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(-) Description

Title :  STRUCTURE OF A PECTATE LYASE FROM AZOSPIRILLUM IRAKENSE
 
Authors :  H. Novoa De Armas, C. Verboven, C. De Ranter, J. Desair, A. Vande Bro J. Vanderleyden, A. Rabijns
Date :  20 Oct 03  (Deposition) - 01 Jun 04  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A
Keywords :  A-Helical Structure, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Novoa De Armas, C. Verboven, C. De Ranter, J. Desair, A. Vande Broek, J. Vanderleyden, A. Rabijns
Azospirillum Irakense Pectate Lyase Displays A Toroidal Fold.
Acta Crystallogr. , Sect. D V. 60 999 2004
PubMed-ID: 15159558  |  Reference-DOI: 10.1107/S090744490400602X

(-) Compounds

Molecule 1 - PECTATE LYASE
    Chains: A
    EC Number: 4.2.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 25-432
    Gene: PELA
    Organism Scientific: AZOSPIRILLUM IRAKENSE
    Organism Taxid: 34011

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL4Ligand/IonGLYCEROL
3HG1Ligand/IonMERCURY (II) ION
4IPA1Ligand/IonISOPROPYL ALCOHOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:215 , CYS A:277BINDING SITE FOR RESIDUE HG A 4000
2AC2SOFTWARELYS A:105 , ARG A:253BINDING SITE FOR RESIDUE CL A 5000
3AC3SOFTWAREMET A:327 , GLU A:328 , ILE A:329 , ARG A:431BINDING SITE FOR RESIDUE IPA A 8244
4AC4SOFTWARELYS A:126 , ASN A:172 , HOH A:1217BINDING SITE FOR RESIDUE GOL A 4901
5AC5SOFTWARESER A:104 , LYS A:105 , ALA A:106 , HOH A:1153BINDING SITE FOR RESIDUE GOL A 5901
6AC6SOFTWAREGLN A:48 , ASP A:398BINDING SITE FOR RESIDUE GOL A 6901

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R76)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Trp A:222 -Pro A:223

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R76)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R76)

(-) Exons   (0, 0)

(no "Exon" information available for 1R76)

(-) 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:384
 aligned with Q9X592_NIVIR | Q9X592 from UniProtKB/TrEMBL  Length:432

    Alignment length:408
                                    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       374       384       394       404       414       424        
         Q9X592_NIVIR    25 AVIGMNEAASALTPSRVSSLPDTQRAAWQEYLARSEAQLSRDKASLAAELAPGQPLPPPPAEGKGADTMPLDKPAAWYTSKAARHVADVIVSFQTPAGGWGKNQPRDGALRLPGQHYTGENVAKVKSGSNDLDAARDRDWHYVGTIDNDATVTEIRFLAQVVSQLAPEEAAPYRDAALKGIEYLLASQFPNGGWPQVWPLEGGYHDAITYNDDALVHVAELLSDIAAGRDGFGFVPPAIRTRALEATNAAIHCIVETQVVQDGKRLGWGQQHDALTLRPTSARNFEPAALSSTESARILLFLMEIEAPSDAVKQAIRGGVAWLNTSVIRDRAWVKSDQGYQLVTEQGAKPLWSRFYSLDGNKPVFGDRDKTIHDDVMGISQERRTGYAWYTTSPQKALSAFTKWEKRS 432
               SCOP domains d1r76a_ A: Polygalacturonic acid lyase (pectate lyase)                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1r76A00 A:25-432  [code=1.50.10.20, no name defined]                                                                                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee.......hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhh....hhhhhhhhhhhhhhhhhhhhh................................---------..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhee...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.ee..ee.....ee.................eehhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....---------------......ee.ee........ee....eee.hhhhhhhhhhh....ee..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1r76 A  25 AVIGMNEAASALTPSRVSSLPDTQRAAWQEYLARSEAQLSRDKASLAAELAPGQPLPPPPAEGKGADTMPLDKPAAWYTSKAARHVADVIVSFQTPAGGWGKNQPRDGALRLPGQHYTGENVAKVK---------RDRDWHYVGTIDNDATVTEIRFLAQVVSQLAPEEAAPYRDAALKGIEYLLASQFPNGGWPQVWPLEGGYHDAITYNDDALVHVAELLSDIAAGRDGFGFVPPAIRTRALEATNAAIHCIVETQVVQDGKRLGWGQQHDALTLRPTSARNFEPAALSSTESARILLFLMEIEAPSDAVKQAIRGGVAWLNTSVIRD---------------QGAKPLWSRFYSLDGNKPVFGDRDKTIHDDVMGISQERRTGYAWYTTSPQKALSAFTKWEKRS 432
                                    34        44        54        64        74        84        94       104       114       124       134       144     |   -     | 164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354         -     | 374       384       394       404       414       424        
                                                                                                                                                       150       160                                                                                                                                                                                               354             370
   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 alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1R76)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9X592_NIVIR | Q9X592)
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.

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  1r76
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 Related Entries

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