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(-) Description

Title :  CRYSTAL STRUCTURE OF COD
 
Authors :  S. -Y. Park, K. Sugiyama, T. Hirano, T. Nishio
Date :  18 Jul 14  (Deposition) - 03 Dec 14  (Release) - 03 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Oligosaccharide Deacetylace, Carbohydrate-Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Hirano, K. Sugiyama, Y. Sakaki, W. Hakamata, S. -Y. Park, T. Nishio
Structural And Functional Analysis Of Chitin Oligosaccharid Deacetylase From Vivrio Parahaemolyticus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CHITIN OLIGOSACCHARIDE DEACETYLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 26-427
    Gene: COD1, COD
    Organism Scientific: VIBRIO PARAHAEMOLYTICUS
    Organism Taxid: 670
    Strain: KN1699
    Synonym: CHITIN OLIGOSACCHARIDE DEACETYLASE COD1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CA2Ligand/IonCALCIUM ION
3GOL4Ligand/IonGLYCEROL
4ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3GOL2Ligand/IonGLYCEROL
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3GOL2Ligand/IonGLYCEROL
4ZN-1Ligand/IonZINC ION
Biological Unit 3 (2, 6)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3GOL4Ligand/IonGLYCEROL
4ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:219 , GLY A:351 , HOH A:1012 , HOH A:1014 , HOH A:1027 , HOH A:1034BINDING SITE FOR RESIDUE CA A 901
02AC2SOFTWAREASP A:36 , HIS A:93 , HIS A:97 , ACT A:903 , HOH A:1131BINDING SITE FOR RESIDUE ZN A 902
03AC3SOFTWAREASP A:35 , ASP A:36 , HIS A:93 , HIS A:97 , PRO A:164 , TYR A:165 , TRP A:225 , HIS A:291 , ZN A:902 , HOH A:1131BINDING SITE FOR RESIDUE ACT A 903
04AC4SOFTWAREPRO A:333 , ASP A:345 , TYR A:346 , HOH A:1025 , HOH A:1266BINDING SITE FOR RESIDUE GOL A 904
05AC5SOFTWAREASN A:383 , TRP A:384 , THR A:397 , TYR A:398 , HOH A:1303 , HOH A:1307 , HOH A:1356 , THR B:150 , SER B:151 , PRO B:153BINDING SITE FOR RESIDUE GOL A 905
06AC6SOFTWAREGLY B:219 , GLY B:351 , HOH B:1016 , HOH B:1031 , HOH B:1040 , HOH B:1049BINDING SITE FOR RESIDUE CA B 901
07AC7SOFTWAREASP B:36 , HIS B:93 , HIS B:97 , ACT B:903 , HOH B:1189BINDING SITE FOR RESIDUE ZN B 902
08AC8SOFTWAREASP B:35 , ASP B:36 , HIS B:93 , HIS B:97 , PRO B:164 , TYR B:165 , TRP B:225 , HIS B:291 , ZN B:902 , HOH B:1189BINDING SITE FOR RESIDUE ACT B 903
09AC9SOFTWAREPRO B:333 , ASP B:345 , TYR B:346 , HOH B:1045 , HOH B:1245BINDING SITE FOR RESIDUE GOL B 904
10BC1SOFTWARETHR A:150 , SER A:151 , PRO A:153 , ASN B:383 , TRP B:384 , THR B:397 , TYR B:398 , HOH B:1439 , HOH B:1457BINDING SITE FOR RESIDUE GOL B 905

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:102 -A:114
2A:181 -A:196
3A:260 -A:277
4B:102 -B:114
5B:181 -B:196
6B:260 -B:277

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:37 -Pro A:38
2Asn A:266 -Pro A:267
3Gly B:37 -Pro B:38
4Asn B:266 -Pro B:267

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WX7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WX7)

(-) Exons   (0, 0)

(no "Exon" information available for 3WX7)

(-) 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:402
 aligned with A6P4T5_VIBPH | A6P4T5 from UniProtKB/TrEMBL  Length:427

