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(-) Description

Title :  MUTANT D189A OF FAMILY 10 POLYSACCHARIDE LYASE FROM CELLVIBRIO CELLULOSA IN COMPLEX WITH TRIGALATURONIC ACID
 
Authors :  S. J. Charnock, I. E. Brown, J. P. Turkenburg, G. W. Black, G. J. Davies
Date :  08 Apr 02  (Deposition) - 04 Oct 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A
Keywords :  Lyase, Pectate, Mechanism, Elimination (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Charnock, I. E. Brown, J. P. Turkenburg, G. W. Black, G. J. Davies
Convergent Evolution Sheds Light On The Anti-Beta- Elimination Mechanism Common To Family 1 And 10 Polysaccharide Lyases
Proc. Natl. Acad. Sci. Usa V. 99 12067 2002
PubMed-ID: 12221284  |  Reference-DOI: 10.1073/PNAS.182431199

(-) Compounds

Molecule 1 - PECTATE LYASE
    Chains: A
    EC Number: 4.2.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Variant: DE3
    Fragment: CATALYTIC MODULE, RESIDUES 327-649
    Mutation: YES
    Organism Scientific: CELLVIBRIO CELLULOSA
    Organism Taxid: 155077
    Other Details: COMPLEX WITH TRIGALACTURONIC ACID
    Synonym: POLYGALACTURONIC ACID LYASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ADA3Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
2CA1Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:524 , TYR A:526 , ARG A:610 , ADA A:1650 , HOH A:2165 , HOH A:2166 , HOH A:2167BINDING SITE FOR RESIDUE ADA A1649
2AC2SOFTWAREASN A:390 , ARG A:524 , ARG A:625 , GLY A:628 , TYR A:629 , ADA A:1649 , ADA A:1651 , CA A:1652 , HOH A:2168BINDING SITE FOR RESIDUE ADA A1650
3AC3SOFTWAREARG A:596 , GLY A:628 , TYR A:629 , SER A:630 , ADA A:1650 , CA A:1652 , HOH A:2149 , HOH A:2169BINDING SITE FOR RESIDUE ADA A1651
4AC4SOFTWAREASN A:390 , ASP A:451 , ADA A:1650 , ADA A:1651 , HOH A:2095 , HOH A:2168 , HOH A:2169BINDING SITE FOR RESIDUE CA A1652

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:437 -Pro A:438
2Ala A:469 -Pro A:470

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1GXO)

(-) 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:320
 aligned with Q9F7L3_CELJA | Q9F7L3 from UniProtKB/TrEMBL  Length:649

    Alignment length:320
                                   338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648
         Q9F7L3_CELJA   329 RMLTLDGNPAANWLNNARTKWSASRADVVLSYQQNNGGWPKNLDYNSVGNGGGGNESGTIDNGATITEMVFLAEVYKSGGNTKYRDAVRKAANFLVNSQYSTGALPQFYPLKGGYSDHATFNDNGMAYALTVLDFAANKRAPFDTDVFSDSDRTRFKTAVTKGTDYILKAQWKQNGVLTVWCAQHGALDYQPKKARAYELESLSGSESVGVLAFLMTQPQTAEIERAVRAGVAWFNSPRTYLEGYTYDSSLAATNPIVPRAGSKMWYRFYDLNTNRGFFSDRDGSKFYDITQMSLERRTGYSWGGNYGTSIINFAQKVGY 648
               SCOP domains d1gxoa_ A: Polygalacturonic acid lyase (pectate lyase)                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1gxoA00 A:329-648  [code=1.50.10.20, no name defined]                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh...hhhhhhhhhhh.........................ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ee...hhhhhhee...hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh.ee..ee.....ee.................ee..hhhhhhhhhh....hhhhhhhhhhhhhhhh.....eeeeee.hhhh....eeeeeeeeeee.ee..................hhhhhhhhhhhhh..ee.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gxo A 329 RMLTLDGNPAANWLNNARTKWSASRADVVLSYQQNNGGWPKNLDYNSVGNGGGGNESGTIANGATITEMVFLAEVYKSGGNTKYRDAVRKAANFLVNSQYSTGALPQFYPLKGGYSDHATFNDNGMAYALTVLDFAANKRAPFDTDVFSDNDRTRFKTAVTKGTDYILKAQWKQNGVLTVWCAQHGALDYQPKKARAYELESLSGSESVGVLAFLMTQPQTAEIEQAVRAGVAWFNSPRTYLEGYTYDSSLAATNPIVPRAGSKMWYRFYDLNTNRGFFSDRDGSKFYDITQMSLERRTGYSWGGNYGTSIINFAQKVGY 648
                                   338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648
   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 1GXO)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9F7L3_CELJA | Q9F7L3)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    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:0030247    polysaccharide binding    Interacting selectively and non-covalently with any polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q9F7L3_CELJA | Q9F7L3: 1gxm 1gxn

(-) Related Entries Specified in the PDB File

1gxm FAMILY 10 POLYSACCHARIDE LYASE FROM PSEUDEMONAS CELLULOSA
1gxn FAMILY 10 POLYSACCHARIDE LYASE FROM PSEUDEMONAS CELLULOSA