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(-) Description

Title :  1,3-ALPHA-1,4-BETA-D-GALACTOSE-4-SULFATE-3,6-ANHYDRO-D-GALACTOSE 4 GALACTOHYDROLASE
 
Authors :  G. Michel, L. Chantalat, O. Dideberg
Date :  04 Feb 00  (Deposition) - 16 Jan 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.54
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Kappa-Carrageenan Double Helix Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Michel, L. Chantalat, E. Duee, T. Barbeyron, B. Henrissat, B. Kloareg, O. Dideberg
The Kappa-Carrageenase Of P. Carrageenovora Features A Tunnel-Shaped Active Site: A Novel Insight In The Evolution Of Clan-B Glycoside Hydrolases
Structure V. 9 513 2001
PubMed-ID: 11435116  |  Reference-DOI: 10.1016/S0969-2126(01)00612-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KAPPA-CARRAGEENASE
    Chains: A
    EC Number: 3.2.1.83
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET20B
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Fragment: CATALYTIC DOMAIN
    Gene: CGKA
    Mutation: YES
    Organism Scientific: PSEUDOALTEROMONAS CARRAGEENOVORA
    Organism Taxid: 227
    Other Details: COMPLEXED WITH CADMIUM CHLORIDE
    Other Details - Source: PROCESSED PROTEIN, HIS-TAG, SELEMETHIONYL PROTEIN
    Plasmid: PET20B

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 19)

Asymmetric/Biological Unit (3, 19)
No.NameCountTypeFull Name
1CD7Ligand/IonCADMIUM ION
2CL7Ligand/IonCHLORIDE ION
3MSE5Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:241 , CL A:1305 , CL A:1306 , HOH A:2344 , HOH A:2376BINDING SITE FOR RESIDUE CD A1298
02AC2SOFTWAREGLU A:48 , GLY A:79 , ASP A:289 , HOH A:2052 , HOH A:2064 , HOH A:2401BINDING SITE FOR RESIDUE CD A1299
03AC3SOFTWAREHIS A:183 , CL A:1307 , CL A:1308 , HOH A:2131 , HOH A:2253 , HOH A:2276BINDING SITE FOR RESIDUE CD A1300
04AC4SOFTWAREGLU A:287 , CL A:1309 , CL A:1310 , HOH A:2398BINDING SITE FOR RESIDUE CD A1301
05AC5SOFTWARESER A:285 , GLU A:287 , CL A:1311 , HOH A:2399BINDING SITE FOR RESIDUE CD A1302
06AC6SOFTWAREARG A:129 , ASP A:289 , HOH A:2041 , HOH A:2115 , HOH A:2139 , HOH A:2400BINDING SITE FOR RESIDUE CD A1303
07AC7SOFTWAREGLU A:72 , HOH A:2221 , HOH A:2403BINDING SITE FOR RESIDUE CD A1304
08AC8SOFTWARETHR A:264 , GLN A:265 , TRP A:266 , CD A:1298BINDING SITE FOR RESIDUE CL A1305
09AC9SOFTWARELYS A:229 , GLU A:241 , CD A:1298 , HOH A:2132BINDING SITE FOR RESIDUE CL A1306
10BC1SOFTWAREHIS A:183 , PRO A:197 , CD A:1300 , CL A:1308 , HOH A:2141 , HOH A:2256BINDING SITE FOR RESIDUE CL A1307
11BC2SOFTWAREHIS A:183 , ARG A:196 , CD A:1300 , CL A:1307 , HOH A:2289BINDING SITE FOR RESIDUE CL A1308
12BC3SOFTWARELYS A:131 , SER A:152 , GLU A:287 , CD A:1301BINDING SITE FOR RESIDUE CL A1309
13BC4SOFTWARECD A:1301BINDING SITE FOR RESIDUE CL A1310
14BC5SOFTWARESER A:134 , THR A:284 , SER A:285 , CD A:1302BINDING SITE FOR RESIDUE CL A1311

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:98 -A:268

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Phe A:136 -Pro A:137
2Ala A:261 -Pro A:262
3Phe A:282 -Pro A:283

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GH16_1PS01034 Glycosyl hydrolases family 16 active sites.CGKA_PSEVC163-174  1A:163-174

(-) Exons   (0, 0)

(no "Exon" information available for 1DYP)

(-) 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:271
 aligned with CGKA_PSEVC | P43478 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:271
                                    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 
           CGKA_PSEVC    27 SMQPPIAKPGETWILQAKRSDEFNVKDATKWNFQTENYGVWSWKNENATVSNGKLKLTTKRESHQRTFWDGCNQQQVANYPLYYTSGVAKSRATGNYGYYEARIKGASTFPGVSPAFWMYSTIDRSLTKEGDVQYSEIDVVELTQKSAVRESDHDLHNIVVKNGKPTWMRPGSFPQTNHNGYHLPFDPRNDFHTYGVNVTKDKITWYVDGEIVGEKDNLYWHRQMNLTLSQGLRAPHTQWKCNQFYPSANKSAEGFPTSMEVDYVRTWVKV 297
               SCOP domains d1dypa_ A: kappa-Carrageenase, catalytic                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1dypA00 A:27-297  [code=2.60.120.200, no name defined]                                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee.hhhh..........ee.....................eeeeeeeeeeeeeeeeehhhh.............eeeeeeee..eeeeeeee.......eeeeeeee............eeeeeeeeee........eee..eeeeeee..eeeee....hhhhhh.eee.........eeeeeee...eeeeee..eeeeeee.......eeeeeeeee....eeee..eeee..........eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------GH16_1      --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dyp A  27 SmQPPIAKPGETWILQAKRSDEFNVKDATKWNFQTENYGVWSWKNENATVSKGKLKLTTKRESHQRTFWDGCNQQQVANYPLYYTSGVAKSRATGNYGYYEARIKGASTFPGVSPAFWmYSTIDRSLTKEGDVQYSEIDVVELTQKSAVRESDHDLHNIVVKNGKPTWmRPGSFPQTNHNGYHLPFDPRNDFHTYGVNVTKDKITWYVDGEIVGEKDNLYWHRQmNLTLSQGLRAPHTQWKCNQFYPSANKSAEGFPTSmEVDYVRTWVKV 297
                             |      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 
                             |                                                                                                                  145-MSE                                           195-MSE                                                 251-MSE                            286-MSE       
                            28-MSE
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CGKA_PSEVC | P43478)
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:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0033918    kappa-carrageenase activity    Catalysis of the endohydrolysis of 1,4-beta-D-linkages between D-galactose 4-sulfate and 3,6-anhydro-D-galactose in kappa-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: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.
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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