    Alignment length:402
                                    35        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  
         A6P4T5_VIBPH    26 TKGTIYLTFDDGPINASIDVINVLNQEEVKATFYFNAWHLDGIGDENEDRALEALKLALDSGHIVANHSYDHMVHNCVEEFGPNSAAECNATGDHQINSYQDPAYDASMFAENLSVLEKYLPNITSYPNYKANEFARLPYTNGWRVTKDFKADGLCATSDDLKPWEPGYACDTANPSNSVKAAIAVQNILANNGYQTHGWDVDWAPENWGIAMPANSLTEAEPFLGYVDSALNTCAPTTINPINSKAQEFPCGTPLHADKVIVLTHEFLFEDGKRGMGATQNLPKLTKFIQLAKQAGYVFDTMDNYTPNWQVGNNYSAGDYVLHLGTVYQAVTSHTAQQDWAPSPTSSLWTNADPATNWTQNVSYKQGDVVTYQGLRYLVNVPHVSQADWSPSSQNTLFTAL 427
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee...hhhhhhhhhhhhhh....eeeehhhhh.........hhhhhhhhhhhh..eeee.....hhhhh......hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh.hhhhh.......ee.......eeee..eee........................hhhhhhhhhhhhhhhhh..ee....ee.........hhhhhh.hhhhhhhhhhhhh..hhhhhh.hhhhh.......hhhhh.eeeeeehhhhh.ee..eehhhhhhhhhhhhhhhhhhhheeeehhhhh........ee....eeee..eeeee...ee.............eee...........ee....eeee..eeeee...ee.hhhhh.......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3wx7 A  26 TKGTIYLTFDDGPINASIDVINVLNQEEVKATFYFNAWHLDGIGDENEDRALEALKLALDSGHIVANHSYDHMVHNCVEEFGPNSAAECNATGDHQINSYQDPAYDASMFAENLSVLEKYLPNITSYPNYKANEFARLPYTNGWRVTKDFKADGLCATSDDLKPWEPGYACDTANPSNSVKAAIAVQNILANNGYQTHGWDVDWAPENWGIAMPANSLTEAEPFLGYVDSALNTCAPTTINPINSKAQEFPCGTPLHADKVIVLTHEFLFEDGKRGMGATQNLPKLTKFIQLAKQAGYVFDTMDNYTPNWQVGNNYSAGDYVLHLGTVYQAVTSHTAQQDWAPSPTSSLWTNADPATNWTQNVSYKQGDVVTYQGLRYLVNVPHVSQADWSPSSQNTLFTAL 427
                                    35        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  


Chain B from PDB  Type:PROTEIN  Length:402
 aligned with A6P4T5_VIBPH | A6P4T5 from UniProtKB/TrEMBL  Length:427

    Alignment length:402
                                    35        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  
         A6P4T5_VIBPH    26 TKGTIYLTFDDGPINASIDVINVLNQEEVKATFYFNAWHLDGIGDENEDRALEALKLALDSGHIVANHSYDHMVHNCVEEFGPNSAAECNATGDHQINSYQDPAYDASMFAENLSVLEKYLPNITSYPNYKANEFARLPYTNGWRVTKDFKADGLCATSDDLKPWEPGYACDTANPSNSVKAAIAVQNILANNGYQTHGWDVDWAPENWGIAMPANSLTEAEPFLGYVDSALNTCAPTTINPINSKAQEFPCGTPLHADKVIVLTHEFLFEDGKRGMGATQNLPKLTKFIQLAKQAGYVFDTMDNYTPNWQVGNNYSAGDYVLHLGTVYQAVTSHTAQQDWAPSPTSSLWTNADPATNWTQNVSYKQGDVVTYQGLRYLVNVPHVSQADWSPSSQNTLFTAL 427
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee...hhhhhhhhhhhhhh....eeeehhhhh.........hhhhhhhhhhhh..eeee.....hhhhhh.....hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh.hhhhh.......ee.......eeee..eee........................hhhhhhhhhhhhhhhhh..ee....ee.........hhhhhh.hhhhhhhhhhhhh..hhhhhh.hhhhh.......hhhhh.eeeeeee.hhh.ee..eehhhhhhhhhhhhhhhhhhh.eeeehhhhh........ee....eeee..eeeee...ee.............eee...........ee....eeee..eeeee...ee.hhhhh.......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3wx7 B  26 TKGTIYLTFDDGPINASIDVINVLNQEEVKATFYFNAWHLDGIGDENEDRALEALKLALDSGHIVANHSYDHMVHNCVEEFGPNSAAECNATGDHQINSYQDPAYDASMFAENLSVLEKYLPNITSYPNYKANEFARLPYTNGWRVTKDFKADGLCATSDDLKPWEPGYACDTANPSNSVKAAIAVQNILANNGYQTHGWDVDWAPENWGIAMPANSLTEAEPFLGYVDSALNTCAPTTINPINSKAQEFPCGTPLHADKVIVLTHEFLFEDGKRGMGATQNLPKLTKFIQLAKQAGYVFDTMDNYTPNWQVGNNYSAGDYVLHLGTVYQAVTSHTAQQDWAPSPTSSLWTNADPATNWTQNVSYKQGDVVTYQGLRYLVNVPHVSQADWSPSSQNTLFTAL 427
                                    35        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
   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 3WX7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WX7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WX7)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A6P4T5_VIBPH | A6P4T5)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016810    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds    Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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.
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.

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  3wx7
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 Related Entries

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

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