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(-) Description

Title :  STRUCTURE OF YERSINIA ENTEROCOLITICA FAMILY 28 EXOPOLYGALACTURONASE
 
Authors :  D. W. Abbott, A. B. Boraston
Date :  09 Mar 07  (Deposition) - 08 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Gh28, Pectin, Cell Wall, Hydrolase, Periplasm, Yersinia Enterocolitica, Beta-Helix, Glycosidase, Exo-Activity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. W. Abbott, A. B. Boraston
The Structural Basis For Exopolygalacturonase Activity In A Family 28 Glycoside Hydrolase.
J. Mol. Biol. V. 368 1215 2007
PubMed-ID: 17397864  |  Reference-DOI: 10.1016/J.JMB.2007.02.083

(-) Compounds

Molecule 1 - EXOPOLYGALACTURONASE
    Atcc: 9610
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: YERSINIA ENTEROCOLITICA
    Organism Taxid: 630
    Synonym: YEGH28

 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  (3, 29)

Asymmetric Unit (3, 29)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2NI9Ligand/IonNICKEL (II) ION
3SO419Ligand/IonSULFATE ION
Biological Unit 1 (1, 11)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2NI-1Ligand/IonNICKEL (II) ION
3SO411Ligand/IonSULFATE ION
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2NI-1Ligand/IonNICKEL (II) ION
3SO48Ligand/IonSULFATE ION

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:376 , GLY A:401 , HIS A:435 , HOH A:2118 , HOH A:2126 , HOH A:2127BINDING SITE FOR RESIDUE NI A1607
02AC2SOFTWAREASP A:270 , ARG A:276BINDING SITE FOR RESIDUE NI A1608
03AC3SOFTWAREASP A:83BINDING SITE FOR RESIDUE NI A1609
04AC4SOFTWAREHOH A:2039 , HOH A:2129BINDING SITE FOR RESIDUE NI A1610
05AC5SOFTWARETYR A:230 , ARG A:231 , GLU A:239 , PRO A:250 , ARG A:337BINDING SITE FOR RESIDUE SO4 A1611
06AC6SOFTWARELYS A:58 , ARG A:483BINDING SITE FOR RESIDUE SO4 A1612
07AC7SOFTWAREASN A:378 , ASN A:379 , HOH A:2172 , HOH A:2173BINDING SITE FOR RESIDUE SO4 A1613
08AC8SOFTWAREPRO A:566 , GLY A:587 , ASP A:588 , THR A:589 , HIS A:592BINDING SITE FOR RESIDUE SO4 A1614
09AC9SOFTWARETYR A:94 , ARG A:288 , ILE A:371 , GLN A:373 , PHE A:397BINDING SITE FOR RESIDUE SO4 A1615
10BC1SOFTWARESER A:575 , GLU A:576 , ASN A:598 , VAL A:599 , LYS A:600BINDING SITE FOR RESIDUE SO4 A1616
11BC2SOFTWAREPHE A:88 , SER A:89 , PRO A:90 , HOH A:2174BINDING SITE FOR RESIDUE SO4 A1617
12BC3SOFTWAREASP A:167 , GLY A:168 , LYS A:169BINDING SITE FOR RESIDUE SO4 A1618
13BC4SOFTWAREARG A:240 , PHE A:354 , HIS A:355 , HOH A:2175 , HOH A:2176BINDING SITE FOR RESIDUE SO4 A1619
14BC5SOFTWAREALA A:47 , TYR A:48 , ASP A:49 , SER A:52 , ARG A:262 , TYR A:343 , HOH A:2177BINDING SITE FOR RESIDUE SO4 A1620
15BC6SOFTWARESER A:442 , LYS A:468BINDING SITE FOR RESIDUE SO4 A1621
16BC7SOFTWAREHIS A:97 , HOH A:2023 , HOH A:2077 , HIS B:97 , HOH B:2049 , HOH B:2155BINDING SITE FOR RESIDUE NI B1607
17BC8SOFTWAREASP B:376 , GLY B:401 , HIS B:435 , HOH B:2200 , HOH B:2213 , HOH B:2214BINDING SITE FOR RESIDUE NI B1608
18BC9SOFTWAREASP B:270BINDING SITE FOR RESIDUE NI B1609
19CC1SOFTWAREHIS B:363 , GLN B:389 , GLU B:419BINDING SITE FOR RESIDUE NI B1610
20CC2SOFTWAREHIS B:302 , GLU B:303BINDING SITE FOR RESIDUE NI B1611
21CC3SOFTWARETYR B:230 , ARG B:231 , GLU B:239 , PRO B:250 , ARG B:337BINDING SITE FOR RESIDUE SO4 B1612
22CC4SOFTWARELYS B:58 , ARG B:483 , HOH B:2282 , HOH B:2283BINDING SITE FOR RESIDUE SO4 B1613
23CC5SOFTWAREPRO B:566 , GLY B:587 , ASP B:588 , THR B:589 , HIS B:592BINDING SITE FOR RESIDUE SO4 B1614
24CC6SOFTWAREASN B:87 , PHE B:88 , SER B:89 , PRO B:90BINDING SITE FOR RESIDUE SO4 B1615
25CC7SOFTWAREGLN B:40 , GLN B:42BINDING SITE FOR RESIDUE SO4 B1616
26CC8SOFTWAREARG B:488 , ASP B:530 , ASN B:531 , HOH B:2284BINDING SITE FOR RESIDUE SO4 B1617
27CC9SOFTWAREASN B:378 , ASN B:379 , SO4 B:1619BINDING SITE FOR RESIDUE SO4 B1618
28DC1SOFTWAREASP B:402 , HIS B:435 , LYS B:468 , SO4 B:1618 , HOH B:2285BINDING SITE FOR RESIDUE SO4 B1619
29DC2SOFTWAREHIS B:97 , TYR B:430 , TYR B:459 , ARG B:488 , HOH B:2046 , HOH B:2048BINDING SITE FOR RESIDUE ACT B1620

