1MWR - JenaLib

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Title :   STRUCTURE OF SEMET PENICILLIN BINDING PROTEIN 2A FROM METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS STRAIN 27R (TRIGONAL FORM) AT 2.45 A RESOLUTION.

Authors :   D. C. Lim, N. C. J. Strynadka

Date :   01 Oct 02 (Deposition) - 06 Nov 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

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

Keywords :   Penicillin Binding Protein, Beta-Lactam, D, D- Transpeptidase, D-Carboxypeptidase, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Lim, N. C. Strynadka
Structural Basis For The Beta Lactam Resistance Of Pbp2A From Methicillin-Resistant Staphylococcus Aureus.
Nat. Struct. Biol. V. 9 870 2002
PubMed-ID: 12389036
(for further references see the PDB file header)

Molecule 1 - PENICILLIN-BINDING PROTEIN 2A
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21 LAMDA DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PET41A DERIVATIVE
	Mutation	:	YES
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Synonym	:	SAUPBP2A

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 38)

No.	Name	Count	Type	Full Name
1	CD	4	Ligand/Ion	CADMIUM ION
2	CL	4	Ligand/Ion	CHLORIDE ION
3	MSE	30	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 15)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MSE	15	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 15)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MSE	15	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:145 , HIS B:143 , GLU B:145 , CL B:1208	BINDING SITE FOR RESIDUE CD B 1201
2	AC2	SOFTWARE	GLY A:135 , HIS A:311 , CL A:1205 , ASP B:209	BINDING SITE FOR RESIDUE CD A 1202
3	AC3	SOFTWARE	ASP A:209 , GLY B:135 , HIS B:311 , CL B:1206	BINDING SITE FOR RESIDUE CD A 1203
4	AC4	SOFTWARE	ASP B:35 , GLU B:480 , ASP B:509	BINDING SITE FOR RESIDUE CD B 1204
5	AC5	SOFTWARE	GLY A:135 , GLN A:137 , GLN A:140 , CD A:1202	BINDING SITE FOR RESIDUE CL A 1205
6	AC6	SOFTWARE	CD A:1203 , GLY B:135 , GLN B:137 , GLN B:140 , HIS B:311	BINDING SITE FOR RESIDUE CL B 1206
7	AC7	SOFTWARE	GLU A:145 , THR A:300	BINDING SITE FOR RESIDUE CL A 1207
8	AC8	SOFTWARE	GLU B:145 , ARG B:298 , THR B:300 , CD B:1201	BINDING SITE FOR RESIDUE CL B 1208

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

Asymmetric Unit

No.	Residues
1	Thr A:363	-	Pro A:364
2	Thr B:363	-	Pro B:364

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

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

(no "Exon" information available for 1MWR)

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:624
 aligned with Q93IC2_STAAU | Q93IC2 from UniProtKB/TrEMBL  Length:668

