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(-) Description

Title :  REFINED ATOMIC MODEL OF WHEAT SERINE CARBOXYPEPTIDASE II AT 2.2-ANGSTROMS RESOLUTION
 
Authors :  D. -I. Liao, S. J. Remington
Date :  01 Jul 92  (Deposition) - 31 Oct 93  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Hydrolase(Carboxypeptidase) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. I. Liao, K. Breddam, R. M. Sweet, T. Bullock, S. J. Remington
Refined Atomic Model Of Wheat Serine Carboxypeptidase Ii At 2. 2-A Resolution.
Biochemistry V. 31 9796 1992
PubMed-ID: 1390755  |  Reference-DOI: 10.1021/BI00155A037
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SERINE CARBOXYPEPTIDASE II (CPDW-II)
    ChainsA
    EC Number3.4.16.1
    EngineeredYES
    Organism CommonBREAD WHEAT
    Organism ScientificTRITICUM AESTIVUM
    Organism Taxid4565
 
Molecule 2 - SERINE CARBOXYPEPTIDASE II (CPDW-II)
    ChainsB
    EC Number3.4.16.1
    EngineeredYES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2MAN2Ligand/IonALPHA-D-MANNOSE
3NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 20)
No.NameCountTypeFull Name
1FUC4Ligand/IonALPHA-L-FUCOSE
2MAN4Ligand/IonALPHA-D-MANNOSE
3NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:27 , TYR A:103 , ASN A:105 , NAG A:249 , FUC A:251ABINDING SITE FOR RESIDUE NAG A 248
02AC2SOFTWARENAG A:248 , MAN A:250 , FUC A:251ABINDING SITE FOR RESIDUE NAG A 249
03AC3SOFTWARENAG A:249BINDING SITE FOR RESIDUE MAN A 250
04AC4SOFTWARENAG A:248 , NAG A:249BINDING SITE FOR RESIDUE FUC A 251A
05AC5SOFTWAREASN A:113 , HIS A:117 , NAG A:253 , FUC A:255BINDING SITE FOR RESIDUE NAG A 252
06AC6SOFTWARENAG A:252 , MAN A:254 , FUC A:255BINDING SITE FOR RESIDUE NAG A 253
07AC7SOFTWARENAG A:253BINDING SITE FOR RESIDUE MAN A 254
08AC8SOFTWARENAG A:252 , NAG A:253BINDING SITE FOR RESIDUE FUC A 255
09AC9SOFTWAREGLN B:285 , ASN B:291 , GLY B:294 , MET B:296 , TYR B:298 , TRP B:300 , NAG B:912BINDING SITE FOR RESIDUE NAG B 911
10BC1SOFTWARETHR B:299 , NAG B:911BINDING SITE FOR RESIDUE NAG B 912

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:56 -B:303
2A:210 -A:222
3A:246 -B:268

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gln A:42 -Pro A:43
2Gly A:53 -Pro A:54
3Ser A:95 -Pro A:96

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SC2)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBOXYPEPT_SER_SERPS00131 Serine carboxypeptidases, serine active site.CBP2_WHEAT154-161  1A:142-149
2CARBOXYPEPT_SER_HISPS00560 Serine carboxypeptidases, histidine active site.CBP2_WHEAT403-420  1B:387-404
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBOXYPEPT_SER_SERPS00131 Serine carboxypeptidases, serine active site.CBP2_WHEAT154-161  2A:142-149
2CARBOXYPEPT_SER_HISPS00560 Serine carboxypeptidases, histidine active site.CBP2_WHEAT403-420  2B:387-404

(-) Exons   (0, 0)

(no "Exon" information available for 3SC2)

(-) 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:254
 aligned with CBP2_WHEAT | P08819 from UniProtKB/Swiss-Prot  Length:444