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:183 -A:187
2B:183 -B:187

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Tyr A:375 -Asp A:376
2Thr A:440 -Gly A:441
3Asp A:602 -Gly A:603
4Lys B:103 -Asp B:104
5Tyr B:375 -Asp B:376
6Ile B:508 -Asp B:509
7Asp B:602 -Gly B:603

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2UVE)

(-) 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:571
 aligned with O68975_YEREN | O68975 from UniProtKB/TrEMBL  Length:601

    Alignment length:571
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 601   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              598  |   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           597  |  |   
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       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 |  |  | - 
         O68975_YEREN    36 DAPQQLQVPTLAYDESSIVLVWKAPEDTRKIVDYQIFSAGKLLGKASDNNDNFSPAKPYIDHFYANDKDNFQHKIVMQNFTVIGLKPETSYQFTVKAQYADGSLSVASKPITAKTSAKPQIVNVRDFGAIDDGKTLNTKAIQQAIDSCKPGCRVEIPAGTYKSGALWLKSDMTLNLQAGAILLGSENPDDYPAGYRLYPYSTIERPASLINAIDPNNSKPGTFRNIRITGSGVIDGNGWLRAKTAEITDELGRSLPQYVASKNSKVHEDGILAKNQVEKAVSDGMDLKNAYGQRRSSLMTLRGVENVYLAGFTVRNPAFHGIMNLENHNVVANGLIHQTYDANNGDGIEFGNSQNVMVFNNFFDTGDDCINFAAGTGEKAQEQEPMKGAWLFNNYFRMGHGAIVTGSHTGAWIEDILAENNVMYLTDIGLRAKSTSTIGGGARNVTFRNNAMRDLAKQVMVMTLDYADSNANIDYPPAKIPAQFYDFTLKNVTVDNSTGKNPSIEIKGDTANKAWHRLVHVNNVQLNNVTPTAIMDLRDSEFNKVTFTELRGDTPWHFSEVK--KCQG---   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..........eeeeee.......eeeeeeee..eeeeehhhhhhhhh.hhhhhhhhh..............eeee.......eeeeeeeeee...........eeee......eee.hhhh........hhhhhhhhhhh....eeeee..eeeee........eeeee...eeeee..hhhhh.eee.........ee................eeeeeee...eee.....eeeeeeee.....eeeee......hhhhhhhhhhhhhhhhhhh..hhhhhhhhh.........eeeeeee..eee............eeeeee..eee...............eeeeee..eee..............hhhhh..eeeeeee..ee................eeeeeee..eee............hhh.eeeeeeeeeeeeeee...........................eeeeeeeeeeeeeee..................eeeeeeeeeeee.....eeeeeeeeeeeeeeee....................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uve A  36 DAPQQLQVPTLAYDESSIVLVWKAPEDTRKIVDYQIFSAGKLLGKASDNNDNFSPAKPYIDHFYVNDKDNFQHKIVMQNFTVIGLKPETSYQFTVKAQYADGSLSVASKPITAKTSAKPQIVNVRDFGAIDDGKTLNTKAIQQAIDSCKPGCRVEIPAGTYKSGALWLKSDMTLNLQAGAILLGSENPDDYPAGYRLYPYSTIERPASLINAIDPNNSKPGTFRNIRITGSGVIDGNGWLRAKTAEITDELGRSLPQYVASKNSKVHEDGILAKNQVEKAVSDGMDLKNAYGQRRSSLMTLRGVENVYLAGFTVRNPAFHGIMNLENHNVVANGLIHQTYDANNGDGIEFGNSQNVMVFNNFFDTGDDCINFAAGTGEKAQEQEPMKGAWLFNNYFRMGHGAIVTGSHTGAWIEDILAENNVMYLTDIGLRAKSTSTIGGGARNVTFRNNAMRDLAKQVMVMTLDYADSNANIDYPPAKIPAQFYDFTLKNVTVDNSTGKNPSIEIKGDTANKAWHRLVHVNNVQLNNVTPTAISDLRDSEFNKVTFTELRGDTPWHFSEVKNVKVDGKPV 606
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       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 


