2Y55 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   UNEXPECTED TRICOVALENT BINDING MODE OF BORONIC ACIDS WITHIN THE ACTIVE SITE OF A PENICILLIN BINDING PROTEIN

Authors :   E. Sauvage, A. Zervosen, R. Herman, F. Kerff, M. Rocaboy, P. Charlier

Date :   12 Jan 11 (Deposition) - 27 Jul 11 (Release) - 27 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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-Inhibitor Complex, Peptidoglycan, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Zervosen, R. Herman, F. Kerff, A. Herman, A. Bouillez, F. Prati, R. F. Pratt, J. M. Frere, B. Joris, A. Luxen, P. Charlier, E. Sauvage
Unexpected Tricovalent Binding Mode Of Boronic Acids Within The Active Site Of A Penicillin- Binding Protein.
J. Am. Chem. Soc. V. 133 10839 2011
PubMed-ID: 21574608 | Reference-DOI: 10.1021/JA200696Y

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

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
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)

Asymmetric Unit (4, 30)

No.	Name	Count	Type	Full Name
1	ACN	5	Ligand/Ion	ACETONE
2	FP5	4	Ligand/Ion	PHENYLACETAMIDOMETHYL BORONIC ACID
3	MG	4	Ligand/Ion	MAGNESIUM ION
4	SO4	17	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 7)

No.	Name	Count	Type	Full Name
1	ACN	1	Ligand/Ion	ACETONE
2	FP5	1	Ligand/Ion	PHENYLACETAMIDOMETHYL BORONIC ACID
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	ACN	1	Ligand/Ion	ACETONE
2	FP5	1	Ligand/Ion	PHENYLACETAMIDOMETHYL BORONIC ACID
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 3 (3, 6)

No.	Name	Count	Type	Full Name
1	ACN	1	Ligand/Ion	ACETONE
2	FP5	1	Ligand/Ion	PHENYLACETAMIDOMETHYL BORONIC ACID
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 4 (3, 7)

No.	Name	Count	Type	Full Name
1	ACN	2	Ligand/Ion	ACETONE
2	FP5	1	Ligand/Ion	PHENYLACETAMIDOMETHYL BORONIC ACID
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (30, 30)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:48 , SER A:49 , LYS A:52 , SER A:298 , ASN A:300 , LYS A:410 , THR A:411 , GLY A:412 , THR A:413 , ACN A:1473	BINDING SITE FOR RESIDUE FP5 A 500
02	AC2	SOFTWARE	ASP A:281 , HIS A:282 , THR A:283	BINDING SITE FOR RESIDUE SO4 A1467
03	AC3	SOFTWARE	ALA A:234 , ARG A:236 , HOH A:2079	BINDING SITE FOR RESIDUE SO4 A1468
04	AC4	SOFTWARE	SER A:131 , GLU A:132 , ARG A:133 , LEU A:134	BINDING SITE FOR RESIDUE SO4 A1469
05	AC5	SOFTWARE	GLY A:159 , GLU A:160 , ARG A:161	BINDING SITE FOR RESIDUE SO4 A1470
06	AC6	SOFTWARE	GLU A:188 , HIS A:247 , GLU A:251	BINDING SITE FOR RESIDUE MG A1471
07	AC7	SOFTWARE	VAL A:406 , HIS A:462	BINDING SITE FOR RESIDUE MG A1472
08	AC8	SOFTWARE	TYR A:147 , THR A:413 , MET A:414 , FP5 A:500	BINDING SITE FOR RESIDUE ACN A1473
09	AC9	SOFTWARE	ARG A:161	BINDING SITE FOR RESIDUE SO4 A1474
10	BC1	SOFTWARE	ALA B:48 , SER B:49 , LYS B:52 , SER B:298 , ASN B:300 , SER B:347 , GLY B:348 , LEU B:349 , LYS B:410 , THR B:411 , GLY B:412 , THR B:413 , ACN B:1471	BINDING SITE FOR RESIDUE FP5 B 500
11	BC2	SOFTWARE	ASP B:281 , HIS B:282 , THR B:283	BINDING SITE FOR RESIDUE SO4 B1467
12	BC3	SOFTWARE	ALA B:234 , ARG B:236 , HOH B:2068	BINDING SITE FOR RESIDUE SO4 B1468
13	BC4	SOFTWARE	SER B:131 , GLU B:132 , ARG B:133 , LEU B:134	BINDING SITE FOR RESIDUE SO4 B1469
14	BC5	SOFTWARE	HIS B:158 , GLY B:159 , GLU B:160 , ARG B:161	BINDING SITE FOR RESIDUE SO4 B1470
15	BC6	SOFTWARE	THR B:413 , FP5 B:500	BINDING SITE FOR RESIDUE ACN B1471
16	BC7	SOFTWARE	ALA C:48 , SER C:49 , LYS C:52 , SER C:298 , ASN C:300 , GLY C:348 , LYS C:410 , GLY C:412 , THR C:413	BINDING SITE FOR RESIDUE FP5 C 500
17	BC8	SOFTWARE	ASP C:281 , HIS C:282 , THR C:283 , HOH C:2064	BINDING SITE FOR RESIDUE SO4 C1467
18	BC9	SOFTWARE	ARG C:236	BINDING SITE FOR RESIDUE SO4 C1468
19	CC1	SOFTWARE	SER C:131 , ARG C:133 , LEU C:134	BINDING SITE FOR RESIDUE SO4 C1469
20	CC2	SOFTWARE	GLY C:159 , GLU C:160 , ARG C:161	BINDING SITE FOR RESIDUE SO4 C1470
21	CC3	SOFTWARE	THR C:413	BINDING SITE FOR RESIDUE ACN C1471
22	CC4	SOFTWARE	SER D:49 , LYS D:52 , SER D:298 , ASN D:300 , LYS D:410 , THR D:411 , THR D:413 , MET D:414 , ACN D:1473	BINDING SITE FOR RESIDUE FP5 D 500
23	CC5	SOFTWARE	ASP D:281 , HIS D:282 , THR D:283 , HOH D:2034	BINDING SITE FOR RESIDUE SO4 D1467
24	CC6	SOFTWARE	ALA D:234 , ARG D:236	BINDING SITE FOR RESIDUE SO4 D1468
25	CC7	SOFTWARE	SER D:131 , GLU D:132 , ARG D:133 , LEU D:134	BINDING SITE FOR RESIDUE SO4 D1469
26	CC8	SOFTWARE	GLY D:159 , GLU D:160 , ARG D:161	BINDING SITE FOR RESIDUE SO4 D1470
27	CC9	SOFTWARE	GLU D:188 , HIS D:247 , GLU D:251	BINDING SITE FOR RESIDUE MG D1471
28	DC1	SOFTWARE	HIS D:462	BINDING SITE FOR RESIDUE MG D1472
29	DC2	SOFTWARE	ASP D:142 , TYR D:147 , LEU D:349 , MET D:414 , FP5 D:500	BINDING SITE FOR RESIDUE ACN D1473
30	DC3	SOFTWARE	THR D:127 , GLY D:318	BINDING SITE FOR RESIDUE ACN D1474

