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(-) Description

Title :  CRYSTAL STRUCTURE OF A COMPLEX BETWEEN ACTINOMADURA R39 DD-PEPTIDASE AND A SULFONAMIDE BORONATE INHIBITOR
 
Authors :  S. E. Cannella, E. Sauvage, R. Herman, F. Kerff, M. Rocaboy, P. Charlier
Date :  02 Aug 12  (Deposition) - 21 Aug 13  (Release) - 21 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
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 :  Hydrolase, Boronic Acid, Peptidoglycan (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Sauvage
Crystal Structure Of A Complex Between Actinomadura R39 Dd-Peptidase And A Boronate Inhibitor
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
    ChainsA, B, C, D
    EC Number3.4.16.4
    FragmentRESIDUES 50-515
    Organism ScientificACTINOMADURA SP. R39
    Organism Taxid72570
    SynonymDD-CARBOXYPEPTIDASE, DD-PEPTIDASE, PENICILLIN-BINDING PROTEIN, PBP

 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  (3, 34)

Asymmetric Unit (3, 34)
No.NameCountTypeFull Name
1BSF4Ligand/Ion{[(BENZYLSULFONYL)AMINO]METHYL}BORONIC ACID
2MG4Ligand/IonMAGNESIUM ION
3SO426Ligand/IonSULFATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1BSF1Ligand/Ion{[(BENZYLSULFONYL)AMINO]METHYL}BORONIC ACID
2MG-1Ligand/IonMAGNESIUM ION
3SO47Ligand/IonSULFATE ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1BSF1Ligand/Ion{[(BENZYLSULFONYL)AMINO]METHYL}BORONIC ACID
2MG-1Ligand/IonMAGNESIUM ION
3SO47Ligand/IonSULFATE ION
Biological Unit 3 (2, 8)
No.NameCountTypeFull Name
1BSF1Ligand/Ion{[(BENZYLSULFONYL)AMINO]METHYL}BORONIC ACID
2MG-1Ligand/IonMAGNESIUM ION
3SO47Ligand/IonSULFATE ION
Biological Unit 4 (2, 6)
No.NameCountTypeFull Name
1BSF1Ligand/Ion{[(BENZYLSULFONYL)AMINO]METHYL}BORONIC ACID
2MG-1Ligand/IonMAGNESIUM ION
3SO45Ligand/IonSULFATE ION

(-) Sites  (34, 34)

