVPAKSYGLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHIYGWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGAAVSKDRRQLTDAQAAEYTQSKVLGDWTPTLP 366
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364  

   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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PMEA_DICCH | P0C1A8)
molecular function
    GO:0045330    aspartyl esterase activity    Catalysis of the hydrolysis of an ester bond by a mechanism involving a catalytically active aspartic acid residue.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0030599    pectinesterase activity    Catalysis of the reaction: pectin + n H2O = n methanol + pectate.
biological process
    GO:0042545    cell wall modification    The series of events leading to chemical and structural alterations of an existing cell wall that can result in loosening, increased extensibility or disassembly.
    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: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:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    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   (PMEA_DICD3 | P0C1A9)
molecular function
    GO:0045330    aspartyl esterase activity    Catalysis of the hydrolysis of an ester bond by a mechanism involving a catalytically active aspartic acid residue.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0030599    pectinesterase activity    Catalysis of the reaction: pectin + n H2O = n methanol + pectate.
biological process
    GO:0042545    cell wall modification    The series of events leading to chemical and structural alterations of an existing cell wall that can result in loosening, increased extensibility or disassembly.
    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: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:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    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)

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        PMEA_DICD3 | P0C1A92nsp 2nst 2nt6 2nt9 2ntb 2ntp 2ntq

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1QJV)