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Title :   PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (ZA5)

Authors :   C. Contreras-Martel, A. Amoroso, E. Woon, A. Zervosen, S. Inglis, A. Ma O. Verlaine, A. Rydzik, V. Job, A. Luxen, B. Joris, C. Schofield, A. Des

Date :   15 Dec 10 (Deposition) - 03 Aug 11 (Release) - 14 Nov 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.09

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Transferase, Infection, Cell Wall, Peptidoglycan, Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Contreras-Martel, A. Amoroso, E. C. Woon, A. Zervosen, S. Inglis, A. Martins, O. Verlaine, A. Rydzik, V. Job, A. Luxen, B. Joris, C. J. Schofield, A. Dessen
Structure-Guided Design Of Cell Wall Biosynthesis Inhibitors That Overcome Beta-Lactam Resistance In Staphylococcus Aureus (Mrsa).
Acs Chem. Biol V. 6 943 2011
PubMed-ID: 21732689 | Reference-DOI: 10.1021/CB2001846

Molecule 1 - PENICILLIN-BINDING PROTEIN 1B
	Chains	:	A
	EC Number	:	2.4.1.129, 2.3.2.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3) PLYS
	Expression System Taxid	:	469008
	Expression System Vector	:	PGEX
	Expression System Vector Type	:	PLASMID
	Fragment	:	TRANSPEPTIDASE DOMAIN, RESIDUES 101-125,323-791
	Mutation	:	YES
	Organism Scientific	:	STREPTOCOCCUS PNEUMONIAE
	Organism Taxid	:	171101
	Other Details	:	ALKYL BORONATE (ZA5) COVALENTLY BOND TO S460
	Strain	:	R6
	Synonym	:	PBP1B

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 21)

No.	Name	Count	Type	Full Name
1	CL	17	Ligand/Ion	CHLORIDE ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	NA	1	Ligand/Ion	SODIUM ION
4	SO4	1	Ligand/Ion	SULFATE ION
5	ZA5	1	Ligand/Ion	[(2,6-DIFLUOROPHENYL)CARBONYLAMINO]METHYL-TRIHYDROXY-BORON

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	NA	-1	Ligand/Ion	SODIUM ION
4	SO4	2	Ligand/Ion	SULFATE ION
5	ZA5	2	Ligand/Ion	[(2,6-DIFLUOROPHENYL)CARBONYLAMINO]METHYL-TRIHYDROXY-BORON

Asymmetric Unit (21, 21)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:459 , SER A:460 , LYS A:463 , SER A:516 , ASN A:518 , MET A:556 , GLY A:653 , THR A:654 , THR A:655 , NA A:1300	BINDING SITE FOR RESIDUE ZA5 A1000
02	AC2	SOFTWARE	THR A:563 , LYS A:583 , HOH A:2206 , HOH A:2207 , HOH A:2208	BINDING SITE FOR RESIDUE SO4 A1100
03	AC3	SOFTWARE	ARG A:529 , HOH A:2107	BINDING SITE FOR RESIDUE CL A1200
04	AC4	SOFTWARE	VAL A:535 , LYS A:536	BINDING SITE FOR RESIDUE CL A1201
05	AC5	SOFTWARE	SER A:625 , ARG A:627 , LYS A:633	BINDING SITE FOR RESIDUE CL A1202
06	AC6	SOFTWARE	ASN A:759 , LYS A:760 , SER A:761	BINDING SITE FOR RESIDUE CL A1203
07	AC7	SOFTWARE	ALA A:591 , ALA A:592 , ASP A:593 , ARG A:595	BINDING SITE FOR RESIDUE CL A1206
08	AC8	SOFTWARE	SER A:726 , GLU A:727	BINDING SITE FOR RESIDUE CL A1208
09	AC9	SOFTWARE	TYR A:544 , GLU A:545 , HOH A:2103 , HOH A:2206	BINDING SITE FOR RESIDUE CL A1211
10	BC1	SOFTWARE	GLU A:346 , HIS A:584 , VAL A:585 , ILE A:586 , HOH A:2129	BINDING SITE FOR RESIDUE CL A1212
11	BC2	SOFTWARE	ASP A:337 , TYR A:338 , LEU A:339 , HIS A:399 , GLN A:403	BINDING SITE FOR RESIDUE CL A1213
12	BC3	SOFTWARE	SER A:609 , LYS A:610	BINDING SITE FOR RESIDUE CL A1214
13	BC4	SOFTWARE	TYR A:110 , SER A:111 , ASP A:395 , GLN A:396	BINDING SITE FOR RESIDUE CL A1216
14	BC5	SOFTWARE	LEU A:729 , LYS A:730 , SER A:731 , SER A:751	BINDING SITE FOR RESIDUE CL A1217
15	BC6	SOFTWARE	THR A:342 , ASN A:449	BINDING SITE FOR RESIDUE CL A1224
16	BC7	SOFTWARE	ASP A:679 , ASP A:680 , HOH A:2173	BINDING SITE FOR RESIDUE CL A1229
17	BC8	SOFTWARE	VAL A:753 , THR A:754	BINDING SITE FOR RESIDUE CL A1237
18	BC9	SOFTWARE	THR A:652 , GLY A:653 , THR A:654 , ZA5 A:1000	BINDING SITE FOR RESIDUE NA A1300
19	CC1	SOFTWARE	LEU A:619 , GLU A:622 , TYR A:756 , HOH A:2073 , HOH A:2074 , HOH A:2141	BINDING SITE FOR RESIDUE EDO A1400
20	CC2	SOFTWARE	SER A:634	BINDING SITE FOR RESIDUE CL A1791
21	CC3	SOFTWARE	ASN A:492 , ASN A:494	BINDING SITE FOR RESIDUE CL A1792

