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(-) Description

Title :  1,3-ALPHA-1,4-BETA-D-GALACTOSE-4-SULFATE-3,6-ANHYDRO-D-GALACTOSE-2-SULFATE 4 GALACTOHYDROLASE
 
Authors :  G. Michel, L. Chantalat, O. Dideberg
Date :  22 Jan 01  (Deposition) - 27 Nov 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
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, L. Chantalat, E. Fanchon, B. Henrissat, B. Kloareg, O. Dideberg
The Iota-Carrageenase Of Alteromonas Fortis. A Beta-Helix Fold-Containing Enzyme For The Degradation Of A Highly Polyanionic Polysaccharide
J. Biol. Chem. V. 276 40202 2001
PubMed-ID: 11493601  |  Reference-DOI: 10.1074/JBC.M100670200
(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
    Expression System Plasmid: PET20B
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Fragment: CATALYTIC DOMAIN RESIDUES 28-491
    Gene: CGIA
    Organism Scientific: ALTEROMONAS SP. ATCC43554
    Organism Taxid: 116059
    Other Details: COMPLEXED WITH CALCIUM, SODIUM AND CHLORIDE
    Other Details - Source: HIS-TAG, SELEMETHIONYL PROTEIN.
    Plasmid: PET20B
    Strain: B834(DE3)

 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  (4, 20)

Asymmetric Unit (4, 20)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2CL2Ligand/IonCHLORIDE ION
3GOL6Ligand/IonGLYCEROL
4NA6Ligand/IonSODIUM ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3GOL3Ligand/IonGLYCEROL
4NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3GOL3Ligand/IonGLYCEROL
4NA-1Ligand/IonSODIUM ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:109 , ASN A:145 , GLY A:146 , HOH A:2161 , HOH A:2164 , HOH A:2213 , HOH A:2214BINDING SITE FOR RESIDUE CA A1492
02AC2SOFTWAREASN A:58 , ASP A:61 , SER A:63 , ASP A:65 , HOH A:2086 , HOH A:2087BINDING SITE FOR RESIDUE CA A1493
03AC3SOFTWARETHR A:438 , ASP A:445 , TYR A:446 , ASP A:447 , HOH A:2449BINDING SITE FOR RESIDUE CA A1494
04AC4SOFTWAREPHE A:184 , ALA A:185 , LEU A:188 , TYR A:218 , GLN A:222 , TYR A:224 , HOH A:2296BINDING SITE FOR RESIDUE CL A1495
05AC5SOFTWAREGLU A:108 , HOH A:2157 , HOH A:2159 , HOH A:2160 , NA B:1498 , HOH B:2072 , HOH B:2096BINDING SITE FOR RESIDUE NA A1496
06AC6SOFTWARELEU A:159 , THR A:182 , ILE A:183 , PHE A:184 , HOH A:2259BINDING SITE FOR RESIDUE NA A1497
07AC7SOFTWAREASP A:54 , HOH A:2045 , HOH A:2046 , HOH A:2073 , HOH A:2074 , NA B:1496 , HOH B:2196BINDING SITE FOR RESIDUE NA A1498
08AC8SOFTWARESER B:109 , ASN B:145 , GLY B:146 , HOH B:2197 , HOH B:2202 , HOH B:2253 , HOH B:2254BINDING SITE FOR RESIDUE CA B1492
09AC9SOFTWAREASN B:58 , ASP B:61 , SER B:63 , ASP B:65 , HOH B:2110 , HOH B:2111BINDING SITE FOR RESIDUE CA B1493
10BC1SOFTWARETHR B:438 , ASP B:445 , TYR B:446 , ASP B:447 , HOH B:2497 , HOH B:2501BINDING SITE FOR RESIDUE CA B1494
11BC2SOFTWAREPHE B:184 , ALA B:185 , LEU B:188 , TYR B:218 , GLN B:222 , TYR B:224 , HOH B:2349BINDING SITE FOR RESIDUE CL B1495
12BC3SOFTWARENA A:1498 , HOH A:2045 , HOH A:2074 , GLU B:108 , HOH B:2193 , HOH B:2194 , HOH B:2196BINDING SITE FOR RESIDUE NA B1496
13BC4SOFTWARELEU B:159 , THR B:182 , ILE B:183 , PHE B:184 , HOH B:2307BINDING SITE FOR RESIDUE NA B1497
14BC5SOFTWARENA A:1496 , HOH A:2157 , ASP B:54 , HOH B:2071 , HOH B:2072 , HOH B:2096BINDING SITE FOR RESIDUE NA B1498
15BC6SOFTWAREASN A:145 , GLY A:146 , ASN A:174 , PHE A:175 , THR A:176 , ARG A:208 , ILE A:209 , LYS A:210 , HOH A:2283 , HOH A:2525 , HOH A:2526BINDING SITE FOR RESIDUE GOL A1499
16BC7SOFTWARETHR A:32 , TYR A:33 , ASP A:37 , PHE A:38 , ASN A:228 , PHE A:263 , HOH A:2529BINDING SITE FOR RESIDUE GOL A1500
17BC8SOFTWAREARG A:168 , ARG A:197 , HIS A:199 , TRP A:200 , ARG A:202 , HOH A:2278 , HOH A:2530 , HOH A:2531BINDING SITE FOR RESIDUE GOL A1501
18BC9SOFTWAREASN B:145 , GLY B:146 , ASN B:174 , PHE B:175 , THR B:176 , ARG B:208 , HOH B:2575 , HOH B:2576BINDING SITE FOR RESIDUE GOL B1499
19CC1SOFTWARETHR B:32 , TYR B:33 , ASP B:37 , PHE B:38 , ASN B:228 , PHE B:263 , HOH B:2577 , HOH B:2578BINDING SITE FOR RESIDUE GOL B1500
20CC2SOFTWAREHIS B:199 , TRP B:200 , ARG B:202 , ASP B:227 , HOH B:2280 , HOH B:2579BINDING SITE FOR RESIDUE GOL B1501

