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(-) Description

Title :  STRUCTURE OF A FAMILY 2 PECTATE LYASE IN A NATIVE FORM
 
Authors :  D. W. Abbott, A. B. Boraston
Date :  08 Aug 07  (Deposition) - 18 Sep 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Lyase, Periplasm, Pectate Lyase, Beta-Elimination, Pectin Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. W. Abbott, A. B. Boraston
A Family 2 Pectate Lyase Displays A Rare Fold And Transition Metal-Assisted -Elimination.
J. Biol. Chem. V. 282 35328 2007
PubMed-ID: 17881361  |  Reference-DOI: 10.1074/JBC.M705511200

(-) Compounds

Molecule 1 - PECTATE LYASE
    Chains: A
    EC Number: 4.2.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: YERSINIA ENTEROCOLITICA
    Organism Taxid: 630

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 51)

Asymmetric/Biological Unit (1, 51)
No.NameCountTypeFull Name
1IOD51Ligand/IonIODIDE ION

(-) Sites  (46, 46)

Asymmetric Unit (46, 46)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:443 , SER A:496BINDING SITE FOR RESIDUE IOD A1547
02AC2SOFTWAREPRO A:545 , IOD A:1597BINDING SITE FOR RESIDUE IOD A1548
03AC3SOFTWARESER A:123 , IOD A:1552BINDING SITE FOR RESIDUE IOD A1549
04AC4SOFTWAREGLN A:544BINDING SITE FOR RESIDUE IOD A1550
05AC5SOFTWARESER A:430 , HOH A:2599BINDING SITE FOR RESIDUE IOD A1551
06AC6SOFTWAREGLY A:516 , ALA A:517 , SER A:528 , IOD A:1549 , IOD A:1576 , HOH A:2726BINDING SITE FOR RESIDUE IOD A1552
07AC7SOFTWARELYS A:368 , ALA A:448BINDING SITE FOR RESIDUE IOD A1553
08AC8SOFTWARELEU A:543 , HOH A:2290 , HOH A:2315BINDING SITE FOR RESIDUE IOD A1554
09AC9SOFTWARELEU A:199 , HOH A:2357BINDING SITE FOR RESIDUE IOD A1555
10BC1SOFTWAREARG A:451 , HOH A:2652BINDING SITE FOR RESIDUE IOD A1556
11BC2SOFTWAREARG A:402 , HOH A:2519BINDING SITE FOR RESIDUE IOD A1557
12BC3SOFTWARETHR A:428 , HOH A:2601 , HOH A:2627BINDING SITE FOR RESIDUE IOD A1558
13BC4SOFTWARELYS A:255BINDING SITE FOR RESIDUE IOD A1559
14BC5SOFTWARETRP A:183 , HOH A:2041 , HOH A:2133 , HOH A:2333BINDING SITE FOR RESIDUE IOD A1560
15BC6SOFTWAREASP A:4 , HOH A:2657BINDING SITE FOR RESIDUE IOD A1561
16BC7SOFTWAREGLU A:184 , HOH A:2131BINDING SITE FOR RESIDUE IOD A1562
17BC8SOFTWARELYS A:312 , HOH A:2486BINDING SITE FOR RESIDUE IOD A1563
18BC9SOFTWAREASP A:145 , SER A:146 , ASP A:147 , GLU A:174 , HOH A:2221 , HOH A:2249BINDING SITE FOR RESIDUE IOD A1564
19CC1SOFTWAREASP A:88 , ARG A:91 , IOD A:1573 , IOD A:1591BINDING SITE FOR RESIDUE IOD A1565
20CC2SOFTWAREGLN A:544BINDING SITE FOR RESIDUE IOD A1566
21CC3SOFTWAREARG A:530 , ASN A:532 , IOD A:1572 , HOH A:2742BINDING SITE FOR RESIDUE IOD A1567
22CC4SOFTWAREPRO A:316 , GLN A:317 , GLY A:318 , GLN A:319 , ASP A:320BINDING SITE FOR RESIDUE IOD A1568
23CC5SOFTWAREARG A:81 , ARG A:85 , HOH A:2136BINDING SITE FOR RESIDUE IOD A1569
24CC6SOFTWAREARG A:91 , VAL A:144 , HOH A:2247BINDING SITE FOR RESIDUE IOD A1570
25CC7SOFTWARELYS A:293 , IOD A:1593 , HOH A:2568BINDING SITE FOR RESIDUE IOD A1571
26CC8SOFTWAREARG A:530 , IOD A:1567 , HOH A:2107 , HOH A:2323BINDING SITE FOR RESIDUE IOD A1572
27CC9SOFTWAREPRO A:31 , IOD A:1565 , HOH A:2018BINDING SITE FOR RESIDUE IOD A1573
28DC1SOFTWAREHOH A:2640BINDING SITE FOR RESIDUE IOD A1574
29DC2SOFTWAREIOD A:1578BINDING SITE FOR RESIDUE IOD A1575
30DC3SOFTWAREGLU A:124 , IOD A:1552 , HOH A:2212 , HOH A:2726BINDING SITE FOR RESIDUE IOD A1576
31DC4SOFTWAREIOD A:1575 , HOH A:2085BINDING SITE FOR RESIDUE IOD A1578
32DC5SOFTWARELYS A:268BINDING SITE FOR RESIDUE IOD A1580
33DC6SOFTWAREARG A:54BINDING SITE FOR RESIDUE IOD A1581
34DC7SOFTWAREHOH A:2053 , HOH A:2111BINDING SITE FOR RESIDUE IOD A1582
35DC8SOFTWAREGLY A:176 , LYS A:177BINDING SITE FOR RESIDUE IOD A1584
36DC9SOFTWAREARG A:256BINDING SITE FOR RESIDUE IOD A1585
37EC1SOFTWAREGLY A:315 , PRO A:316 , GLN A:319BINDING SITE FOR RESIDUE IOD A1586
38EC2SOFTWAREASN A:356 , HOH A:2537BINDING SITE FOR RESIDUE IOD A1587
39EC3SOFTWARELYS A:500 , GLN A:502 , HOH A:2713BINDING SITE FOR RESIDUE IOD A1588
40EC4SOFTWAREARG A:154 , LEU A:215 , ASP A:221 , HOH A:2092 , HOH A:2215BINDING SITE FOR RESIDUE IOD A1589
41EC5SOFTWAREPHE A:187BINDING SITE FOR RESIDUE IOD A1590
42EC6SOFTWAREIOD A:1565BINDING SITE FOR RESIDUE IOD A1591
43EC7SOFTWARETYR A:210 , HOH A:2242 , HOH A:2494BINDING SITE FOR RESIDUE IOD A1592
44EC8SOFTWAREIOD A:1571 , HOH A:2472 , HOH A:2556BINDING SITE FOR RESIDUE IOD A1593
45EC9SOFTWAREILE A:391BINDING SITE FOR RESIDUE IOD A1596
46FC1SOFTWAREIOD A:1548BINDING SITE FOR RESIDUE IOD A1597

