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(-) Description

Title :  HEXASACCHARIDE I BOUND TO BACILLUS SUBTILIS PECTATE LYASE
 
Authors :  R. W. Pickersgill, A. Seyedarabi
Date :  24 Nov 06  (Deposition) - 20 Nov 07  (Release) - 28 Apr 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Michaelis Complex, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Seyedarabi, T. T. To, S. Ali, S. Hussain, M. Fries, R. Madsen, M. H. Clausen, S. Teixteira, K. Brocklehurst, R. W. Pickersgill
Structural Insights Into Substrate Specificity And The Anti Beta-Elimination Mechanism Of Pectate Lyase.
Biochemistry V. 49 539 2010
PubMed-ID: 20000851  |  Reference-DOI: 10.1021/BI901503G

(-) Compounds

Molecule 1 - PECTATE LYASE
    Chains: A
    EC Number: 4.2.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET3D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PEL, BSU07560
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: PL

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1ADA5Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
2CA3Ligand/IonCALCIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:173 , ASN A:178 , GLN A:278 , ARG A:282 , PHE A:339 , ADA A:401 , CA A:406 , HOH A:489 , HOH A:562 , HOH A:564 , HOH A:685 , HOH A:694 , HOH A:864 , HOH A:934BINDING SITE FOR RESIDUE ADA A 400
2AC2SOFTWAREASN A:180 , ASP A:223 , LYS A:247 , ILE A:250 , ARG A:284 , ADA A:400 , ADA A:402 , CA A:406 , CA A:407 , HOH A:501 , HOH A:671 , HOH A:965BINDING SITE FOR RESIDUE ADA A 401
3AC3SOFTWAREASP A:223 , ASP A:227 , ADA A:401 , ADA A:403 , CA A:405 , CA A:407 , HOH A:457 , HOH A:501 , HOH A:528 , HOH A:565 , HOH A:731 , HOH A:980BINDING SITE FOR RESIDUE ADA A 402
4AC4SOFTWAREGLN A:182 , SER A:229 , SER A:253 , LYS A:257 , ADA A:402 , ADA A:404 , HOH A:980BINDING SITE FOR RESIDUE ADA A 403
5AC5SOFTWARELYS A:118 , ASN A:189 , ASN A:230 , ADA A:403 , HOH A:609 , HOH A:674 , HOH A:781 , HOH A:837BINDING SITE FOR RESIDUE ADA A 404
6AC6SOFTWAREASP A:184 , ASP A:223 , ASP A:227 , ADA A:402 , HOH A:457 , HOH A:896BINDING SITE FOR RESIDUE CA A 405
7AC7SOFTWAREASP A:173 , ASN A:180 , ADA A:400 , ADA A:401 , HOH A:564 , HOH A:565BINDING SITE FOR RESIDUE CA A 406
8AC8SOFTWAREASP A:223 , ADA A:401 , ADA A:402 , HOH A:501 , HOH A:524 , HOH A:671BINDING SITE FOR RESIDUE CA A 407

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2NZM)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:280 -Pro A:281

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2NZM)

(-) 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:399
 aligned with PLY_BACSU | P39116 from UniProtKB/Swiss-Prot  Length:420

    Alignment length:399
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411         
            PLY_BACSU    22 ADLGHQTLGSNDGWGAYSTGTTGGSKASSSNVYTVSNRNQLVSALGKETNTTPKIIYIKGTIDMNVDDNLKPLGLNDYKDPEYDLDKYLKAYDPSTWGKKEPSGTQEEARARSQKNQKARVMVDIPANTTIVGSGTNAKVVGGNFQIKSDNVIIRNIEFQDAYDYFPQWDPTDGSSGNWNSQYDNITINGGTHIWIDHCTFNDGSRPDSTSPKYYGRKYQHHDGQTDASNGANYITMSYNYYHDHDKSSIFGSSDSKTSDDGKLKITLHHNRYKNIVQRAPRVRFGQVHVYNNYYEGSTSSSSYPFSYAWGIGKSSKIYAQNNVIDVPGLSAAKTISVFSGGTALYDSGTLLNGTQINASAANGLSSSVGWTPSLHGSIDASANVKSNVINQAGAGKLN 420
               SCOP domains d2nzma_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2nzmA00 A:1-399 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------Pec_lyase_C-2nzmA01 A:51-325                                                                                                                                                                                                                                                       -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhh..........hhh.eeee.hhhhhhhhhh.......eeeee..eee..........hhhhhh....hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhheee....eeeee.....eee..eeee..eeeeee..eee.......eee.......eee.....eeee..eeeeee..eee....hhhhh.ee..ee.......eeee...eeeeee..eeeeeee..ee.....hhhhh....eeee..eeeeeee...ee....eeee..eee.............eee......eee..eee.....hhh.eee.......eee..ee..ee.hhhhhh.................hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nzm A   1 ADLGHQTLGSNDGWGAYSTGTTGGSKASSSNVYTVSNRNQLVSALGKETNTTPKIIYIKGTIDMNVDDNLKPLGLNDYKDPEYDLDKYLKAYDPSTWGKKEPSGTQEEARARSQKNQKARVMVDIPANTTIVGSGTNAKVVGGNFQIKSDNVIIRNIEFQDAYDYFPQWDPTDGSSGNWNSQYDNITINGGTHIWIDHCTFNDGSRPDSTSPKYYGRKYQHHDGQTDASNGANYITMSYNYYHDHDKSSIFGSSDSKTSDDGKLKITLHHNRYKNIVQAAPRVRFGQVHVYNNYYEGSTSSSSYPFSYAWGIGKSSKIYAQNNVIDVPGLSAAKTISVFSGGTALYDSGTLLNGTQINASAANGLSSSVGWTPSLHGSIDASANVKSNVINQAGAGKLN 399
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390
   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 beta proteins (24004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Pec_lyase (42)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PLY_BACSU | P39116)
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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0030570    pectate lyase activity    Catalysis of the reaction: a pectate = a pectate + a pectate oligosaccharide with 4-(4-deoxy-alpha-D-galact-4-enuronosyl)-D-galacturonate end. This reaction is the eliminative cleavage of pectate to give oligosaccharides with 4-deoxy-alpha-D-gluc-4-enuronosyl groups at their non-reducing ends.
biological process
    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: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)

UniProtKB/Swiss-Prot
        PLY_BACSU | P39116: 1bn8 2bsp 2o04 2o0v 2o0w 2o17 2o1d 3krg 5amv

(-) Related Entries Specified in the PDB File

1bn8 PECTATE LYASE WITH ONE CALCIUM
2o04 PECTATE LYASE IN COMPLEX WITH HEXASACCHARIDE II (THREE CALCIUMS)
2o0v PECTATE LYASE IN COMPLEX WITH HEXASACCHARIDE III (THREE CALCIUMS)
2o0w PECTATE LYASE WITH ONE CALCIUM (NO COMPLEX FORMED WITH COMPOUND IV)
2o17 PECTATE LYASE IN COMPLEX WITH HEXASACCHARIDE (THREE CALCIUMS)
2o1d PECTATE LYASE IN COMPLEX WITH TRISACCHARIDE (THREE CALCIUMS)