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:269 -A:298
2A:269 -A:298
3A:336 -A:360
4A:408 -A:476
5A:408 -A:476
6A:412 -A:484
7B:269 -B:298
8B:269 -B:298
9B:336 -B:360
10B:408 -B:476
11B:408 -B:476
12B:412 -B:484

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1H80)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H80)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1H80)

(-) Exons   (0, 0)

(no "Exon" information available for 1H80)

(-) 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:433
 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 d1h80a_ A: iota-carrageenase                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1h80A00 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.......eeeeeeeeeeeeeeee......eeeee................eeeeee..hhhhhhhh..................eeeeee......................eee.....ee..---------------------......----------.ee...hhhhhhhhhhhh......................eeehhhhhhhhhh......................eee.....eee............................ee..................hhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h80 A  28 VSPKTYKDADFYVAPTQQDVNYDLVDDFGANGNDTSDDSNALQRAINAISRKPNGGTLLIPNGTYHFLGIQMKSNVHIRVESDVIIKPTWNGDGKNHRLFEVGVNNIVRNFSFQGLGNGFLVDFKDSRDKNLAVFKLGDVRNYKISNFTIDDNKTIFASILVDVTERNGRLHWSRNGIIERIKQNNALFGYGLIQTYGADNILFRNLHSEGGIALRMETDNLLMKNYKQGGIRNIFADNIRCSKGLAAVMFGPHFMKNGDVQVTNVSSVSCGSAVRSDSGFVELFS---------------------GCAQTP----------AARVTQKDACLDKAKLEYGIEPGSFGTVKVFDVTARFGYNADLKQDQLDYFSTSNPMCKRVCLPTKEQWSKQGQIYIGPSLAAVIDTTPETSKYDYDVKTFNVKRINFPVNSHKTIDTNTESSRVCNYYGMSECSSSRWER 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     |   -         -       337  |      -   |   357       367       377       387       397       407       417       427       437       447       457       467       477       487    
                                                                                                                                                                                                                                                                                                                       313                   335  340        351                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:430
 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 d1h80b_ B: iota-carrageenase                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1h80B00 B: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.......eeeeeeeeeeeeeeee......eeeee................eeeeee..hhhhhhhh..................eeeeee......................eee........----------------------.....------------.....hhhhhhhhhhhh......................eeehhhhhhhhhh......................eee.....eee............................ee..................hhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h80 B  28 VSPKTYKDADFYVAPTQQDVNYDLVDDFGANGNDTSDDSNALQRAINAISRKPNGGTLLIPNGTYHFLGIQMKSNVHIRVESDVIIKPTWNGDGKNHRLFEVGVNNIVRNFSFQGLGNGFLVDFKDSRDKNLAVFKLGDVRNYKISNFTIDDNKTIFASILVDVTERNGRLHWSRNGIIERIKQNNALFGYGLIQTYGADNILFRNLHSEGGIALRMETDNLLMKNYKQGGIRNIFADNIRCSKGLAAVMFGPHFMKNGDVQVTNVSSVSCGSAVRSDSGFVELF----------------------GCAQT------------ARVTQKDACLDKAKLEYGIEPGSFGTVKVFDVTARFGYNADLKQDQLDYFSTSNPMCKRVCLPTKEQWSKQGQIYIGPSLAAVIDTTPETSKYDYDVKTFNVKRINFPVNSHKTIDTNTESSRVCNYYGMSECSSSRWER 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    |    -         -       337 |       -    |  357       367       377       387       397       407       417       427       437       447       457       467       477       487    
                                                                                                                                                                                                                                                                                                                      312                    335 339          352
   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  (0, 0)

(no "Pfam Domain" information available for 1H80)

(-) 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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  1h80
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1ktw IOTA-CARRAGEENASE COMPLEXED TO IOTA- CARRAGEENAN FRAGMENTS