    Alignment length:254
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255    
          CBP2_WHEAT      6 HAADRIARLPGQPAVDFDMYSGYITVDEGAGRSLFYLLQEAPEDAQPAPLVLWLNGGPGCSSVAYGASEELGAFRVKPRGAGLVLNEYRWNKVANVLFLDSPAGVGFSYTNTSSDIYTSGDNRTAHDSYAFLAKWFERFPHYKYRDFYIAGESYAGHYVPELSQLVHRSKNPVINLKGFMVGNGLIDDYHDYVGTFEFWWNHGIVSDDTYRRLKEACLHDSFIHPSPACDAATDVATAEQGNIDMYSLYTPVCN  259
               SCOP domains d3sc2.1 A:,B: Serine carboxypeptidase II                                                                                                                                                                                                                       SCOP domains
               CATH domains 3sc2A00 A:-4A-247  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee............eeeeeeeee....eeeeeee...hhhhh...eeeee...........hhhh....eee......eee...hhhhheeeee.........eeee.........hhhhhhhhhhhhhhhhhh.......eeeeeee..hhhhhhhhhhhhhh......eeeeeeee.....hhhhhhhhhhhhhh.....hhhhhhhhhhh.........hhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------CARBOXYP-------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3sc2 A  -4A HAADRIARLPGQPAVDFDMYSGYITVDEGAGRSLFYLLQEAPEDAQPAPLVLWLNGGPGCSSVAYGASEELGAFRVKPAGAGLVLNEYRWNKVANVLFLDSPAGVGFSYTNTSSDIYTSGDNRTAHDSYAFLAKWFERFPHYKYRDFYIAGESYAGHYVPELSQLVHRSKNPVINLKGFMVGNGLIDDYHDYVGTFEFWWNHGIVSDDTYRRLKEACLHDSFIHPSPACDAATDVATAEQGNIDMYSLYTPVCN  247
                            ||||     5     || 17      | 26        36        46        56  |     65        75 |      84        94       104      112B|      121       131  ||   143       153       163       173       183       193       203       213       223       233       243    
                            ||||          11|       23A                                 58A                76A                                 112A||                   134|                                                                                                              
                          -4A|||           14                                                                                                   112B|                    137                                                                                                              
                           -3A||                                                                                                                 112C                                                                                                                                     
                            -2A|                                                                                                                                                                                                                                                          
                             -1A                                                                                                                                                                                                                                                          

Chain B from PDB  Type:PROTEIN  Length:152
 aligned with CBP2_WHEAT | P08819 from UniProtKB/Swiss-Prot  Length:444

    Alignment length:152
                                   296       306       316       326       336       346       356       366       376       386       396       406       416       426       436  
          CBP2_WHEAT    287 SYDPCTERYSTAYYNRRDVQMALHANVTGAMNYTWATCSDTINTHWHDAPRSMLPIYRELIAAGLRIWVFSGDTDAVVPLTATRYSIGALGLPTTTSWYPWYDDQEVGGWSQVYKGLTLVSVRGAGHEVPLHRPRQALVLFQYFLQGKPMPG  438
               SCOP domains d3sc2.1 A:,B: Serine carboxypeptidase II                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Peptidase_S10-3sc2B01 B:264-417                                                                                                                    ----- Pfam domains (1)
           Pfam domains (2) Peptidase_S10-3sc2B02 B:264-417                                                                                                                    ----- Pfam domains (2)
         Sec.struct. author .....hhhhhhhhh..hhhhhhh................hhhhh.........hhhhhhhh....eeeeeee.......hhhhhhhhh......eeeeeeee...eeeeeeeee..eeeeee......hhhh.hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------CARBOXYPEPT_SER_HI------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3sc2 B  264 SYDPCTERYSTAYYNRRDVQMALHANVTGAMNYTWATCSDTINTHWHDAPRSMLPIYRELIAAGLRIWVFSGDTDAVVPLTATRYSIGALGLPTTTSWYPWYDDQEVGGWSQVYKGLTLVSVRGAGHEVPLHRPRQALVLFQYFLQGKPMPG  422
                                || 275       285       295      303B     ||310       320   ||  333       343       353|      371    |  380       390       400       410       420  
                              268|                             303A|  308A||             324|                      353|          375A                                               
                               271                              303B   308B|              328                       362                                                             
                                                                        308C                                                                                                        

   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)

Asymmetric Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CBP2_WHEAT | P08819)
molecular function
    GO:0004180    carboxypeptidase activity    Catalysis of the hydrolysis of the terminal or penultimate peptide bond at the C-terminal end of a peptide or polypeptide.
    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:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0004185    serine-type carboxypeptidase activity    Catalysis of the hydrolysis of a peptide bond not more than three residues from the C-terminus of a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CBP2_WHEAT | P088191bcr 1bcs 1whs 1wht

(-) Related Entries Specified in the PDB File

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