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(-) Description

Title :  CARBOXYPEPTIDASE T WITH L-BENZYLSUCCINIC ACID
 
Authors :  S. A. Kuznetsov, V. I. Timofeev, V. K. Akparov, I. P. Kuranova
Date :  22 Feb 12  (Deposition) - 27 Feb 13  (Release) - 30 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. K. H. Akparov, V. I. Timofeev, I. G. Khaliullin, V. Svedas, G. G. Chestukhina, I. P. Kuranova
Structural Insights Into The Broad Substrate Specificity Of Carboxypeptidase T From Thermoactinomyces Vulgaris.
Febs J. V. 282 1214 2015
PubMed-ID: 25619204  |  Reference-DOI: 10.1111/FEBS.13210

(-) Compounds

Molecule 1 - CARBOXYPEPTIDASE T
    Chains: A
    EC Number: 3.4.17.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CPT
    Organism Scientific: THERMOACTINOMYCES VULGARIS
    Organism Taxid: 2026

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 32)

Asymmetric/Biological Unit (5, 32)
No.NameCountTypeFull Name
1BZS1Ligand/IonL-BENZYLSUCCINIC ACID
2CA4Ligand/IonCALCIUM ION
3GOL24Ligand/IonGLYCEROL
4SO42Ligand/IonSULFATE ION
5ZN1Ligand/IonZINC ION

(-) Sites  (32, 32)

Asymmetric Unit (32, 32)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:69 , GLU A:72 , HIS A:204 , BZS A:405BINDING SITE FOR RESIDUE ZN A 401
02AC2SOFTWARESER A:7 , TYR A:9 , GLU A:14 , HOH A:507 , HOH A:569 , HOH A:748BINDING SITE FOR RESIDUE CA A 402
03AC3SOFTWARESER A:50 , ASP A:51 , GLU A:57 , GLU A:59 , HOH A:595 , HOH A:685BINDING SITE FOR RESIDUE CA A 403
04AC4SOFTWARETYR A:5 , ASP A:291 , GLU A:292 , HOH A:577 , HOH A:673BINDING SITE FOR RESIDUE CA A 404
05AC5SOFTWAREHIS A:69 , GLU A:72 , ARG A:129 , ASN A:146 , ARG A:147 , HIS A:204 , THR A:205 , ALA A:251 , LEU A:254 , TYR A:255 , THR A:257 , ASP A:260 , GLU A:277 , ZN A:401BINDING SITE FOR RESIDUE BZS A 405
06AC6SOFTWAREVAL A:16 , ASN A:20 , THR A:21 , ASN A:25 , LYS A:32 , TRP A:45 , HOH A:549 , HOH A:728BINDING SITE FOR RESIDUE SO4 A 406
07AC7SOFTWAREHIS A:10 , LYS A:18 , ASP A:84 , GOL A:414BINDING SITE FOR RESIDUE GOL A 407
08AC8SOFTWARETYR A:12 , ASN A:13 , ARG A:42 , GLU A:117 , GOL A:415 , HOH A:687BINDING SITE FOR RESIDUE GOL A 408
09AC9SOFTWAREPHE A:33 , ASP A:184 , PHE A:185 , GOL A:410 , HOH A:556BINDING SITE FOR RESIDUE GOL A 409
10BC1SOFTWARELYS A:31 , TYR A:106 , GOL A:409 , HOH A:571 , HOH A:798 , HOH A:799BINDING SITE FOR RESIDUE GOL A 410
11BC2SOFTWAREARG A:71 , LYS A:152 , GLU A:166 , TYR A:216 , GOL A:412 , HOH A:738 , HOH A:758BINDING SITE FOR RESIDUE GOL A 411
12BC3SOFTWAREARG A:71 , ARG A:129 , GLU A:166 , TYR A:255 , GOL A:411 , GOL A:417 , HOH A:625 , HOH A:750BINDING SITE FOR RESIDUE GOL A 412
13BC4SOFTWARETHR A:226 , GLN A:227 , HOH A:534 , HOH A:642 , HOH A:773BINDING SITE FOR RESIDUE GOL A 413
14BC5SOFTWAREHIS A:10 , GLU A:77 , LEU A:80 , TYR A:81 , ASP A:84 , GOL A:407 , HOH A:579 , HOH A:716BINDING SITE FOR RESIDUE GOL A 414
15BC6SOFTWAREASP A:1 , ASN A:11 , GLU A:117 , GOL A:408 , HOH A:559 , HOH A:609 , HOH A:699BINDING SITE FOR RESIDUE GOL A 415
16BC7SOFTWAREASN A:25 , ASN A:28 , LYS A:31 , LYS A:32 , HOH A:617BINDING SITE FOR RESIDUE GOL A 416
17BC8SOFTWARETYR A:206 , SER A:207 , GOL A:412 , HOH A:646BINDING SITE FOR RESIDUE GOL A 417
18BC9SOFTWARETRP A:128 , ARG A:132 , HOH A:519 , HOH A:683 , HOH A:689BINDING SITE FOR RESIDUE GOL A 418
19CC1SOFTWAREGLY A:193 , GLN A:195 , HIS A:269 , HOH A:705 , HOH A:710BINDING SITE FOR RESIDUE GOL A 419
20CC2SOFTWAREGLY A:157 , GLY A:158 , SER A:159 , THR A:167 , HOH A:542 , HOH A:567 , HOH A:636 , HOH A:776BINDING SITE FOR RESIDUE GOL A 420
21CC3SOFTWARELEU A:209 , GLN A:249 , ASP A:253 , LEU A:254 , HOH A:722BINDING SITE FOR RESIDUE GOL A 421
22CC4SOFTWAREHOH A:576 , HOH A:583 , HOH A:597 , HOH A:638 , HOH A:775BINDING SITE FOR RESIDUE GOL A 422
23CC5SOFTWAREGLY A:137 , SER A:138 , SER A:139 , TYR A:140 , ARG A:171 , SER A:172 , HOH A:565 , HOH A:586BINDING SITE FOR RESIDUE GOL A 423
24CC6SOFTWAREGLU A:292 , ARG A:296 , SER A:299 , LYS A:302 , GLU A:303 , HOH A:530 , HOH A:783BINDING SITE FOR RESIDUE GOL A 424
25CC7SOFTWAREGLY A:8 , ASP A:291 , HOH A:747BINDING SITE FOR RESIDUE GOL A 425
26CC8SOFTWAREASN A:58 , PRO A:60 , ASN A:102 , ASP A:313 , HOH A:784BINDING SITE FOR RESIDUE GOL A 426
27CC9SOFTWAREASP A:56 , GLU A:57 , GLU A:59 , GLU A:61 , GLU A:104 , HOH A:678 , HOH A:679BINDING SITE FOR RESIDUE CA A 427
28DC1SOFTWAREARG A:183 , ASN A:187 , TRP A:264 , GLN A:268 , GOL A:429 , HOH A:711BINDING SITE FOR RESIDUE SO4 A 428
29DC2SOFTWAREGLY A:150 , PHE A:174 , TRP A:264 , SO4 A:428 , HOH A:603 , HOH A:702BINDING SITE FOR RESIDUE GOL A 429
30DC3SOFTWAREGLU A:310 , LYS A:311 , HOH A:774 , HOH A:800BINDING SITE FOR RESIDUE GOL A 430
31DC4SOFTWAREASN A:89 , ASP A:93 , LYS A:302 , GOL A:432 , HOH A:752BINDING SITE FOR RESIDUE GOL A 431
32DC5SOFTWARETYR A:81 , SER A:299 , GOL A:431 , HOH A:795BINDING SITE FOR RESIDUE GOL A 432

