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(-) Description

Title :  STRUCTURE OF THE COMPLEX OF L-BENZYLSUCCINATE WITH WHEAT SERINE CARBOXYPEPTIDASE II AT 2.0 ANGSTROMS RESOLUTION
 
Authors :  T. L. Bullock, S. J. Remington
Date :  07 Mar 94  (Deposition) - 22 Jun 94  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Serine Carboxypeptidase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. L. Bullock, B. Branchaud, S. J. Remington
Structure Of The Complex Of L-Benzylsuccinate With Wheat Serine Carboxypeptidase Ii At 2. 0-A Resolution.
Biochemistry V. 33 11127 1994
PubMed-ID: 7727364  |  Reference-DOI: 10.1021/BI00203A009
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SERINE CARBOXYPEPTIDASE II
    ChainsA
    EC Number3.4.16.1
    EngineeredYES
    Organism CommonCOMMON WHEAT
    Organism ScientificTRITICUM AESTIVUM
    Organism Taxid4565
 
Molecule 2 - SERINE CARBOXYPEPTIDASE II
    ChainsB
    EC Number3.4.16.1
    EngineeredYES
    Organism CommonCOMMON WHEAT
    Organism ScientificTRITICUM AESTIVUM
    Organism Taxid4565

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2FUC1Ligand/IonALPHA-L-FUCOSE
3GOL1Ligand/IonGLYCEROL
4NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (4, 18)
No.NameCountTypeFull Name
1ACY4Ligand/IonACETIC ACID
2FUC2Ligand/IonALPHA-L-FUCOSE
3GOL2Ligand/IonGLYCEROL
4NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:113 , HIS A:117 , HOH A:1342 , HOH A:1358 , HOH A:1359BINDING SITE FOR RESIDUE NAG A 1131
02AC2SOFTWARETYR A:103 , NAG A:1133 , NAG A:1134 , THR B:293BINDING SITE FOR RESIDUE FUC A 1132
03AC3SOFTWARETHR A:22 , GLY A:27 , TYR A:103 , ASN A:105 , FUC A:1132 , NAG A:1134BINDING SITE FOR RESIDUE NAG A 1133
04AC4SOFTWAREFUC A:1132 , NAG A:1133 , THR B:293BINDING SITE FOR RESIDUE NAG A 1134
05AC5SOFTWAREASN B:280 , ARG B:282 , GLN B:285 , ASN B:291 , GLY B:294 , MET B:296 , TYR B:298 , THR B:299 , TRP B:300 , NAG B:2912BINDING SITE FOR RESIDUE NAG B 2911
06AC6SOFTWAREASN B:280 , NAG B:2911 , HOH B:3031BINDING SITE FOR RESIDUE NAG B 2912
07AC7SOFTWAREPHE A:14 , ASP A:15 , GLU A:36 , ALA A:37 , GLU A:39 , GLN A:42 , HIS A:212BINDING SITE FOR RESIDUE GOL A 450
08AC8SOFTWAREASN A:51 , GLY A:52 , GLU A:145 , SER A:146BINDING SITE FOR RESIDUE ACY A 460
09AC9SOFTWAREASN A:235 , THR A:243 , PRO A:244 , GLU B:376 , VAL B:377 , ARG B:393BINDING SITE FOR RESIDUE ACY B 461
10ACTUNKNOWNASP B:338 , HIS B:397 , SER A:146 , GLU A:145NULL

(-) 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 1WHS)

(-) 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 1WHS)

(-) 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:255
 aligned with CBP2_WHEAT | P08819 from UniProtKB/Swiss-Prot  Length:444

    Alignment length:255
                                    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 HAADRIARLPGQPAVDFDMYSGYITVDEGAGRSLFYLLQEAPEDAQPAPLVLWLNGGPGCSSVAYGASEELGAFRVKPRGAGLVLNEYRWNKVANVLFLDSPAGVGFSYTNTSSDIYTSGDNRTAHDSYAFLAKWFERFPHYKYRDFYIAGESYAGHYVPELSQLVHRSKNPVINLKGFMVGNGLIDDYHDYVGTFEFWWNHGIVSDDTYRRLKEACLHDSFIHPSPACDAATDVATAEQGNIDMYSLYTPVCNI  260
               SCOP domains d1whs.1 A:,B: Serine carboxypeptidase II                                                                                                                                                                                                                        SCOP domains
               CATH domains 1whsA00 A:-4-248  [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
                1whs A   -4 HAADRIARLPGQPAVDFDMYSGYITVDEGAGRSLFYLLQEAPEDAQPAPLVLWLNGGPGCSSVAYGASEELGAFRVKPRGAGLVLNEYRWNKVANVLFLDSPAGVGFSYTNTSSDIYTSGDNRTAHDSYAFLAKWFERFPHYKYRDFYIAGESYAGHYVPELSQLVHRSKNPVINLKGFMVGNGLIDDYHDYVGTFEFWWNHGIVSDDTYRRLKEACLHDSFIHPSPACDAATDVATAEQGNIDMYSLYTPVCNI  248
                                     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|                                                                                                               
                                           14                                                                                                   112B|                    137                                                                                                               
                                                                                                                                                 112C                                                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:153
 aligned with CBP2_WHEAT | P08819 from UniProtKB/Swiss-Prot  Length:444

    Alignment length:153
                                   296       306       316       326       336       346       356       366       376       386       396       406       416       426       436   
          CBP2_WHEAT    287 SYDPCTERYSTAYYNRRDVQMALHANVTGAMNYTWATCSDTINTHWHDAPRSMLPIYRELIAAGLRIWVFSGDTDAVVPLTATRYSIGALGLPTTTSWYPWYDDQEVGGWSQVYKGLTLVSVRGAGHEVPLHRPRQALVLFQYFLQGKPMPGQ  439
               SCOP domains d1whs.1 A:,B: Serine carboxypeptidase II                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Peptidase_S10-1whsB01 B:264-417                                                                                                                    ------ Pfam domains (1)
           Pfam domains (2) Peptidase_S10-1whsB02 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
                1whs B  264 SYDPCTERYSTAYYNRRDVQMALHANVTGAMNYTWATCSDTINTHWHDAPRSMLPIYRELIAAGLRIWVFSGDTDAVVPLTATRYSIGALGLPTTTSWYPWYDDQEVGGWSQVYKGLTLVSVRGAGHEVPLHRPRQALVLFQYFLQGKPMPGQ  423
                                || 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 1wht 3sc2

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