Chain B from PDB  Type:PROTEIN  Length:566
 aligned with O68975_YEREN | O68975 from UniProtKB/TrEMBL  Length:601

    Alignment length:571
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 601   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              598  |   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           597  |  |   
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       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 |  |  | - 
         O68975_YEREN    36 DAPQQLQVPTLAYDESSIVLVWKAPEDTRKIVDYQIFSAGKLLGKASDNNDNFSPAKPYIDHFYANDKDNFQHKIVMQNFTVIGLKPETSYQFTVKAQYADGSLSVASKPITAKTSAKPQIVNVRDFGAIDDGKTLNTKAIQQAIDSCKPGCRVEIPAGTYKSGALWLKSDMTLNLQAGAILLGSENPDDYPAGYRLYPYSTIERPASLINAIDPNNSKPGTFRNIRITGSGVIDGNGWLRAKTAEITDELGRSLPQYVASKNSKVHEDGILAKNQVEKAVSDGMDLKNAYGQRRSSLMTLRGVENVYLAGFTVRNPAFHGIMNLENHNVVANGLIHQTYDANNGDGIEFGNSQNVMVFNNFFDTGDDCINFAAGTGEKAQEQEPMKGAWLFNNYFRMGHGAIVTGSHTGAWIEDILAENNVMYLTDIGLRAKSTSTIGGGARNVTFRNNAMRDLAKQVMVMTLDYADSNANIDYPPAKIPAQFYDFTLKNVTVDNSTGKNPSIEIKGDTANKAWHRLVHVNNVQLNNVTPTAIMDLRDSEFNKVTFTELRGDTPWHFSEVK--KCQG---   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..........eeeeee.......eeeeeeee..eeeeehhhhhhhhh.hhhhhhhhh..............eeee.......eeeeeeeeee...........eeee......eee.hhhh........hhhhhhhhhhhh...eeeee..eeeee..ee....eeeee...eeeee..hhhhh.eee.........ee...eee..........eeeeeee...eee.....eeeeeeee.....eeeee...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeee.eeeeeee..eee......eeee..eeeeee..eee.........eeee..eeeeee..eee.....eeee...hhhhhhh..eeeeeee..ee......eeee......eeeeeee..eee...eeeeeee......eeeeeeeeeeeeeee..eeeeeee...-----..........eeeeeeeeeeeeeee......eeee..hhhh..eeeeeeeeeeee.....eee.eeeeeeeeeeee.........ee..eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uve B  36 DAPQQLQVPTLAYDESSIVLVWKAPEDTRKIVDYQIFSAGKLLGKASDNNDNFSPAKPYIDHFYVNDKDNFQHKIVMQNFTVIGLKPETSYQFTVKAQYADGSLSVASKPITAKTSAKPQIVNVRDFGAIDDGKTLNTKAIQQAIDSCKPGCRVEIPAGTYKSGALWLKSDMTLNLQAGAILLGSENPDDYPAGYRLYPYSTIERPASLINAIDPNNSKPGTFRNIRITGSGVIDGNGWLRAKTAEITDELGRSLPQYVASKNSKVHEDGILAKNQVEKAVSDGMDLKNAYGQRRSSLMTLRGVENVYLAGFTVRNPAFHGIMNLENHNVVANGLIHQTYDANNGDGIEFGNSQNVMVFNNFFDTGDDCINFAAGTGEKAQEQEPMKGAWLFNNYFRMGHGAIVTGSHTGAWIEDILAENNVMYLTDIGLRAKSTSTIGGGARNVTFRNNAMRDLAKQVMVMTLDYA-----IDYPPAKIPAQFYDFTLKNVTVDNSTGKNPSIEIKGDTANKAWHRLVHVNNVQLNNVTPTAISDLRDSEFNKVTFTELRGDTPWHFSEVKNVKVDGKPV 606
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495      |  -  |    515       525       535       545       555       565       575       585       595       605 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            502   508
   Legend:   → Mismatch (orange background)
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  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 2UVE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2UVE)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (O68975_YEREN | O68975)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0004650    polygalacturonase activity    Catalysis of the random hydrolysis of (1->4)-alpha-D-galactosiduronic linkages in pectate and other galacturonans.
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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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  2uve
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  O68975_YEREN | O68975
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 Related Entries

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

UniProtKB/TrEMBL
        O68975_YEREN | O68975: 2uvf

(-) Related Entries Specified in the PDB File

2uvf STRUCTURE OF YERSINIA ENTEROCOLITICA FAMILY 28 EXOPOLYGALACTURONASE