1MWS - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF NITROCEFIN ACYL-PENICILLIN BINDING PROTEIN 2A FROM METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS STRAIN 27R AT 2.00 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 :   2.00

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, Nitrocefin, 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
	Fragment	:	RESIDUES 23-668
	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, 14)

No.	Name	Count	Type	Full Name
1	CD	8	Ligand/Ion	CADMIUM ION
2	CL	4	Ligand/Ion	CHLORIDE ION
3	NC1	2	Mod. Amino Acid	NITROCEFIN ACYL-SERINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	NC1	1	Mod. Amino Acid	NITROCEFIN ACYL-SERINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	NC1	1	Mod. Amino Acid	NITROCEFIN ACYL-SERINE

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:143 , GLU A:145 , CL A:1010 , HOH A:1016 , GLU B:145	BINDING SITE FOR RESIDUE CD A 1001
02	AC2	SOFTWARE	GLU A:145 , HIS B:143 , GLU B:145 , CL B:1009 , HOH B:1056	BINDING SITE FOR RESIDUE CD B 1002
03	AC3	SOFTWARE	ASP A:209 , GLY B:135 , HIS B:311 , CL B:1012 , HOH B:1082	BINDING SITE FOR RESIDUE CD A 1003
04	AC4	SOFTWARE	HIS A:232 , HOH A:1149 , HOH A:1160 , GLU B:378	BINDING SITE FOR RESIDUE CD A 1004
05	AC5	SOFTWARE	GLY A:135 , HIS A:311 , CL A:1011 , HOH A:1024 , ASP B:209	BINDING SITE FOR RESIDUE CD A 1005
06	AC6	SOFTWARE	GLU A:59 , HIS B:232 , HOH B:1140	BINDING SITE FOR RESIDUE CD B 1006
07	AC7	SOFTWARE	ASN B:569 , ASP B:573 , HOH B:1027 , HOH B:1036 , HOH B:1137	BINDING SITE FOR RESIDUE CD B 1007
08	AC8	SOFTWARE	ASP A:320 , GLU B:150	BINDING SITE FOR RESIDUE CD A 1008
09	AC9	SOFTWARE	GLU A:145 , GLU B:145 , ARG B:298 , THR B:300 , CD B:1002	BINDING SITE FOR RESIDUE CL B 1009
10	BC1	SOFTWARE	THR A:300 , CD A:1001 , GLU B:145	BINDING SITE FOR RESIDUE CL A 1010
11	BC2	SOFTWARE	GLN A:137 , GLN A:140 , HIS A:311 , CD A:1005 , HOH A:1079 , GLN B:207	BINDING SITE FOR RESIDUE CL A 1011
12	BC3	SOFTWARE	GLN A:207 , CD A:1003 , GLY B:135 , GLN B:137 , GLN B:140 , HIS B:311	BINDING SITE FOR RESIDUE CL B 1012

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

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 1MWS)

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

(no "Exon" information available for 1MWS)

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:634
 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 d1mwsa1 A:27-138 Penicillin binding protein 2a (PBP2A), N-terminal domain                                       d1mwsa2 A:139-327 Penicillin binding protein 2a (PBP2A), middle domain                                                                                                                       d1mwsa3 A:328-668 Penicillin binding protein 2a (PBP2A), C-terminal domain                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1mwsA01 A:27-135 NTF2-like; domain 1                                                                         1mwsA02 A:136-167,A:238-326     1mwsA03 A:168-237 Penicillin-binding protein 2a; domain 3             1mwsA02 A:136-167,A:238-326 Penicillin-binding protein 2a (Domain 2)                     1mwsA04 A:327-665 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                                                          --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeeee..eeeeeeeeeeee..eeeeeeeeeeeee....eee..hhhhh.......eeeeeeee......ee.....eeeeeeeeeeeee.....hhhhhhhhhhhh..hhhhhhhhh..........eeeeee...hhhhhhhhhhhh.eeeeeeeee..hhhhhhhhhh.eee.hhhhhhhhhhh......eee.hhhhhhhhhhhh...eeeeeeee.....eeeeeeee.......ee...hhhhhhhhhhhhh...eeeeee......eeeeeee....hhhhhhh.hhhhhhhhhhh..............hhhhhhhhhhhhhhhh.......eeee...ee..hhhhh...ee......eeeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhh.......hhhhhhhhhhhhhh...ee...........eee....hhhhhhhhhhhhhhhhhh............eeeeeeee...--------.eeeeeeee......eeeeeee......hhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1mws A  27 DKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQNWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETESRNYPLEKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGsTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELK--------QIGWFISYDKDNPNMMMAINVKDVQDKGMASYNAKISGKVYDELYENGNKKYDIDE 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  
                                                                                                                                                                                                                                                                                                                                                                                                                  403-NC1                                                                                                                                                                                                  604      613

