2Y2M - JenaLib

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Title :   PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (E08)

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

Date :   15 Dec 10 (Deposition) - 03 Aug 11 (Release) - 28 Sep 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.62

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)
	Expression System Taxid	:	469008
	Expression System Variant	:	PLYS
	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 (E08) 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 (3, 16)

No.	Name	Count	Type	Full Name
1	CL	14	Ligand/Ion	CHLORIDE ION
2	E08	1	Ligand/Ion	TRIHYDROXY-[(1S)-1-[(2-PROPAN-2-YLPHENYL)CARBONYLAMINO]ETHYL]BORON
3	NA	1	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	E08	2	Ligand/Ion	TRIHYDROXY-[(1S)-1-[(2-PROPAN-2-YLPHENYL)CARBONYLAMINO]ETHYL]BORON
3	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:459 , SER A:460 , SER A:516 , ASN A:518 , GLY A:653 , THR A:654 , THR A:655 , GLY A:656 , ASP A:658 , NA A:1300 , HOH A:2379	BINDING SITE FOR RESIDUE E08 A1000
02	AC2	SOFTWARE	ARG A:529 , HOH A:2203	BINDING SITE FOR RESIDUE CL A1200
03	AC3	SOFTWARE	VAL A:535 , LYS A:536 , HOH A:2146 , HOH A:2166	BINDING SITE FOR RESIDUE CL A1201
04	AC4	SOFTWARE	SER A:625 , ARG A:627 , LYS A:633 , HOH A:2268	BINDING SITE FOR RESIDUE CL A1202
05	AC5	SOFTWARE	ASP A:593 , ARG A:595	BINDING SITE FOR RESIDUE CL A1206
06	AC6	SOFTWARE	TYR A:544 , GLU A:545 , HOH A:2212 , HOH A:2213	BINDING SITE FOR RESIDUE CL A1211
07	AC7	SOFTWARE	GLU A:346 , HIS A:584 , VAL A:585 , ILE A:586 , HOH A:2243	BINDING SITE FOR RESIDUE CL A1212
08	AC8	SOFTWARE	ASP A:337 , TYR A:338 , LEU A:339 , HIS A:399 , GLN A:403	BINDING SITE FOR RESIDUE CL A1213
09	AC9	SOFTWARE	LYS A:610	BINDING SITE FOR RESIDUE CL A1214
10	BC1	SOFTWARE	SER A:111 , ASP A:112 , ASP A:395 , GLN A:396	BINDING SITE FOR RESIDUE CL A1216
11	BC2	SOFTWARE	ASP A:679 , ASP A:680 , HOH A:2288	BINDING SITE FOR RESIDUE CL A1222
12	BC3	SOFTWARE	PHE A:341 , THR A:342 , ASN A:449	BINDING SITE FOR RESIDUE CL A1224
13	BC4	SOFTWARE	ARG A:358 , ASN A:645	BINDING SITE FOR RESIDUE CL A1227
14	BC5	SOFTWARE	SER A:634	BINDING SITE FOR RESIDUE CL A1791
15	BC6	SOFTWARE	PHE A:490 , ASN A:492 , ASN A:494	BINDING SITE FOR RESIDUE CL A1792
16	BC7	SOFTWARE	THR A:652 , GLY A:653 , THR A:654 , E08 A:1000	BINDING SITE FOR RESIDUE NA A1300

(no "SS Bond" information available for 2Y2M)

(no "Cis Peptide Bond" information available for 2Y2M)

(no "SAP(SNP)/Variant" information available for 2Y2M)

(no "PROSITE Motif" information available for 2Y2M)

(no "Exon" information available for 2Y2M)

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:471
 aligned with Q7CRA4_STRR6 | Q7CRA4 from UniProtKB/TrEMBL  Length:821

    Alignment length:686
                                   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       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784      
         Q7CRA4_STRR6   105 ISEITYSDGTVIASIESDLLRTSISSEQISENLKKAIIATEDEHFKEHKGVVPKAVIRATLGKFVGLGSSSGGSTLTQQLIKQQVVGDAPTLARKAAEIVDALALERAMNKDEILTTYLNVAPFGRNNKGQNIAGARQAAEGIFGVDASQLTVPQAAFLAGLPQSPITYSPYENTGELKSDEDLEIGLRRAKAVLYSMYRTGALSKDEYSQYKDYDLKQDFLPSGTVTGISRDYLYFTTLAEAQERMYDYLAQRDNVSAKELKNEATQKFYRDLAAKEIENGGYKITTTIDQKIHSAMQSAVADYGYLLDDGTGRVEVGNVLMDNQTGAILGFVGGRNYQENQNNHAFDTKRSPASTTKPLLAYGIAIDQGLMGSETILSNYPTNFANGNPIMYANSKGTGMMTLGEALNYSWNIPAYWTYRMLRENGVDVKGYMEKMGYEIPEYGIESLPMGGGIEVTVAQHTNGYQTLANNGVYHQKHVISKIEAADGRVVYEYQDKPVQVYSKATATIMQGLLREVLSSRVTTTFKSNLTSLNPTLANADWIGKTGTTNQDENMWLMLSTPRLTLGGWIGHDDNHSLSRRAGYSNNSNYMAHLVNAIQQASPSIWGNERFALDPSVVKSEVLKSTGQKPGKVSVEGKEVEVTGSTVTSYWANKSGAPATSYRFAIGGSDADYQNAWSSIVGSL 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.hhhhhhhhhhhhhhh.hhhhhhhhh..........hhhhh.....hhhhhhhhhhhhhh..ee.....eeeee.....eeee.....ee..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...eeeeee.....eeeeeee...eeeeeeee.............hhhhhhhhhhhhhhhhhh...............eeeeee.......eeeee..eeeee...eeeeee.................hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y2m A 105 ISEITYSDGTVIASI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SRDYLYFTTLAEAQERMYDYLAQRDNVSAKELKNEATQKFYRDLAAKEIENGGYKITTTIDQKIHSAMQSAVADYGYLLDDGTGRVEVGNVLMDNQTGAILGFVGGRNYQENQNNHAFDTKRSPASTTKPLLAYGIAIDQGLMGSETILSNYPTNFANGNPIMYANSKGTGMMTLGEALNYSWNIPAYWTYRMLRENGVDVKGYMEKMGYEIPEYGIESLPMGGGIEVTVAQHTNGYQTLANNGVYHQKHVISKIEAADGRVVYEYQDKPVQVYSKATATIMQGLLREVLSSRVTTTFKSNLTSLNPTLANADWIGKTGTTGQDENMWLMLSTPRLTLGGWIGHDDNHSLSQQAGYSNNSNYMAHLVNAIQQASPSIWGNERFALDPSVVKSEVLKSTGQKPGKVSVEGKEVEVTGSTVTSYWANKSGAPATSYRFAIGGSDADYQNAWSSIVGSL 790
                                   114    |    -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -|      344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784      
                                        119                                                                                                                                                                                                                     335

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 2Y2M)

(no "CATH Domain" information available for 2Y2M)

(no "Pfam Domain" information available for 2Y2M)

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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		E08	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2y2m)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	2y2m
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	Q7CRA4_STRR6 \| Q7CRA4
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	2.3.2.-
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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)
2y2k	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (ZA5)
2y2l	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (E06)
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 (3, 16)

Sites (16, 16)

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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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