(no "SS Bond" information available for 2Y55)

(no "Cis Peptide Bond" information available for 2Y55)

(no "SAP(SNP)/Variant" information available for 2Y55)

(no "PROSITE Motif" information available for 2Y55)

(no "Exon" information available for 2Y55)

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 d2y55a_ A: D-alanyl-D-alanine carboxypeptidase Dac                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeee.......hhhhhhhhhhhhhhhhhh...eeeeeeee........ee..eeeee......hhhhhhhhhhhhhhh...ee...eeee.............hhhhh..hhhh.......ee....ee.eeeeeee........eeehhhhh...eeee..eee........eee......eeeee.eee.....eeeeee..hhhhhhhhhhhhhhhhh..ee...eee..........eeeeeeeeeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhh..hhhhhhh........hhhhhhhhh............eee..ee..eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y55 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 d2y55b_ 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......hhhhhhhhhhhhhh....ee...eeee.............hhhhh..hhhh.......ee....ee.eeeeeee........eeehhhhh...eeee..eee........eee......eeeee.eee.....eeeeee..hhhhhhhhhhhhhhhhh..ee...eee..........eeeeeee..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhh.hhhhhhhh.......hhhhhhhhh............eeeeeee..eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y55 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 d2y55c_ C: D-alanyl-D-alanine carboxypeptidase Dac                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.hhhhh..eeeeeeee.....eeeee.......hhhhhhhhhhhhhhhhh......eeeeee........ee..eeeee......hhhhhhhhhhhhhhh...ee...eeee.............hhhhh..hhhh.......ee....ee.eeeeeee........eeehhhhh...eeee..eee........eee......eeeee.eee.....eeeeee..hhhhhhhhhhhhhhhhh..ee...eee..........eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh......................hhhhhhhhhhhhh...hhhhhhhhh......hhhhhhhhh............eee..ee..eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y55 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: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 d2y55d_ D: D-alanyl-D-alanine carboxypeptidase Dac                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh...eeeeeee.......eee.......hhhhhhhhhhhhhhhhhh.....eeeeee........ee..eeeee......hhhhhhhhhhhhhh....ee...eeee.............hhhhh.hhhhh.......ee....ee.eeeeeee........eeehhhh....eeee..eee........eee......eeeee.eee.....eeeeee..hhhhhhhhhhhhhhhhhh.ee...eee..........eeeeeee..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh......................hhhhhhhhhhhhhh..hhhhhhhhh......hhhhhhhhh............eee..ee..eeeeeee.......eeeeeeee......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y55 D   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

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: beta-lactamase/transpeptidase-like (515)

Superfamily: beta-lactamase/transpeptidase-like (515)

Family: Dac-like (29)

Protein domain: D-alanyl-D-alanine carboxypeptidase Dac (17)

Actinomadura sp. [TaxId: 1989] (17)

1a	d2y55a_	A:
1b	d2y55b_	B:
1c	d2y55c_	C:
1d	d2y55d_	D:

(no "CATH Domain" information available for 2Y55)

(no "Pfam Domain" information available for 2Y55)

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.

Asymmetric Unit
	Complete Structure
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	Cis Peptide Bonds
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	2y55
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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
2y59	UNEXPECTED TRICOVALENT BINDING MODE OF BORONIC ACIDS WITHIN THE ACTIVE SITE OF A PENICILLIN BINDING PROTEIN
2y5o	UNEXPECTED TRICOVALENT BINDING MODE OF BORONIC ACIDS WITHIN THE ACTIVE SITE OF A PENICILLIN BINDING PROTEIN
2y5r	UNEXPECTED TRICOVALENT BINDING MODE OF BORONIC ACIDS WITHIN THE ACTIVE SITE OF A PENICILLIN BINDING PROTEIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 30)

Sites (30, 30)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File