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 d1mwsb1 B:27-138 Penicillin binding protein 2a (PBP2A), N-term   inal domain                                    d1mwsb2 B:139-327 Penicillin binding protein 2a (PBP2A), middle domain                                                                                                                       d1mwsb3 B:328-668 Penicillin binding protein 2a (PBP2A), C-terminal domain                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1mwsB01 B:27-135 NTF2-like; domain 1                                                                         1mwsB02 B:136-167,B:238-326     1mwsB03 B:168-237 Penicillin-binding protein 2a; domain 3             1mwsB02 B:136-167,B:238-326 Penicillin-binding protein 2a (Domain 2)                     1mwsB04 B:327-665 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                                                          --- CATH domains
           Pfam domains (1) MecA_N-1mwsB03 B:27-140                                                                                           -----PBP_dimer-1mwsB05 B:146-313                                                                                                                                             -------------------------------Transpeptidase-1mwsB01 B:345-658                                                                                                                                                                                                                                                                                          ---------- Pfam domains (1)
           Pfam domains (2) MecA_N-1mwsB04 B:27-140                                                                                           -----PBP_dimer-1mwsB06 B:146-313                                                                                                                                             -------------------------------Transpeptidase-1mwsB02 B:345-658                                                                                                                                                                                                                                                                                          ---------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee..---..eeeeeeeeee..eeeeeeeeeeeee....eee..hhhhh.......eeeeeeee......ee.....eeeeeeeeeeeeehhhhhhhhhhhhhhhhh..hhhhhhhhhhh........eeeeee...hhhhhhhhhhhh.eeeeeeeee..hhhhhhhhhheeee.hhhhhhh..........eeeeehhhhhhhhhhh...eeeeeeee.....eeeeeeee.......ee...hhhhhhhhhhh.....eeeeee......eeeeeee....hhhhhhh.hhhhhhhhhh...............hhhhhhhhhhhhhhhh.......eeee...ee..hhhhh...ee......eeeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.................----..hhhhhhhhhh.......hhhhhhhhhhhhhh...ee...........eee....hhhhhhhhhhhhhhhhhh.hhhhhh.....eeee..eee..------..eeeeeeeee......eeeeeee.......hhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1mws B  27 DKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKV---KKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQNWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETESRNYPLEKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGsTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQI----LDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELK------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      |  - |     516       526       536       546       556       566       576       586       596       | -    |  616       626       636       646       656       666  
                                                                                        88  92                                                                                                                                                                                                                                                                                                                    403-NC1                                                                                             503  508                                                                                             604    611

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-1mwsB01	B:345-658
1b	Transpeptidase-1mwsB02	B:345-658

Clan: NTF2 (66)

Family: MecA_N (5)

Staphylococcus aureus (5)

2a	MecA_N-1mwsB03	B:27-140
2b	MecA_N-1mwsB04	B:27-140

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

Family: PBP_dimer (15)

Staphylococcus aureus (5)

3a	PBP_dimer-1mwsB05	B:146-313
3b	PBP_dimer-1mwsB06	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.

Asymmetric Unit
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	Cis Peptide Bonds
		Thr A:363 - Pro A:364	[ RasMol ]
		Thr B:363 - Pro B:364	[ RasMol ]

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

1mwr	STRUCTURE OF SEMET PENICILLIN BINDING PROTEIN 2A FROM METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS STRAIN 27R (TRIGONAL FORM) AT 2.45 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, 14)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 6)

CATH Domains (4, 8)

Pfam Domains (3, 6)

Gene Ontology (2, 2)

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