    Alignment length:642
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666  
         Q93IC2_STAAU    27 DKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQKWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETESRNYPLEKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELKMKQGETGRQIGWFISYDKDNPNMMMAINVKDVQDKGMASYNAKISGKVYDELYENGNKKYDIDE 668
               SCOP domains d1mwra1 A:27-138 Penicillin binding protein 2a (PBP2A), N-ter      minal domain                                 d1mwra2 A:139-327 Penicillin binding protein 2a (PBP2A), middle domain                                                                                                                       d1mwra3 A:328-668 Penicillin binding protein 2a (PBP2A), C-terminal domain                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1mwrA01 A:27-135 NTF2-like; domain 1                                                                         -1mwrA02 A:137-167,A:238-326    1mwrA03 A:168-237 Penicillin-binding protein 2a; domain 3             1mwrA02 A:137-167,A:238-326 Penicillin-binding protein 2a (Domain 2 )                    1mwrA04 A:327-665 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                                                          --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee..------.eeeeeeeee..eeeeeeeee.eee....eee..hhhhh.......eeeee.........ee.....eeeeeeeeeeeeehhhhh...hhhhhhhhhh.hhhhhhhhhh.........eeeeee.....hhhhhh.....eeeeeeeee..hhhhhhhhhh.eee.hhhhhhh..........eee.hhhhhhhhhhhh....eeeeeee.-...eeeeeeee.......ee...hhhhhhhhhhh....eeeeeee......eeeeeee....hhhhhhh.hhhhhhhhhh...............hhhhhhhhhhhhhhhh........eee...ee..hhhhh...ee......eeehhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.................----..hhhhhhhhhh.......hhhhhhhhhhhhhh...ee...........eee....hhhhhhhhhhhhhhhhhh............eeee..eee..-------.eeeeeeeee......eeeeeee.......hhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1mwr A  27 DKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEmTERPIKIYNSLGVKDINIQDRKIKK------RVDAQYKIKTNYGNIDRNVQFNFVKEDGmWKLDWDHSVIIPGmQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQmDQNWVQDDTFVPLKTVKKmDEYLSDFAKKFHLTTNETESRNYPLEKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDD-SNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNmKNDYGSGTAIHPQTGELLALVSTPSYDVYPFmYGmSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAmIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGmKKLGVGEDIPSDYPFYNAQI----LDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGmQQVVNKTHKEDIYRSYANLIGKSGTAELK-------RQIGWFISYDKDNPNmmmAINVKDVQDKGmASYNAKISGKVYDELYENGNKKYDIDE 668
                                    36        46        56     |  66        76        86|      |96       106       116     | 126       136       146       156       166       176       186       196    |  206       216   |   226       236       246       256       266       276       286       296       306       316       326       336   |   346       356       366     | 376       386       396       406    |  416       426       436       446       456       466       476      |486       496      |  - |     516       526       536       546       556       566       576       586       596       | -     | 616       626|||    636    |  646       656       666  
                                                              62-MSE                   87     94                         122-MSE       136-MSE                                                          201-MSE            220-MSE                                                                             304 |                               340-MSE                         372-MSE                                411-MSE                                                                 483-MSE             503  508                                                                575-MSE                      604     612            627-MSE       641-MSE                       
                                                                                                                                                                                                                                                                                                                 306                                                                  375-MSE                                                                                                                                                                                                                                                      628-MSE                                    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    629-MSE

Chain B from PDB  Type:PROTEIN  Length:629
 aligned with Q93IC2_STAAU | Q93IC2 from UniProtKB/TrEMBL  Length:668

