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(-) Description

Title :  IOTA-CARRAGEENASE COMPLEXED TO IOTA-CARRAGEENAN FRAGMENTS
 
Authors :  G. Michel, R. Kahn, O. Dideberg
Date :  18 Jan 02  (Deposition) - 10 Jun 03  (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 :  Hydrolase, Iota-Carrageenan Double Helix Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Michel, W. Helbert, R. Kahn, O. Dideberg, B. Kloareg
The Structural Bases Of The Processive Degradation Of Iota-Carrageenan, A Main Cell Wall Polysaccharide Of Red Algae.
J. Mol. Biol. V. 334 421 2003
PubMed-ID: 14623184  |  Reference-DOI: 10.1016/J.JMB.2003.09.056
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IOTA-CARRAGEENASE
    Chains: A, B
    EC Number: 3.2.1.157
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET20B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, RESIDUES 28-491
    Organism Scientific: ALTEROMONAS SP. ATCC 43554
    Organism Taxid: 116059

 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  (5, 22)

Asymmetric Unit (5, 22)
No.NameCountTypeFull Name
1CA10Ligand/IonCALCIUM ION
2CL2Ligand/IonCHLORIDE ION
3DGS3Ligand/Ion3,6-ANHYDRO-D-GALACTOSE-2-SULFATE
4G4S3Ligand/Ion4-O-SULFO-BETA-D-GALACTOPYRANOSE
5NA4Ligand/IonSODIUM ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3DGS3Ligand/Ion3,6-ANHYDRO-D-GALACTOSE-2-SULFATE
4G4S3Ligand/Ion4-O-SULFO-BETA-D-GALACTOPYRANOSE
5NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3DGS-1Ligand/Ion3,6-ANHYDRO-D-GALACTOSE-2-SULFATE
4G4S-1Ligand/Ion4-O-SULFO-BETA-D-GALACTOPYRANOSE
5NA-1Ligand/IonSODIUM ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREG4S A:2 , LYS A:122 , ASN A:123BINDING SITE FOR RESIDUE DGS A 1
02AC2SOFTWAREDGS A:1 , ASN A:123 , ARG A:125 , LYS A:163BINDING SITE FOR RESIDUE G4S A 2
03AC3SOFTWAREPHE A:216 , ARG A:243 , GLU A:245 , LEU A:273 , ARG A:303 , TYR A:341 , LYS A:394 , G4S A:493 , HOH A:741 , HOH A:756 , HOH A:793BINDING SITE FOR RESIDUE DGS A 492
04AC4SOFTWARETYR A:341 , ARG A:353 , LYS A:394 , GLN A:424 , DGS A:492 , DGS A:494 , HOH A:678 , HOH A:733 , HOH A:756BINDING SITE FOR RESIDUE G4S A 493
05AC5SOFTWAREARG A:321 , TYR A:341 , ALA A:342 , GLY A:423 , GLN A:424 , TYR A:479 , G4S A:493 , G4S A:495BINDING SITE FOR RESIDUE DGS A 494
06AC6SOFTWAREARG A:321 , TYR A:479 , DGS A:494 , HOH A:757BINDING SITE FOR RESIDUE G4S A 495
07AC7SOFTWAREGLU A:108BINDING SITE FOR RESIDUE CA A 496
08AC8SOFTWAREGLU B:108 , HOH B:565 , HOH B:623 , HOH B:631BINDING SITE FOR RESIDUE CA B 2
09AC9SOFTWARETHR A:438 , ASP A:445 , TYR A:446 , ASP A:447 , HOH A:654BINDING SITE FOR RESIDUE CA A 3
10BC1SOFTWARETHR B:438 , ASP B:445 , TYR B:446 , ASP B:447 , HOH B:637BINDING SITE FOR RESIDUE CA B 4
11BC2SOFTWARESER A:109 , ASN A:145 , GLY A:146 , HOH A:705BINDING SITE FOR RESIDUE CA A 5
12BC3SOFTWARESER B:109 , ASN B:145 , GLY B:146 , HOH B:589 , HOH B:698BINDING SITE FOR RESIDUE CA B 6
13BC4SOFTWAREASN A:58 , ASP A:61 , SER A:63 , ASP A:65 , HOH A:596 , HOH A:605BINDING SITE FOR RESIDUE CA A 7
14BC5SOFTWAREASN B:58 , ASP B:61 , SER B:63 , ASP B:65 , HOH B:731BINDING SITE FOR RESIDUE CA B 8
15BC6SOFTWAREASP A:445 , ASP A:447 , HOH A:780BINDING SITE FOR RESIDUE CA A 9
16BC7SOFTWAREASP B:445 , ASP B:447 , HOH B:691BINDING SITE FOR RESIDUE CA B 10
17BC8SOFTWARELEU A:159 , THR A:182 , ILE A:183 , PHE A:184 , HOH A:531BINDING SITE FOR RESIDUE NA A 11
18BC9SOFTWARELEU B:159 , THR B:182 , ILE B:183 , PHE B:184 , HOH B:537BINDING SITE FOR RESIDUE NA B 12
19CC1SOFTWAREASP A:178 , HOH A:724BINDING SITE FOR RESIDUE NA A 13
20CC2SOFTWAREASP B:178 , HOH B:748BINDING SITE FOR RESIDUE NA B 14
21CC3SOFTWAREPHE A:184 , ALA A:185 , LEU A:188 , TYR A:218 , GLN A:222 , TYR A:224 , HOH A:729BINDING SITE FOR RESIDUE CL A 530
22CC4SOFTWAREALA B:185 , TYR B:218 , GLN B:222 , TYR B:224BINDING SITE FOR RESIDUE CL B 531