Asymmetric Unit (34, 34)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:49 , LYS A:52 , PHE A:297 , SER A:298 , LYS A:410 , THR A:411 , GLY A:412 , THR A:413 , HOH A:2028 , ALA B:175BINDING SITE FOR RESIDUE BSF A 500
02AC2SOFTWAREHIS A:282 , THR A:283 , HOH A:2209 , HOH A:2210BINDING SITE FOR RESIDUE SO4 A1467
03AC3SOFTWAREALA A:234 , ARG A:236 , HOH A:2278BINDING SITE FOR RESIDUE SO4 A1468
04AC4SOFTWARESER A:131 , ARG A:133 , LEU A:134BINDING SITE FOR RESIDUE SO4 A1469
05AC5SOFTWAREGLY A:159 , GLU A:160 , ARG A:161 , SO4 A:1473 , HOH A:2133 , HOH A:2280BINDING SITE FOR RESIDUE SO4 A1470
06AC6SOFTWAREGLU A:188 , HIS A:247 , GLU A:251BINDING SITE FOR RESIDUE MG A 610
07AC7SOFTWAREGLU A:404BINDING SITE FOR RESIDUE MG A 611
08AC8SOFTWARESER B:49 , LYS B:52 , SER B:298 , LYS B:410 , THR B:411 , GLY B:412 , THR B:413 , HOH B:2204 , HOH B:2206BINDING SITE FOR RESIDUE BSF B 500
09AC9SOFTWAREHIS B:282 , THR B:283BINDING SITE FOR RESIDUE SO4 B1466
10BC1SOFTWAREALA B:234 , ARG B:236 , HOH B:2180 , HOH B:2271 , HOH B:2272BINDING SITE FOR RESIDUE SO4 B1467
11BC2SOFTWARESER B:131 , ARG B:133 , LEU B:134BINDING SITE FOR RESIDUE SO4 B1468
12BC3SOFTWAREGLY B:159 , GLU B:160 , ARG B:161 , SO4 B:1472 , HOH B:2131BINDING SITE FOR RESIDUE SO4 B1469
13BC4SOFTWARESER C:49 , PHE C:297 , SER C:298 , LYS C:410 , THR C:411 , GLY C:412 , THR C:413 , HOH C:2229 , HOH C:2276BINDING SITE FOR RESIDUE BSF C 500
14BC5SOFTWAREHIS C:282 , THR C:283 , HOH C:2087BINDING SITE FOR RESIDUE SO4 C1466
15BC6SOFTWAREARG C:236 , HOH C:2294BINDING SITE FOR RESIDUE SO4 C1467
16BC7SOFTWARESER C:131 , GLU C:132 , ARG C:133 , LEU C:134 , HOH C:2103BINDING SITE FOR RESIDUE SO4 C1468
17BC8SOFTWAREGLY C:159 , GLU C:160 , ARG C:161 , SO4 C:1472 , HOH C:2145BINDING SITE FOR RESIDUE SO4 C1469
18BC9SOFTWARESER D:49 , LYS D:52 , SER D:298 , LYS D:410 , THR D:411 , GLY D:412 , THR D:413 , HOH D:2016 , HOH D:2187BINDING SITE FOR RESIDUE BSF D 500
19CC1SOFTWAREASP D:281 , HIS D:282 , THR D:283 , HOH D:2053BINDING SITE FOR RESIDUE SO4 D1467
20CC2SOFTWAREALA D:234 , ARG D:236 , HOH D:2199BINDING SITE FOR RESIDUE SO4 D1468
21CC3SOFTWARESER D:131 , ARG D:133 , LEU D:134 , HOH D:2201 , HOH D:2202 , HOH D:2203BINDING SITE FOR RESIDUE SO4 D1469
22CC4SOFTWAREGLY D:159 , GLU D:160 , ARG D:161 , SO4 D:1471 , HOH D:2106BINDING SITE FOR RESIDUE SO4 D1470
23CC5SOFTWAREGLU D:188 , HIS D:247 , GLU D:251BINDING SITE FOR RESIDUE MG D 610
24CC6SOFTWAREVAL D:406 , HIS D:462BINDING SITE FOR RESIDUE MG D 611
25CC7SOFTWAREHIS C:158 , GLY C:159 , SO4 C:1472 , HOH C:2082BINDING SITE FOR RESIDUE SO4 C1470
26CC8SOFTWAREARG A:39 , ASP A:40 , HOH A:2023BINDING SITE FOR RESIDUE SO4 A1471
27CC9SOFTWAREGLU A:192 , LEU A:193 , HOH A:2156BINDING SITE FOR RESIDUE SO4 A1472
28DC1SOFTWAREARG B:39 , ASP B:40BINDING SITE FOR RESIDUE SO4 B1470
29DC2SOFTWARETRP B:139 , SER B:415 , HOH B:2257BINDING SITE FOR RESIDUE SO4 B1471
30DC3SOFTWARETHR C:413 , HOH C:2122 , HOH C:2134BINDING SITE FOR RESIDUE SO4 C1471
31DC4SOFTWAREGLY A:203 , HIS B:158 , GLU B:168 , LEU B:235 , SO4 B:1469BINDING SITE FOR RESIDUE SO4 B1472
32DC5SOFTWAREHIS C:158 , GLU C:168 , SO4 C:1469 , SO4 C:1470BINDING SITE FOR RESIDUE SO4 C1472
33DC6SOFTWAREHIS D:158 , GLU D:168 , SO4 D:1470 , HOH D:2104BINDING SITE FOR RESIDUE SO4 D1471
34DC7SOFTWAREHIS A:158 , GLU A:168 , SO4 A:1470 , HOH A:2146 , HOH A:2279 , HOH A:2280BINDING SITE FOR RESIDUE SO4 A1473

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B4Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4B4Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B4Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4B4Z)

(-) Exons   (0, 0)

(no "Exon" information available for 4B4Z)

(-) 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: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 d4b4za_ A: D-alanyl-D-alanine carboxypeptidase Dac                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeee.......hhhhhhhhhhhhhhhhhh.....eeeeee........ee..eeeee......hhhhhhhhhhhhhhh...ee...eeee.............hhhhh..hhhh.......ee....ee.eeeeeee........eeehhhhh...eeee..eee........eee......eeeee.eee.....eeeeee..hhhhhhhhhhhhhhhhh..ee...eee..........eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhh..hhhhhhhh.......hhhhhhhhh............eeeeeee..eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b4z A   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 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 d4b4zb_ B: D-alanyl-D-alanine carboxypeptidase Dac                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeee.......hhhhhhhhhhhhhhhhhh.....eeeeee........ee..eeeee......hhhhhhhhhhhhhhh...ee...eeee.............hhhhh..hhhh.......ee....ee.eeeeeee........eeehhhhh...eeeeeeeee........eee......eeeeeeeee.....eeeeee..hhhhhhhhhhhhhhhhh..ee...eee..........eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhh..hhhhhhhhh......hhhhhhhhh............eee..ee..eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b4z 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 d4b4zc_ C: D-alanyl-D-alanine carboxypeptidase Dac                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeee.......hhhhhhhhhhhhhhhhhh...eeeeeeee........ee..eeeee......hhhhhhhhhhhhhhh...ee...eeee.............hhhhh..hhhh.......ee....ee.eeeeeee........eeehhhh....eeee..eee........eee......eeeee.eee.....eeeeee..hhhhhhhhhhhhhhhhh..ee...eee..........eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhh..hhhhhhhhh......hhhhhhhhh............eee..ee..eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b4z 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:461
 aligned with DAC_ACTSP | P39045 from UniProtKB/Swiss-Prot  Length:538