    Alignment length:642
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666  
         Q93IC2_STAAU    27 DKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQKWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETESRNYPLEKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELKMKQGETGRQIGWFISYDKDNPNMMMAINVKDVQDKGMASYNAKISGKVYDELYENGNKKYDIDE 668
               SCOP domains d1mwrb1 B:27-138 Penicillin binding protein 2a (PBP2A), N-ter      minal domain                                 d1mwrb2 B:139-327 Penicillin binding protein 2a (PBP2A), middle domain                                                                                                                       d1mwrb3 B:328-668 Penicillin binding protein 2a (PBP2A), C-terminal domain                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1mwrB01 B:27-135 NTF2-like; domain 1                                                                         -1mwrB02 B:137-167,B:238-326    1mwrB03 B:168-237 Penicillin-binding protein 2a; domain 3             1mwrB02 B:137-167,B:238-326 Penicillin-binding protein 2a (Domain 2 )                    1mwrB04 B:327-665 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                                                          --- CATH domains
           Pfam domains (1) MecA_N-1mwrB03 B:27-140                                                                                           -----PBP_dimer-1mwrB05 B:146-313                                                                                                                                             -------------------------------Transpeptidase-1mwrB01 B:345-658                                                                                                                                                                                                                                                                                          ---------- Pfam domains (1)
           Pfam domains (2) MecA_N-1mwrB04 B:27-140                                                                                           -----PBP_dimer-1mwrB06 B:146-313                                                                                                                                             -------------------------------Transpeptidase-1mwrB02 B:345-658                                                                                                                                                                                                                                                                                          ---------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee..------.eeeeeeeee..eeeeeeeee.eeee..eeee..hhhhh.......eeeeeeee......ee.....eeeeeeeeeeeeehhhhhhhhhhhhhhhhh..hhhhhhhhhh.........eeeeee...hhhhhhhhhhh..eeeeeeeee..hhhhhhhhhh.eee.hhhhhh...........eee.hhhhhhhhhhhh...eeeeeeee.-...eeeeeeee.......ee...hhhhhhhhhhh.....eeeeee......eeeeeee....hhhhhhh.hhhhhhhhhh...............hhhhhhhhhhhhhhhh........ee.........................eehhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh......................hhhhhhhhh........hhhhhhhhhhhhhh...ee...........eee....hhhhhhhhhhhhhhhhhh............eeee..eee..------..eeeeeeeee......eeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1mwr B  27 DKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEmTERPIKIYNSLGVKDINIQDRKIKK------RVDAQYKIKTNYGNIDRNVQFNFVKEDGmWKLDWDHSVIIPGmQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQmDQNWVQDDTFVPLKTVKKmDEYLSDFAKKFHLTTNETESRNYPLEKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDD-SNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNmKNDYGSGTAIHPQTGELLALVSTPSYDVYPFmYGmSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAmIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGmKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGmQQVVNKTHKEDIYRSYANLIGKSGTAELK------GRQIGWFISYDKDNPNmmmAINVKDVQDKGmASYNAKISGKVYDELYENGNKKYDIDE 668
                                    36        46        56     |  66        76        86|      |96       106       116     | 126       136       146       156       166       176       186       196    |  206       216   |   226       236       246       256       266       276       286       296       306       316       326       336   |   346       356       366     | 376       386       396       406    |  416       426       436       446       456       466       476      |486       496       506       516       526       536       546       556       566       576       586       596       | -    |  616       626|||    636    |  646       656       666  
                                                              62-MSE                   87     94                         122-MSE       136-MSE                                                          201-MSE            220-MSE                                                                             304 |                               340-MSE                         372-MSE                                411-MSE                                                                 483-MSE                                                                                     575-MSE                      604    611             627-MSE       641-MSE                       
                                                                                                                                                                                                                                                                                                                 306                                                                  375-MSE                                                                                                                                                                                                                                                      628-MSE                                    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    629-MSE

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

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Beta-lactamase (210)

Family: Transpeptidase (31)

Staphylococcus aureus (10)

1a	Transpeptidase-1mwrB01	B:345-658
1b	Transpeptidase-1mwrB02	B:345-658

Clan: NTF2 (66)

Family: MecA_N (5)

Staphylococcus aureus (5)

2a	MecA_N-1mwrB03	B:27-140
2b	MecA_N-1mwrB04	B:27-140

Clan: no clan defined [family: PBP_dimer] (15)

Family: PBP_dimer (15)

Staphylococcus aureus (5)

3a	PBP_dimer-1mwrB05	B:146-313
3b	PBP_dimer-1mwrB06	B:146-313

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q93IC2_STAAU | Q93IC2)

molecular function
	GO:0008658	penicillin binding	Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
biological process
	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.

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		Thr A:363 - Pro A:364	[ RasMol ]
		Thr B:363 - Pro B:364	[ RasMol ]

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	1mwr
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	Q93IC2_STAAU \| Q93IC2	:	1mws 1mwt 1mwu

1mws	STRUCTURE OF NITROCEFIN ACYL-PENICILLIN BINDING PROTEIN 2A FROM METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS STRAIN 27R AT 2.00 A RESOLUTION.
1mwt	STRUCTURE OF PENICILLIN G ACYL-PENICILLIN BINDING PROTEIN 2A FROM METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS STRAIN 27R AT 2.45 A RESOLUTION.
1mwu	STRUCTURE OF METHICILLIN ACYL-PENICILLIN BINDING PROTEIN 2A FROM METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS STRAIN 27R AT 2.60 A RESOLUTION.
1mwx	STRUCTURE OF PENICILLIN BINDING PROTEIN 2A FROM METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS STRAIN 27R AT 1.80 A RESOLUTION.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 38)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (3, 6)

CATH Domains (4, 8)

Pfam Domains (3, 6)

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