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:269 -A:298
2A:336 -A:360
3A:408 -A:476
4A:412 -A:484
5B:269 -B:298
6B:336 -B:360
7B:408 -B:476
8B:412 -B:484

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1KTW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1KTW)

(-) 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:457
 aligned with CGIA_ALTFO | Q9F5I8 from UniProtKB/Swiss-Prot  Length:491

    Alignment length:464
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487    
           CGIA_ALTFO    28 VSPKTYKDADFYVAPTQQDVNYDLVDDFGANGNDTSDDSNALQRAINAISRKPNGGTLLIPNGTYHFLGIQMKSNVHIRVESDVIIKPTWNGDGKNHRLFEVGVNNIVRNFSFQGLGNGFLVDFKDSRDKNLAVFKLGDVRNYKISNFTIDDNKTIFASILVDVTERNGRLHWSRNGIIERIKQNNALFGYGLIQTYGADNILFRNLHSEGGIALRMETDNLLMKNYKQGGIRNIFADNIRCSKGLAAVMFGPHFMKNGDVQVTNVSSVSCGSAVRSDSGFVELFSPTDEVHTRQSWKQAVESKLGRGCAQTPYARGNGGTRWAARVTQKDACLDKAKLEYGIEPGSFGTVKVFDVTARFGYNADLKQDQLDYFSTSNPMCKRVCLPTKEQWSKQGQIYIGPSLAAVIDTTPETSKYDYDVKTFNVKRINFPVNSHKTIDTNTESSRVCNYYGMSECSSSRWER 491
               SCOP domains d1ktwa_ A: iota-carrageenase                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1ktwA00 A:28-491 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh........eeeehhhhhh........hhhhhhhhhhhhhh....eeeee...eeee..ee....eeeee....eeee........eeeeee.....eeeeeeee....eeee........eeeeee..eeeeeeeeeeee........eee.eeee..eeeeeeeeeeeeeeee......eeeee.eeeeeeeeeeeee..eeeeee..hhhhhhhh..eeeeeeeeeeeee...eeeeee........eeeeeeeee.....eee.....eee.......hhhhhhhhhhhhhh.........-------.eee...hhhhhhhhhhhhh........eeeeeeeee....eeehhhhhhhhhh......................eee.....eee............eeeeeeee........eee.................hhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ktw A  28 VSPKTYKDADFYVAPTQQDVNYDLVDDFGANGNDTSDDSNALQRAINAISRKPNGGTLLIPNGTYHFLGIQMKSNVHIRVESDVIIKPTWNGDGKNHRLFEVGVNNIVRNFSFQGLGNGFLVDFKDSRDKNLAVFKLGDVRNYKISNFTIDDNKTIFASILVDVTERNGRLHWSRNGIIERIKQNNALFGYGLIQTYGADNILFRNLHSEGGIALRMETDNLLMKNYKQGGIRNIFADNIRCSKGLAAVMFGPHFMKNGDVQVTNVSSVSCGSAVRSDSGFVELFSPTDEVHTRQSWKQAVESKLGRGCAQTPYA-------WAARVTQKDACLDKAKLEYGIEPGSFGTVKVFDVTARFGYNADLKQDQLDYFSTSNPMCKRVCLPTKEQWSKQGQIYIGPSLAAVIDTTPETSKYDYDVKTFNVKRINFPVNSHKTIDTNTESSRVCNYYGMSECSSSRWER 491
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337    |    -  |    357       367       377       387       397       407       417       427       437       447       457       467       477       487    
                                                                                                                                                                                                                                                                                                                                                    342     350                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:457
 aligned with CGIA_ALTFO | Q9F5I8 from UniProtKB/Swiss-Prot  Length:491

