Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF PECTATE LYASE II FROM XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS STR. ATCC 33913
 
Authors :  M. L. Garron, D. Shaya
Date :  10 Aug 07  (Deposition) - 04 Mar 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Parallel Beta Helix, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. C. Lau, Z. Z. Xiao, T. Sulea, H. Bergeron, S. Grosse, M. Beauchemin
A Seductive Method To Improve The Thermostability And Activity Of An Enzyme
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PECTATE LYASE II
    Chains: A, B
    EC Number: 4.2.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PELB
    Organism Scientific: XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS
    Organism Taxid: 340
    Strain: ATCC 33913

 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, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1PO45Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1PO43Ligand/IonPHOSPHATE ION

(-) Sites  (0, 0)

(no "Site" information available for 2QX3)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:79 -A:166
2B:79 -B:166

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:231 -Pro A:232
2Val B:231 -Pro B:232

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QX3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QX3)

(-) Exons   (0, 0)

(no "Exon" information available for 2QX3)

(-) 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:330
 aligned with Q8P6Z9_XANCP | Q8P6Z9 from UniProtKB/TrEMBL  Length:353

    Alignment length:330
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353
         Q8P6Z9_XANCP    24 GPVGYGAATTGGGNKVPVNVATFEAMQSAIDSYSGSGGLVLNYTGKFDFGTIKDVCAQWKLPAKTVQIKNKSDVTIKGANGSAANFGIRVVGNAHNVIIQNMTIGLLQGGEDADSISLEGNSSGEPSKIWVDHNTVFASLTKCSGAGDASFDGGIDMKKGVHHVTVSYNYVYNYQKVALNGYSDSDTKNSAARTTYHHNRFENVESRVPLQRRGLSHIYNNYFNNVTTSGINVRMGGIAKIESNYFENIKNPVTSRDSSEIGYWDLINNYVGSGITWGTPDGSKPYANATNWISTKVFPESLGYIYTVTPAAQVKAKVIATAGAGKNLAE 353
               SCOP domains d2qx3a_ A: automated matches                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2qx3A00 A:24-353 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................eee.hhhhhhhhhhhh.....eeeee....hhhhh............eeeee....eeeee........eeeee...eeeeee..eee...hhhhh..eeee.......eeeeee..eee.................eeee...eeeeee..eeeeeee..ee.....hhhhhh.eeeee..eeeeeee...eee..eeeee..eeeee....eeee...eeeee..eeeeee..eee.......eeeee..ee...ee..........ee.....................hhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qx3 A  24 GPVGYGAATTGGGNKVPVNVATFEAMQSAIDSYSGSGGLVLNYTGKFDFGTIKDVCAQWKLPAKTVQIKNKSDVTIKGANGSAANFGIRVVGNAHNVIIQNMTIGLLQGGEDADSISLEGNSSGEPSKIWVDHNTVFASLTKCSGAGDASFDGGIDMKKGVHHVTVSYNYVYNYQKVALNGYSDSDTKNSAARTTYHHNRFENVESRVPLQRRGLSHIYNNYFNNVTTSGINVRMGGIAKIESNYFENIKNPVTSRDSSEIGYWDLINNYVGSGITWGTPDGSKPYANATNWISTKVFPESLGYIYTVTPAAQVKAKVIATAGAGKNLAE 353
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353


Chain B from PDB  Type:PROTEIN  Length:330
 aligned with Q8P6Z9_XANCP | Q8P6Z9 from UniProtKB/TrEMBL  Length:353

    Alignment length:330
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353
         Q8P6Z9_XANCP    24 GPVGYGAATTGGGNKVPVNVATFEAMQSAIDSYSGSGGLVLNYTGKFDFGTIKDVCAQWKLPAKTVQIKNKSDVTIKGANGSAANFGIRVVGNAHNVIIQNMTIGLLQGGEDADSISLEGNSSGEPSKIWVDHNTVFASLTKCSGAGDASFDGGIDMKKGVHHVTVSYNYVYNYQKVALNGYSDSDTKNSAARTTYHHNRFENVESRVPLQRRGLSHIYNNYFNNVTTSGINVRMGGIAKIESNYFENIKNPVTSRDSSEIGYWDLINNYVGSGITWGTPDGSKPYANATNWISTKVFPESLGYIYTVTPAAQVKAKVIATAGAGKNLAE 353
               SCOP domains d2qx3b_ B: automated matches                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2qx3B00 B:24-353 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                CATH domains
           Pfam domains (1) ------------------------------------Pec_lyase_C-2qx3B01 B:60-269                                                                                                                                                                                      ------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ------------------------------------Pec_lyase_C-2qx3B02 B:60-269                                                                                                                                                                                      ------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author .................eee.hhhhhhhhhhhh.....eeeee....hhhhh.hhhhh......eeeee....eeeee........eeeee...eeeeee..eee...hhhhh..eeee.......eeeeee..eee.................eeee...eeeeee..eeeeeee..ee.....hhhhhh.eeeee..eeeeeee...eee..eeeee..eeeee....eeee...eeeee..eeeeee..eee.......eeeee..ee...ee..........ee.....................hhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qx3 B  24 GPVGYGAATTGGGNKVPVNVATFEAMQSAIDSYSGSGGLVLNYTGKFDFGTIKDVCAQWKLPAKTVQIKNKSDVTIKGANGSAANFGIRVVGNAHNVIIQNMTIGLLQGGEDADSISLEGNSSGEPSKIWVDHNTVFASLTKCSGAGDASFDGGIDMKKGVHHVTVSYNYVYNYQKVALNGYSDSDTKNSAARTTYHHNRFENVESRVPLQRRGLSHIYNNYFNNVTTSGINVRMGGIAKIESNYFENIKNPVTSRDSSEIGYWDLINNYVGSGITWGTPDGSKPYANATNWISTKVFPESLGYIYTVTPAAQVKAKVIATAGAGKNLAE 353
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353
   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  (1, 2)

Asymmetric Unit
(-)
Clan: Pec_lyase (42)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8P6Z9_XANCP | Q8P6Z9)
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.
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.
    GO:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 2qx3)
 
  Cis Peptide Bonds
    Val A:231 - Pro A:232   [ RasMol ]  
    Val B:231 - Pro B:232   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2qx3
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q8P6Z9_XANCP | Q8P6Z9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  4.2.2.2
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q8P6Z9_XANCP | Q8P6Z9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8P6Z9_XANCP | Q8P6Z9: 2qxz 2qy1

(-) Related Entries Specified in the PDB File

2qxz