(no "SS Bond" information available for 2Y2K)

(no "Cis Peptide Bond" information available for 2Y2K)

(no "SAP(SNP)/Variant" information available for 2Y2K)

(no "PROSITE Motif" information available for 2Y2K)

(no "Exon" information available for 2Y2K)

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
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Chain A from PDB  Type:PROTEIN  Length:469
 aligned with Q7CRA4_STRR6 | Q7CRA4 from UniProtKB/TrEMBL  Length:821

    Alignment length:685
                                   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       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785     
         Q7CRA4_STRR6   106 SEITYSDGTVIASIESDLLRTSISSEQISENLKKAIIATEDEHFKEHKGVVPKAVIRATLGKFVGLGSSSGGSTLTQQLIKQQVVGDAPTLARKAAEIVDALALERAMNKDEILTTYLNVAPFGRNNKGQNIAGARQAAEGIFGVDASQLTVPQAAFLAGLPQSPITYSPYENTGELKSDEDLEIGLRRAKAVLYSMYRTGALSKDEYSQYKDYDLKQDFLPSGTVTGISRDYLYFTTLAEAQERMYDYLAQRDNVSAKELKNEATQKFYRDLAAKEIENGGYKITTTIDQKIHSAMQSAVADYGYLLDDGTGRVEVGNVLMDNQTGAILGFVGGRNYQENQNNHAFDTKRSPASTTKPLLAYGIAIDQGLMGSETILSNYPTNFANGNPIMYANSKGTGMMTLGEALNYSWNIPAYWTYRMLRENGVDVKGYMEKMGYEIPEYGIESLPMGGGIEVTVAQHTNGYQTLANNGVYHQKHVISKIEAADGRVVYEYQDKPVQVYSKATATIMQGLLREVLSSRVTTTFKSNLTSLNPTLANADWIGKTGTTNQDENMWLMLSTPRLTLGGWIGHDDNHSLSRRAGYSNNSNYMAHLVNAIQQASPSIWGNERFALDPSVVKSEVLKSTGQKPGKVSVEGKEVEVTGSTVTSYWANKSGAPATSYRFAIGGSDADYQNAWSSIVGSL 790
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eeee.------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhhh......eeeeeeee.....eeeee...................hhhhhhhhhhhhhhhhh.......eee.....................eeehhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhh..........hhhhh.....hhhhhhhhhhhhhh..ee.....eeeee.....eeee.....ee..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeeeee.....eeeeeee...eeeeeeee.............hhhhhhhhhhhhhhhhhh...............eeeeee.......eeee....eeee...eeeeee.................hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y2k A 106 SEITYSDGTVIASI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RDYLYFTTLAEAQERMYDYLAQRDNVSAKELKNEATQKFYRDLAAKEIENGGYKITTTIDQKIHSAMQSAVADYGYLLDDGTGRVEVGNVLMDNQTGAILGFVGGRNYQENQNNHAFDTKRSPASTTKPLLAYGIAIDQGLMGSETILSNYPTNFANGNPIMYANSKGTGMMTLGEALNYSWNIPAYWTYRMLRENGVDVKGYMEKMGYEIPEYGIESLPMGGGIEVTVAQHTNGYQTLANNGVYHQKHVISKIEAADGRVVYEYQDKPVQVYSKATATIMQGLLREVLSSRVTTTFKSNLTSLNPTLANADWIGKTGTTGQDENMWLMLSTPRLTLGGWIGHDDNHSLSQQAGYSNNSNYMAHLVNAIQQASPSIWGNERFALDPSVVKSEVLKSTGQKPGKVSVEGKEVEVTGSTVTSYWANKSGAPATSYRFAIGGSDADYQNAWSSIVGSL 790
                                   115   |     -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -|      345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785     
                                       119                                                                                                                                                                                                                      336

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 '\|'

(no "SCOP Domain" information available for 2Y2K)

(no "CATH Domain" information available for 2Y2K)

(no "Pfam Domain" information available for 2Y2K)

Asymmetric Unit(hide GO term definitions)

Chain A (Q7CRA4_STRR6 | Q7CRA4)

molecular function
	GO:0008658	penicillin binding	Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
	GO:0008955	peptidoglycan glycosyltransferase activity	Catalysis of the reaction: [GlcNAc-(1,4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n)-diphosphoundecaprenol + GlcNAc-(1,4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol = [GlcNAc-(1,4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n+1)-diphosphoundecaprenol + undecaprenyl diphosphate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0016746	transferase activity, transferring acyl groups	Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
	GO:0016757	transferase activity, transferring glycosyl groups	Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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	Cis Peptide Bonds
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Biological Unit
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	2.4.1.129
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2uwx	ACTIVE SITE RESTRUCTURING REGULATES LIGAND RECOGNITION IN CLASS A PENICILLIN-BINDING PROTEINS
2xd1	ACTIVE SITE RESTRUCTURING REGULATES LIGAND RECOGNITION IN CLASS A PENICILLIN-BINDING PROTEINS
2xd5	STRUCTURAL INSIGHTS INTO THE CATALYTIC MECHANISM AND THE ROLE OF STREPTOCOCCUS PNEUMONIAE PBP1B
2y2g	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (A01)
2y2h	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (ZA2)
2y2i	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (ZA3)
2y2j	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (ZA4)
2y2l	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (E06)
2y2m	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (E08)
2y2n	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (E07)
2y2o	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (EO9)
2y2p	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (Z10)
2y2q	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (Z06)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 21)

Sites (21, 21)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (7, 7)

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