    Alignment length:464
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487    
           CGIA_ALTFO    28 VSPKTYKDADFYVAPTQQDVNYDLVDDFGANGNDTSDDSNALQRAINAISRKPNGGTLLIPNGTYHFLGIQMKSNVHIRVESDVIIKPTWNGDGKNHRLFEVGVNNIVRNFSFQGLGNGFLVDFKDSRDKNLAVFKLGDVRNYKISNFTIDDNKTIFASILVDVTERNGRLHWSRNGIIERIKQNNALFGYGLIQTYGADNILFRNLHSEGGIALRMETDNLLMKNYKQGGIRNIFADNIRCSKGLAAVMFGPHFMKNGDVQVTNVSSVSCGSAVRSDSGFVELFSPTDEVHTRQSWKQAVESKLGRGCAQTPYARGNGGTRWAARVTQKDACLDKAKLEYGIEPGSFGTVKVFDVTARFGYNADLKQDQLDYFSTSNPMCKRVCLPTKEQWSKQGQIYIGPSLAAVIDTTPETSKYDYDVKTFNVKRINFPVNSHKTIDTNTESSRVCNYYGMSECSSSRWER 491
               SCOP domains d1ktwb_ B: iota-carrageenase                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1ktwB00 B:28-491 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                                                                                                                                                      CATH domains
           Pfam domains (1) ---------------------Pectate_lyase_3-1ktwB01 B:49-279                                                                                                                                                                                                       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------Pectate_lyase_3-1ktwB02 B:49-279                                                                                                                                                                                                       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ......hhhhh........eeee..............hhhhhhhhhhhhhh....eeeee...eeee..ee....eeeee....eeee........eeeeee.....eeeeeeee....eeee........eeeeee..eeeeeeeeeeee........eee.eeee..eeeeeeeeeeeeeeee......eeeee.eeeeeeeeeeeee..eeeeee..hhhhhhhh..eee.eeeeeeeee...eeeeee........eeeeeeeee.....eee.....eee.......hhhhhhhhhhhhhh.........-------.eee...hhhhhhhhhhhhh........eeeeeeeee....eeehhhhhhhhh.........ee............eee.....eee............eeeeeeee........ee...............ee.hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ktw B  28 VSPKTYKDADFYVAPTQQDVNYDLVDDFGANGNDTSDDSNALQRAINAISRKPNGGTLLIPNGTYHFLGIQMKSNVHIRVESDVIIKPTWNGDGKNHRLFEVGVNNIVRNFSFQGLGNGFLVDFKDSRDKNLAVFKLGDVRNYKISNFTIDDNKTIFASILVDVTERNGRLHWSRNGIIERIKQNNALFGYGLIQTYGADNILFRNLHSEGGIALRMETDNLLMKNYKQGGIRNIFADNIRCSKGLAAVMFGPHFMKNGDVQVTNVSSVSCGSAVRSDSGFVELFSPTDEVHTRQSWKQAVESKLGRGCAQTPYA-------WAARVTQKDACLDKAKLEYGIEPGSFGTVKVFDVTARFGYNADLKQDQLDYFSTSNPMCKRVCLPTKEQWSKQGQIYIGPSLAAVIDTTPETSKYDYDVKTFNVKRINFPVNSHKTIDTNTESSRVCNYYGMSECSSSRWER 491
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337    |    -  |    357       367       377       387       397       407       417       427       437       447       457       467       477       487    
                                                                                                                                                                                                                                                                                                                                                    342     350
   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  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CGIA_ALTFO | Q9F5I8)
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:0033952    iota-carrageenase activity    Catalysis of the endohydrolysis of 1,4-beta-D-linkages between D-galactose 4-sulfate and 3,6-anhydro-D-galactose-2-sulfate in iota-carrageenans.
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:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    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.
    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.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CGIA_ALTFO | Q9F5I8: 1h80 3lmw

(-) Related Entries Specified in the PDB File

1h80 THIS STRUCTURE IS THE NATIVE PROTEIN COMPLEXED WITH CALCIUM, SODIUM AND CHLORIDE.