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(-) Description

Title :  FAMILY 10 POLYSACCHARIDE LYASE FROM CELLVIBRIO CELLULOSA
 
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) - 19 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.32
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
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, B
    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
    Organism Scientific: CELLVIBRIO CELLULOSA
    Organism Taxid: 155077
    Synonym: POLYGALACTURONIC ACID LYASE

 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
1GOL4Ligand/IonGLYCEROL
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:428 , ASP A:445 , HIS A:446 , GLY A:514 , ALA A:515 , HOH A:2400BINDING SITE FOR RESIDUE GOL A1650
2AC2SOFTWAREARG A:417 , ALA A:420 , ASN A:421 , PHE A:476 , ASP A:480 , ARG A:483 , PHE A:484 , HOH A:2187 , HOH A:2401BINDING SITE FOR RESIDUE GOL A1651
3AC3SOFTWARELYS A:348 , TRP A:349 , ASN A:390 , GLY A:391 , ALA A:392 , GLU A:396 , HOH A:2402 , HOH A:2403BINDING SITE FOR RESIDUE GOL A1652
4AC4SOFTWARELYS B:348 , ASN B:370 , LEU B:371 , GLY B:391 , GLU B:396 , HOH B:2064 , HOH B:2432BINDING SITE FOR RESIDUE GOL B1650

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:437 -Pro A:438
2Ala A:469 -Pro A:470
3Tyr B:437 -Pro B:438
4Ala B:469 -Pro B:470

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1GXM)

(-) 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:324
 aligned with Q9F7L3_CELJA | Q9F7L3 from UniProtKB/TrEMBL  Length:649

    Alignment length:324
                                   335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645    
         Q9F7L3_CELJA   326 ATGRMLTLDGNPAANWLNNARTKWSASRADVVLSYQQNNGGWPKNLDYNSVGNGGGGNESGTIDNGATITEMVFLAEVYKSGGNTKYRDAVRKAANFLVNSQYSTGALPQFYPLKGGYSDHATFNDNGMAYALTVLDFAANKRAPFDTDVFSDSDRTRFKTAVTKGTDYILKAQWKQNGVLTVWCAQHGALDYQPKKARAYELESLSGSESVGVLAFLMTQPQTAEIERAVRAGVAWFNSPRTYLEGYTYDSSLAATNPIVPRAGSKMWYRFYDLNTNRGFFSDRDGSKFYDITQMSLERRTGYSWGGNYGTSIINFAQKVGYL 649
               SCOP domains d1gxma_ A: Polygalacturonic acid lyase (pectate lyase)                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1gxmA00 A:326-649  [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........ee.....ee.hhhhhhhhhhhhh..ee.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1gxm A 326 MTGRMLTLDGNPAANWLNNARTKWSASRADVVLSYQQNNGGWPKNLDYNSVGNGGGGNESGTIDNGATITEMVFLAEVYKSGGNTKYRDAVRKAANFLVNSQYSTGALPQFYPLKGGYSDHATFNDNGMAYALTVLDFAANKRAPFDTDVFSDNDRTRFKTAVTKGTDYILKAQWKQNGVLTVWCAQHGALDYQPKKARAYELESLSGSESVGVLAFLMTQPQTAEIEQAVRAGVAWFNSPRTYLEGYTYDSSLAATNPIVPRAGSKMWYRFYDLNTNRGFFSDRDGSKFYDITQMSLERRTGYSWGGNYGTSIINFAQKVGYL 649
                                   335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645    


Chain B from PDB  Type:PROTEIN  Length:332
 aligned with Q9F7L3_CELJA | Q9F7L3 from UniProtKB/TrEMBL  Length:649

    Alignment length:382
                                   277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647  
         Q9F7L3_CELJA   268 GNNLVQLTSRTADGLANIDYLRVEGASTTAGSCSGNTGSSVSSVRSSSSVASSSSSSQATGRMLTLDGNPAANWLNNARTKWSASRADVVLSYQQNNGGWPKNLDYNSVGNGGGGNESGTIDNGATITEMVFLAEVYKSGGNTKYRDAVRKAANFLVNSQYSTGALPQFYPLKGGYSDHATFNDNGMAYALTVLDFAANKRAPFDTDVFSDSDRTRFKTAVTKGTDYILKAQWKQNGVLTVWCAQHGALDYQPKKARAYELESLSGSESVGVLAFLMTQPQTAEIERAVRAGVAWFNSPRTYLEGYTYDSSLAATNPIVPRAGSKMWYRFYDLNTNRGFFSDRDGSKFYDITQMSLERRTGYSWGGNYGTSIINFAQKVGYL 649
               SCOP domains d     1gxm                                             b_ B: Polygalacturonic acid lyase (pectate lyase)                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1     gxmB                                             00 B:318-649  [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..hhhhhhhhhhh...hhhhhhhhhhhhhhhh.....eeeeee.hhhh....eeeeeeeeeee.ee..................hhhhhhhhhhhhh..ee.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gxm B 318 G-----LVPR---------------------------------------------GSHMTGRMLTLDGNPAANWLNNARTKWSASRADVVLSYQQNNGGWPKNLDYNSVGNGGGGNESGTIDNGATITEMVFLAEVYKSGGNTKYRDAVRKAANFLVNSQYSTGALPQFYPLKGGYSDHATFNDNGMAYALTVLDFAANKRAPFDTDVFSDNDRTRFKTAVTKGTDYILKAQWKQNGVLTVWCAQHGALDYQPKKARAYELESLSGSESVGVLAFLMTQPQTAEIEQAVRAGVAWFNSPRTYLEGYTYDSSLAATNPIVPRAGSKMWYRFYDLNTNRGFFSDRDGSKFYDITQMSLERRTGYSWGGNYGTSIINFAQKVGYL 649
                            |     |322         -         -         -         -     | 327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647  
                          318   319  |                                           323                                                                                                                                                                                                                                                                                                                                      
                                   322
   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 alpha proteins (14657)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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: 1gxn 1gxo

(-) Related Entries Specified in the PDB File

1gxn FAMILY 10 POLYSACCHARIDE LYASE FROM PSEUDEMONAS CELLULOSA
1gxo MUTANT D189A OF FAMILY 10 POLYSACCHARIDE LYASE FROM PSEUDEMONAS CELLULOSA IN COMPLEX WITH TRIGALATURONIC ACID