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:155 -A:156
2A:314 -A:323

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Thr A:205 -Tyr A:206
2Pro A:213 -Tyr A:214
3Tyr A:279 -Pro A:280
4Asn A:284 -Pro A:285

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DUK)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBOXYPEPT_ZN_1PS00132 Zinc carboxypeptidases, zinc-binding region 1 signature.CBPT_THEVU158-180  1A:60-82
2CARBOXYPEPT_ZN_2PS00133 Zinc carboxypeptidases, zinc-binding region 2 signature.CBPT_THEVU302-312  1A:204-214

(-) Exons   (0, 0)

(no "Exon" information available for 4DUK)

(-) 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:323
 aligned with CBPT_THEVU | P29068 from UniProtKB/Swiss-Prot  Length:424

    Alignment length:323
                                   108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418   
           CBPT_THEVU    99 DFPSYDSGYHNYNEMVNKINTVASNYPNIVKKFSIGKSYEGRELWAVKISDNVGTDENEPEVLYTALHHAREHLTVEMALYTLDLFTQNYNLDSRITNLVNNREIYIVFNINPDGGEYDISSGSYKSWRKNRQPNSGSSYVGTDLNRNYGYKWGCCGGSSGSPSSETYRGRSAFSAPETAAMRDFINSRVVGGKQQIKTLITFHTYSELILYPYGYTYTDVPSDMTQDDFNVFKTMANTMAQTNGYTPQQASDLYITDGDMTDWAYGQHKIFAFTFEMYPTSYNPGFYPPDEVIGRETSRNKEAVLYVAEKADCPYSVIGKSC 421
               SCOP domains d4duka_ A: Carboxypeptidase T                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...hhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee...........eeeeee......hhhhhhhhhhhhhhhhh...hhhhhhhhhhheeeee...hhhhhhhhhh......................hhhhh...........................hhhhhhhhhhhhhhee..ee.eeeeeeee....eeee.............hhhhhhhhhhhhhhhhhhhh.eeee.hhh.....hhhhhhhhhhh.eeeeee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------CARBOXYPEPT_ZN_1       -------------------------------------------------------------------------------------------------------------------------CARBOXYPEPT------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4duk A   1 DFPSYDSGYHNYNEMVNKINTVASNYPNIVKKFSIGKSYEGRELWAVKISDNVGTDENEPEVLYTALHHAREHLTVEMALYTLDLFTQNYNLDSRITNLVNNREIYIVFNINPDGGEYDISSGSYKSWRKNRQPNSGSSYVGTDLNRNYGYKWGCCGGSSGSPSSETYRGRSAFSAPETAAMRDFINSRVVGGKQQIKTLITFHTYSELILYPYGYTYTDVPSDMTQDDFNVFKTMANTMAQTNGYTPQQASDLYITDGDMTDWAYGQHKIFAFTFEMYPTSYNPGFYPPDEVIGRETSRNKEAVLYVAEKADCPYSVIGKSC 323
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DUK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DUK)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CBPT_THEVU | P29068)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004181    metallocarboxypeptidase activity    Catalysis of the hydrolysis of C-terminal amino acid residues from a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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
        CBPT_THEVU | P29068: 1obr 3prt 3qnv 3v38 3v7z 4djl 4f8z 4gm5 4iav 4ihm 4ik2

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4DUK)