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(-) Description

Title :  THE SOLUTION STRUCTURE OF TYPE II ANTIFREEZE PROTEIN REVEALS A NEW MEMBER OF THE LECTIN FAMILY
 
Authors :  W. Gronwald, M. C. Loewen, B. Lix, A. J. Daugulis, F. D. Sonnichsen, P. L. Davies, B. D. Sykes
Date :  14 Dec 98  (Deposition) - 23 Dec 98  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (5x)
Keywords :  Recombinant Sea Raven Protein, Solution Backbone Fold, C- Type Lectin, Antifreeze Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Gronwald, M. C. Loewen, B. Lix, A. J. Daugulis, F. D. Sonnichsen, P. L. Davies, B. D. Sykes
The Solution Structure Of Type Ii Antifreeze Protein Reveals A New Member Of The Lectin Family.
Biochemistry V. 37 4712 1998
PubMed-ID: 9537986  |  Reference-DOI: 10.1021/BI972788C
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (SEA RAVEN TYPE II ANTIFREEZE PROTEIN)
    Chains: A
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Gene: SRAFP GENE
    Expression System Plasmid: PPIC9-SRM-CTHT
    Expression System Strain: GS115
    Expression System Taxid: 4922
    Organ: BLOOD
    Organism Common: SEA RAVEN
    Organism Scientific: HEMITRIPTERUS AMERICANUS
    Organism Taxid: 8094
    Other Details: SIX AMINO ACID HIS TAG WAS ADDED AT THE C- TERMINAL END TO FACILITATE RECOVERY OF THE SECRETED AFP FROM THE MEDIUM USING AFFINITY CHROMATOGRAPHY.

 Structural Features

(-) Chains, Units

  
NMR Structure (5x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2AFP)

(-) Sites  (0, 0)

(no "Site" information available for 2AFP)

(-) SS Bonds  (5, 5)

NMR Structure
No.Residues
1A:7 -A:18
2A:35 -A:125
3A:69 -A:100
4A:89 -A:111
5A:101 -A:117

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2AFP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.ISP2_HEMAM48-160  1A:14-126
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.ISP2_HEMAM135-159  1A:101-125

(-) Exons   (0, 0)

(no "Exon" information available for 2AFP)

(-) Sequences/Alignments

NMR Structure
   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:129
 aligned with ISP2_HEMAM | P05140 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:129
                                    44        54        64        74        84        94       104       114       124       134       144       154         
           ISP2_HEMAM    35 QRAPPNCPAGWQPLGDRCIYYETTAMTWALAETNCMKLGGHLASIHSQEEHSFIQTLNAGVVWIGGSACLQAGAWTWSDGTPMNFRSWCSTKPDDVLAACCMQMTAAADQCWDDLPCPASHKSVCAMTF 163
               SCOP domains d2afpa_ A: Type II antifreeze protein                                                                                             SCOP domains
               CATH domains 2afpA00 A:1-129 Mannose-Binding Protein A, subunit A                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeeee..eeee.hhhhhhhhheeee....hhhhhhhhhhh...eeee.eeee....eeee......................eeeeeee...eeeeee.......eeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------C_TYPE_LECTIN_2  PDB: A:14-126 UniProt: 48-160                                                                   --- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1          ---- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2afp A   1 QRAGPNCPAGWQPLGDRCIYYETTAMTWALAETNCMKLGGHLASIHSQEEHSFIQTLNAGVVWIGGSACLQAGAWTWSDGTPMNFRSWCSTKPDDVLAACCMQMTAAADQCWDDLPCPASHKSVCAMTF 129
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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, 1)

NMR Structure
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

NMR Structure(hide GO term definitions)
Chain A   (ISP2_HEMAM | P05140)
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.
biological process
    GO:0050826    response to freezing    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a freezing stimulus, temperatures below 0 degrees Celsius.
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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 Databases and Analysis Tools

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  2afp
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 Related Entries

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