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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DD-TRANSPEPTIDASE-CARBOXYPEPTIDASE FROM ACTINOMADURA R39
 
Authors :  E. Sauvage, R. Herman, S. Petrella, C. Duez, J. M. Frere, P. Charlier
Date :  24 Sep 04  (Deposition) - 28 Jun 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Penicillin-Binding, Peptidoglycan, Actinomadura, Transpeptidase, Antibiotic Resistance, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Sauvage, R. Herman, S. Petrella, C. Duez, F. Bouillenne, J. M. Frere, P. Charlier
Crystal Structure Of The Actinomadura R39 Dd- Peptidase Reveals New Domains In Penicillin- Binding Proteins.
J. Biol. Chem. V. 280 31249 2005
PubMed-ID: 15987687  |  Reference-DOI: 10.1074/JBC.M503271200

(-) Compounds

Molecule 1 - D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
    Chains: A, B, C, D
    EC Number: 3.4.16.4
    Organism Scientific: ACTINOMADURA SP.
    Organism Taxid: 72570
    Strain: R39
    Synonym: DD-CARBOXYPEPTIDASE, DD-PEPTIDASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 38)

Asymmetric Unit (2, 38)
No.NameCountTypeFull Name
1CO18Ligand/IonCOBALT (II) ION
2SO420Ligand/IonSULFATE ION
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2SO45Ligand/IonSULFATE ION
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2SO45Ligand/IonSULFATE ION
Biological Unit 3 (1, 5)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2SO45Ligand/IonSULFATE ION
Biological Unit 4 (1, 5)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2SO45Ligand/IonSULFATE ION

(-) Sites  (38, 38)

Asymmetric Unit (38, 38)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:49 , SER A:298 , LYS A:410 , THR A:411 , GLY A:412 , THR A:413BINDING SITE FOR RESIDUE SO4 A 500
02AC2SOFTWAREHIS A:282 , THR A:283BINDING SITE FOR RESIDUE SO4 A 501
03AC3SOFTWAREARG A:236BINDING SITE FOR RESIDUE SO4 A 502
04AC4SOFTWARESER A:131 , GLU A:132 , ARG A:133 , LEU A:134BINDING SITE FOR RESIDUE SO4 A 503
05AC5SOFTWAREGLY A:159 , GLU A:160 , ARG A:161 , CO A:513BINDING SITE FOR RESIDUE SO4 A 504
06AC6SOFTWAREGLU A:188 , HIS A:247 , GLU A:251BINDING SITE FOR RESIDUE CO A 510
07AC7SOFTWAREVAL A:406 , HIS A:462BINDING SITE FOR RESIDUE CO A 511
08AC8SOFTWARELEU A:63 , ASP A:66 , HIS A:67BINDING SITE FOR RESIDUE CO A 512
09AC9SOFTWAREHIS A:158 , GLU A:168 , SO4 A:504BINDING SITE FOR RESIDUE CO A 513
10BC1SOFTWAREASP A:102 , HIS A:282BINDING SITE FOR RESIDUE CO A 514
11BC2SOFTWARESER B:49 , SER B:298 , THR B:393 , LYS B:410 , THR B:411 , GLY B:412 , THR B:413BINDING SITE FOR RESIDUE SO4 B 500
12BC3SOFTWAREASP B:281 , HIS B:282 , THR B:283BINDING SITE FOR RESIDUE SO4 B 501
13BC4SOFTWAREALA B:234 , ARG B:236BINDING SITE FOR RESIDUE SO4 B 502
14BC5SOFTWARESER B:131 , GLU B:132 , ARG B:133 , LEU B:134BINDING SITE FOR RESIDUE SO4 B 503
15BC6SOFTWAREGLY B:159 , GLU B:160 , ARG B:161BINDING SITE FOR RESIDUE SO4 B 504
16BC7SOFTWAREGLU B:188 , HIS B:247 , GLU B:251BINDING SITE FOR RESIDUE CO B 510
17BC8SOFTWARELEU B:63 , HIS B:67 , GLU B:313BINDING SITE FOR RESIDUE CO B 512
18BC9SOFTWAREHIS B:158 , GLU B:168BINDING SITE FOR RESIDUE CO B 513
19CC1SOFTWAREASP B:102 , HIS B:282BINDING SITE FOR RESIDUE CO B 514
20CC2SOFTWARESER C:49 , SER C:298 , LYS C:410 , THR C:411 , GLY C:412 , THR C:413BINDING SITE FOR RESIDUE SO4 C 500
21CC3SOFTWAREASP C:281 , HIS C:282 , THR C:283BINDING SITE FOR RESIDUE SO4 C 501
22CC4SOFTWAREALA C:234 , ARG C:236 , HOH C:2011BINDING SITE FOR RESIDUE SO4 C 502
23CC5SOFTWARESER C:131 , GLU C:132 , ARG C:133 , LEU C:134BINDING SITE FOR RESIDUE SO4 C 503
24CC6SOFTWAREGLY C:159 , GLU C:160 , ARG C:161BINDING SITE FOR RESIDUE SO4 C 504
25CC7SOFTWAREGLU C:188 , HIS C:247 , GLU C:251BINDING SITE FOR RESIDUE CO C 510
26CC8SOFTWARELEU C:63 , HIS C:67BINDING SITE FOR RESIDUE CO C 512
27CC9SOFTWAREHIS C:158 , GLU C:168BINDING SITE FOR RESIDUE CO C 513
28DC1SOFTWAREASP C:102 , HIS C:282BINDING SITE FOR RESIDUE CO C 514
29DC2SOFTWARESER D:49 , SER D:298 , LYS D:410 , THR D:411 , GLY D:412 , THR D:413BINDING SITE FOR RESIDUE SO4 D 500
30DC3SOFTWAREASP D:281 , HIS D:282 , THR D:283BINDING SITE FOR RESIDUE SO4 D 501
31DC4SOFTWAREARG D:236BINDING SITE FOR RESIDUE SO4 D 502
32DC5SOFTWAREGLU D:132 , ARG D:133 , LEU D:134 , HOH D:2023BINDING SITE FOR RESIDUE SO4 D 503
33DC6SOFTWAREGLY D:159 , GLU D:160 , ARG D:161 , CO D:513BINDING SITE FOR RESIDUE SO4 D 504
34DC7SOFTWAREGLU D:188 , HIS D:247 , GLU D:251BINDING SITE FOR RESIDUE CO D 510
35DC8SOFTWAREHIS D:462BINDING SITE FOR RESIDUE CO D 511
36DC9SOFTWARELEU D:63 , HIS D:67BINDING SITE FOR RESIDUE CO D 512
37EC1SOFTWAREHIS D:158 , GLU D:168 , SO4 D:504BINDING SITE FOR RESIDUE CO D 513
38EC2SOFTWARETHR D:97 , ASP D:102 , HIS D:282BINDING SITE FOR RESIDUE CO D 514