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V8I)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:246 -Val A:247

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V8I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V8I)

(-) Exons   (0, 0)

(no "Exon" information available for 2V8I)

(-) 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:543
 aligned with A1JSS8_YERE8 | A1JSS8 from UniProtKB/TrEMBL  Length:572

    Alignment length:543
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566   
         A1JSS8_YERE8    27 DRLTVVKQYVDNVLNKASDTYHGDKPSPLLADGVDPRTGQQLEWIFPDGRRAVLSNFSAQQNLMRVMSGLSQLSGDPRYQKRAEDIVRYHFQNYQDPSGLLYWGGHRFVDLKTLQPEGPSEKEMVHELKNAYPYYDLMFSVDSDATARFIRGFWNAHVYDWRILETSRHGEYGKPMGALWESKFEQQPPFFATKGLSFLNAGNDLIYSASLLYKHQQDQGALTWAKRLADQYVLPRDAKTGLGVYQFTQALKREEPTDDADTHSKFGDRAQRQFGPEFGPTALEGNMMLKGRTSTLYSENALMQLQLGKDLGPQGQDLLKWTVDGLKAFAKYAYNDQDNTFRPMIANGQDLSNYTLPRDGYYGKKGTVLKPYKAGNEFLISYARAYAIDNDPLLWKVARGIANDQGLGDIGTAPGKEVKVNMDTTNSDPYALFALLDLYHASQVADYRKLAEKIGDNIIKIRYIDGFFMASSDRQYADVDAIEPYALLALEASLRNKPQAVAPFLNGAGFTEGAYRMDDGSARVSTRDNELFLLNVGEKLQPN 569
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Pectate_lyase_2-2v8iA01 A:4-546                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh...............ee........eee.....eeeeehhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.............eee.....ee................hhhhhhhhhhhhhhhhhhhhhhhheee....ee...........hhhhh........eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............eee............hhhhhhhhhhhhhhhhh...hhh.ee..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhee....ee..ee........ee............ee..ee.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..ee.........ee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..ee........ee...hhhhhhhhhhhhhh.hhhhh..........eeeee.....eeeeeehhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v8i A   4 DRLTVVKQYVDNVLNKASDTYHGDKPSPLLADGVDPRTGQQLEWIFPDGRRAVLSNFSAQQNLMRVMSGLSQLSGDPRYQKRAEDIVRYHFQNYQDPSGLLYWGGHRFVDLKTLQPEGPSEKEMVHELKNAYPYYDLMFSVDSDATARFIRGFWNAHVYDWRILETSRHGEYGKPMGALWESKFEQQPPFFATKGLSFLNAGNDLIYSASLLYKHQQDQGALTWAKRLADQYVLPRDAKTGLGVYQFTQALKREEPTDDADTHSKFGDRAQRQFGPEFGPTALEGNMMLKGRTSTLYSENALMQLQLGKDLGPQGQDLLKWTVDGLKAFAKYAYNDQDNTFRPMIANGQDLSNYTLPRDGYYGKKGTVLKPYKAGNEFLISYARAYAIDNDPLLWKVARGIANDQGLGDIGTAPGKEVKVNMDTTNSDPYALFALLDLYHASQVADYRKLAEKIGDNIIKIRYIDGFFMASSDRQYADVDAIEPYALLALEASLRNKPQAVAPFLNGAGFTEGAYRMDDGSARVSTRDNELFLLNVGEKLQPN 546
                                    13        23        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       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543
   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  (0, 0)

(no "SCOP Domain" information available for 2V8I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V8I)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Pectate_lyase_2] (3)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A1JSS8_YERE8 | A1JSS8)
molecular function
    GO:0016837    carbon-oxygen lyase activity, acting on polysaccharides    Catalysis of the cleavage of a carbon-oxygen bond by the elimination of an alcohol from a polysaccharide.
    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.
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:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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UniProtKB/TrEMBL
        A1JSS8_YERE8 | A1JSS8: 2v8j 2v8k

(-) Related Entries Specified in the PDB File

2v8j STRUCTURE OF A FAMILY 2 PECTATE LYASE IN COMPLEX WITH A TRANSITION METAL
2v8k STRUCTURE OF A FAMILY 2 PECTATE LYASE IN COMPLEX WITH TRIGALACTURONIC ACID