    Alignment length:461
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514 
            DAC_ACTSP    55 REDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASNMKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSAEDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTGAAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFEEALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNNGHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLSRGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRGTAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQDAIAVRLAEYAGHQAPE 515
               SCOP domains d4b4zd_ D: D-alanyl-D-alanine carboxypeptidase Dac                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..eeeeeeee.....eeeee.......hhhhhhhhhhhhhhhhhh...eeeeeeee........ee..eeeee......hhhhhhhhhhhhhhh...ee...eeee.............hhhhh..hhhh.......ee....ee.eeeeeee........eeehhhhh...eeee..eee........eee......eeeee.eee.....eeeeee..hhhhhhhhhhhhhhhhh..ee...eee..........eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhh.hhhhhhh........hhhhhhhhh............eeeeeee..eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b4z D   6 REDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASNMKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSAEDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTGAAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFEEALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNNGHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLSRGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRGTAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQDAIAVRLAEYAGHQAPE 466
                                    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       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465 

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B4Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B4Z)

(-) 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 | P390451w79 1w8q 1w8y 2vgj 2vgk 2wke 2xdm 2xk1 2xln 2y4a 2y55 2y59 3zcz 3zvt 3zvw 4b4x 4ben

(-) Related Entries Specified in the PDB File

1w79 CRYSTAL STRUCTURE OF THE DD-TRANSPEPTIDASE- CARBOXYPEPTIDASE FROM ACTINOMADURA R39
1w8q CRYSTAL STRUCTURE OF THE DD-PEPTIDASE FROM ACTINOMADURA R39 WITH COBALT IONS
1w8y CRYSTAL STRUCTURE OF THE NITROCEFIN ACYL-DD-PEPTIDASE FROM ACTINOMADURA R39.
2vgj CRYSTAL STRUCTURE OF ACTINOMADURA R39 DD-PEPTIDASE COMPLEXED WITH A PEPTIDOGLYCAN-MIMETIC CEPHALOSPORIN
2vgk CRYSTAL STRUCTURE OF ACTINOMADURA R39 DD-PEPTIDASE COMPLEXED WITH A PEPTIDOGLYCAN-MIMETIC CEPHALOSPORIN
2wke CRYSTAL STRUCTURE OF THE ACTINOMADURA R39 DD-PEPTIDASE INHIBITED BY 6-BETA-IODOPENICILLANATE.
2xdm CRYSTAL STRUCTURE OF A COMPLEX BETWEEN ACTINOMADURA R39 DD-PEPTIDASE AND A PEPTIDOGLYCAN MIMETIC BORONATE INHIBITOR
2xk1 CRYSTAL STRUCTURE OF A COMPLEX BETWEEN ACTINOMADURA R39 DD-PEPTIDASE AND A BORONATE INHIBITOR
2xln CRYSTAL STRUCTURE OF A COMPLEX BETWEEN ACTINOMADURA R39 DD-PEPTIDASE AND A BORONATE INHIBITOR
2y4a UNEXPECTED TRICOVALENT BINDING MODE OF BORONIC ACIDS WITHIN THE ACTIVE SITE OF A PENICILLIN BINDING PROTEIN
2y55 UNEXPECTED TRICOVALENT BINDING MODE OF BORONIC ACIDS WITHIN THE ACTIVE SITE OF A PENICILLIN BINDING PROTEIN
2y59 UNEXPECTED TRICOVALENT BINDING MODE OF BORONIC ACIDS WITHIN THE ACTIVE SITE OF A PENICILLIN BINDING PROTEIN
3zvt UNEXPECTED TRICOVALENT BINDING MODE OF BORONIC ACIDS WITHIN THE ACTIVE SITE OF A PENICILLIN BINDING PROTEIN
3zvw UNEXPECTED TRICOVALENT BINDING MODE OF BORONIC ACIDS WITHIN THE ACTIVE SITE OF A PENICILLIN BINDING PROTEIN
4b4x CRYSTAL STRUCTURE OF A COMPLEX BETWEEN ACTINOMADURA R39 DD-PEPTIDASE AND A SULFONAMIDE BORONATE INHIBITOR