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W8Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1W8Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W8Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1W8Q)

(-) Exons   (0, 0)

(no "Exon" information available for 1W8Q)

(-) 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:467
 aligned with DAC_ACTSP | P39045 from UniProtKB/Swiss-Prot  Length:538

    Alignment length:467
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       
            DAC_ACTSP    50 RLTELREDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASNMKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSAEDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTGAAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFEEALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNNGHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLSRGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRGTAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQDAIAVRLAEYAGHQAPEG 516
               SCOP domains d1w8qa_ A: D-alanyl-D-alanine carboxypeptidase Dac                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1w8qA01 A:1-68,A:285-467 DD-peptidase/beta-lactamase superfamily    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1w8qA01 A:1-68,A:285-467 DD-peptidase/beta-lactamase superfamily                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh..eeeeeeee.......eee....ee.hhhhhhhhhhhhhhhhh....eeeeeeee........ee..eeeee......hhhhhhhhhhhhhhh...ee...eeee.............hhhhh.hhhhh.......ee....ee.eeeeeee........eeehhhhh...eeee..eee........eee......eeeee.eee.....eeeeee..hhhhhhhhhhhhhhhhh..ee...eee..........eeeeeeeeeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....................eehhhhhhhhhhhhhh.hhhhhhh........hhhhhhhhh............eee..ee..eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w8q A   1 RLTELREDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASNMKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSAEDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTGAAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFEEALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNNGHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLSRGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRGTAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQDAIAVRLAEYAGHQAPEG 467
                                    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       330       340       350       360       370       380       390       400       410       420       430       440       450       460       


Chain B from PDB  Type:PROTEIN  Length:466
 aligned with DAC_ACTSP | P39045 from UniProtKB/Swiss-Prot  Length:538

    Alignment length:466
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509      
            DAC_ACTSP    50 RLTELREDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASNMKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSAEDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTGAAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFEEALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNNGHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLSRGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRGTAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQDAIAVRLAEYAGHQAPE 515
               SCOP domains d1w8qb_ B: D-alanyl-D-alanine carboxypeptidase Dac                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1w8qB01 B:1-68,B:285-466 DD-peptidase/beta-lactamase superfamily    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1w8qB01 B:1-68,B:285-466 DD-peptidase/beta-lactamase superfamily                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh..eeeeeeee.......eee.......hhhhhhhhhhhhhhhhh....eeeeeeee........ee..eeeee......hhhhhhhhhhhhhhh...ee...eeee.............hhhhh..hhhh................eeeeeee........eeehhhhh...eeee..eee........eee......eeeee.eee.....eeeeee..hhhhhhhhhhhhhhhh...ee...eee..........eeeeeeeeeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh......................hhhhhhhhhhhhhh..hhhhhhhhh......hhhhhhhhh............eeeeeee..eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w8q B   1 RLTELREDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASNMKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSAEDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTGAAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFEEALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNNGHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLSRGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRGTAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQDAIAVRLAEYAGHQAPE 466
                                    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       330       340       350       360       370       380       390       400       410       420       430       440       450       460      


Chain C from PDB  Type:PROTEIN  Length:466
 aligned with DAC_ACTSP | P39045 from UniProtKB/Swiss-Prot  Length:538

    Alignment length:466
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509      
            DAC_ACTSP    50 RLTELREDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASNMKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSAEDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTGAAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFEEALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNNGHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLSRGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRGTAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQDAIAVRLAEYAGHQAPE 515
               SCOP domains d1w8qc_ C: D-alanyl-D-alanine carboxypeptidase Dac                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1w8qC01 C:1-68,C:285-466 DD-peptidase/beta-lactamase superfamily    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1w8qC01 C:1-68,C:285-466 DD-peptidase/beta-lactamase superfamily                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh..eeeeeeee....eeeeee.......hhhhhhhhhhhhhhhhh......eeeeee........ee..eeeee......hhhhhhhhhhhhhh....ee...eeee...................hhhhh.......ee....ee.eeeeeee........eeehhhhh...eeee..eee........eee......eeeee.eee.....eeeeee..hhhhhhhhhhhhhhhhh..ee...eee..........eeeeeee..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhh..hhhhhhhh.......hhhhhhhhh............eeeeeee..eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w8q C   1 RLTELREDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASNMKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSAEDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTGAAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFEEALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNNGHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLSRGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRGTAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQDAIAVRLAEYAGHQAPE 466
                                    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       330       340       350       360       370       380       390       400       410       420       430       440       450       460      


Chain D from PDB  Type:PROTEIN  Length:467
 aligned with DAC_ACTSP | P39045 from UniProtKB/Swiss-Prot  Length:538

    Alignment length:467
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       
            DAC_ACTSP    50 RLTELREDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASNMKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSAEDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTGAAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFEEALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNNGHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLSRGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRGTAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQDAIAVRLAEYAGHQAPEG 516
               SCOP domains d1w8qd_ D: D-alanyl-D-alanine carboxypeptidase Dac                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1w8qD01 D:1-68,D:285-467 DD-peptidase/beta-lactamase superfamily    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1w8qD01 D:1-68,D:285-467 DD-peptidase/beta-lactamase superfamily                                                                                                                        CATH domains
           Pfam domains (1) ----Peptidase_S13-1w8qD01 D:5-459                                                                                                                                                                                                                                                                                                                                                                                                                                          -------- Pfam domains (1)
           Pfam domains (2) ----Peptidase_S13-1w8qD02 D:5-459                                                                                                                                                                                                                                                                                                                                                                                                                                          -------- Pfam domains (2)
           Pfam domains (3) ----Peptidase_S13-1w8qD03 D:5-459                                                                                                                                                                                                                                                                                                                                                                                                                                          -------- Pfam domains (3)
           Pfam domains (4) ----Peptidase_S13-1w8qD04 D:5-459                                                                                                                                                                                                                                                                                                                                                                                                                                          -------- Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeee.......hhhhhhhhhhhhhhhhh......eeeeee........ee..eeeee......hhhhhhhhhhhhhh....ee...eeee....................hhhh.......ee....ee.eeeeeee........eeehhhh....eeee..eee........eee......eeeee.eee.....eeeeee..hhhhhhhhhhhhhhhh...ee...eee..........eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhh..hhhhhhhh.......hhhhhhhhh............eeeeeee..eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w8q D   1 RLTELREDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASNMKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSAEDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTGAAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFEEALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNNGHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLSRGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRGTAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQDAIAVRLAEYAGHQAPEG 467
                                    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       330       340       350       360       370       380       390       400       410       420       430       440       450       460
   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, 4)

Asymmetric Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Beta-lactamase (210)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (DAC_ACTSP | P39045)
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:0009002    serine-type D-Ala-D-Ala carboxypeptidase activity    Catalysis of the reaction: (Ac)2-L-Lys-D-alanyl-D-alanine + H2O = (Ac)2-L-Lys-D-alanine + D-alanine.
    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:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0009252    peptidoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0046677    response to antibiotic    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 an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        DAC_ACTSP | P39045: 1w79 1w8y 2vgj 2vgk 2wke 2xdm 2xk1 2xln 2y4a 2y55 2y59 3zcz 3zvt 3zvw 4b4x 4b4z 4ben

(-) Related Entries Specified in the PDB File

1w79 CRYSTAL STRUCTURE OF THE DD-TRANSPEPTIDASE- CARBOXYPEPTIDASE FROM ACTINOMADURA R39
1w8y CRYSTAL STRUCTURE OF THE NITROCEFIN ACYL-DD -PEPTIDASE FROM ACTINOMADURA R39.