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Title :   CRYSTAL STRUCTURE OF PENISCILLIN-BINDING PROTEIN 4 FROM LISTERIA MONOCYTOGENES IN THE CARBENICILLIN BOUND FORM

Authors :   J. H. Jeong, Y. G. Kim

Date :   17 Dec 12 (Deposition) - 29 May 13 (Release) - 31 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B

Keywords :   Penicillin-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Jeong, Y. Kim, C. Rojviriya, S. Ha, B. S. Kang, Y. Kim
Crystal Structures Of Bifunctional Penicillin-Binding Protein 4 From Listeria Monocytogenes.
Antimicrob. Agents Chemother. V. 57 3507 2013
PubMed-ID: 23669378 | Reference-DOI: 10.1128/AAC.00144-13

Compounds

Molecule 1 - PENICILLIN-BINDING PROTEIN 4
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PPROEXHTA
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	RIL
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 73-119
	Organism Scientific	:	LISTERIA MONOCYTOGENES
	Organism Taxid	:	1639
	Other Details	:	PROTEOLYSIS FROM 120-177
	Synonym	:	LMO2229 PROTEIN

Molecule 2 - PENICILLIN-BINDING PROTEIN 4
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PPROEXHTA
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	RIL
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 178-714
	Organism Scientific	:	LISTERIA MONOCYTOGENES
	Organism Taxid	:	1639
	Other Details	:	CARBENICILLIN BOUND TO SER394, PROTEOLYSIS FROM 120-177
	Synonym	:	LMO2229 PROTEIN

Structural Features

Chains, Units

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 4)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CB9	1	Ligand/Ion	(2R,4S)-2-[(1R)-1-{[(2S)-2-CARBOXY-2-PHENYLACETYL]AMINO}-2-OXOETHYL]-5,5-DIMETHYL-1,3-THIAZOLIDINE-4-CARBOXYLIC ACID
2	GOL	3	Ligand/Ion	GLYCEROL

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA B:347 , ASN B:348 , GLU B:615 , TYR B:617	BINDING SITE FOR RESIDUE GOL B1642
2	AC2	SOFTWARE	LYS B:389 , ALA B:390 , GLN B:391 , ASP B:591 , HOH B:2104	BINDING SITE FOR RESIDUE GOL B1643
3	AC3	SOFTWARE	PRO B:429 , THR B:430 , CB9 B:801	BINDING SITE FOR RESIDUE GOL B1644
4	AC4	SOFTWARE	SER B:394 , VAL B:432 , SER B:449 , ASN B:451 , THR B:576 , GLY B:577 , SER B:578 , THR B:579 , GLN B:580 , SER B:623 , GOL B:1644	BINDING SITE FOR LIGAND CB9 B 801 BOUND TO SER B 394

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

Asymmetric/Biological 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:41
 aligned with Q8Y547_LISMO | Q8Y547 from UniProtKB/TrEMBL  Length:714

    Alignment length:41
                                    86        96       106       116 
         Q8Y547_LISMO    77 ATIIYDKDGDKAGELSSTDATFVSIDKISKNLQNAVVSIED 117
               SCOP domains ----------------------------------------- SCOP domains
               CATH domains ----------------------------------------- CATH domains
               Pfam domains ----------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeeee........hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------- PROSITE
                 Transcript ----------------------------------------- Transcript
                 3zga A  77 ATIIYDKDGDKAGELSSTDATFVSIDKISKNLQNAVVSIED 117
                                    86        96       106       116

Chain B from PDB  Type:PROTEIN  Length:458
 aligned with Q8Y547_LISMO | Q8Y547 from UniProtKB/TrEMBL  Length:714

    Alignment length:458
                                   193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633        
         Q8Y547_LISMO   184 YSKDEIMEMYLNRSYFGNGEWGVENASLKYFGKSAADLNIPEAATIAGLLQAPSAYDPYQHIDKATNRRNMVLNAMVETGTISKAEGDKYKATKIVLNDQSKDPLANKYPWYVDAVINEAVNEADITQDEIMQKGYKIYTELDQNYQTSLENVYNNDGLFPSNANDGTLVQSGAVLMDPATGGIRALVGGRGEHVFRGFNRATQMKAQPGSTMKPLAVYTPALQSGYDVDSMLKDEKITYKGNYTPTNVGGVYSGEVPMYKAVANSINAPAVWLLDQIGIDKGVKSVEKFGITVPEKDRTLGLALGGMSKGASPVEMATAYATFANNGAKPESHIITKIVDPSGNTVYENVPKTKQIISETVSNEMTSMLLDVINTGTGQSAAVSGHEMAGKTGSTQVPFDDTSGTKDQWFVGYTPNLVGAVWMGYDKTDKEHYLTTTSSAGVSSLAHYVMNSGLQYQ 641
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh......hhhhhhhhhhhh......hhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...............hhhhhhhhhhhhhhhh..hhhhhhhh..eeee..hhhhhhhhhhhhhhhhhh..........eeeeeeee....eeeeee....................hhhhhhhhhhhhhhhh.......eeee...................eeeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh......hhhhhhhhhhhhhh..eee....eeeee.....eeee....eee..hhhhhhhhhhhhhhhhhh..hhhhh......eeeeeeee........eeeeeeeeee..eeeeeeee..............hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zga B 184 YSKDEIMEMYLNRSYFGNGEWGVENASLKYFGKSAADLNIPEAATIAGLLQAPSAYDPYQHIDKATNRRNMVLNAMVETGTISKAEGDKYKATKIVLNDQSKDPLANKYPWYVDAVINEAVNEADITQDEIMQKGYKIYTELDQNYQTSLENVYNNDGLFPSNANDGTLVQSGAVLMDPATGGIRALVGGRGEHVFRGFNRATQMKAQPGSTMKPLAVYTPALQSGYDVDSMLKDEKITYKGNYTPTNVGGVYSGEVPMYKAVANSINAPAVWLLDQIGIDKGVKSVEKFGITVPEKDRTLGLALGGMSKGASPVEMATAYATFANNGAKPESHIITKIVDPSGNTVYENVPKTKQIISETVSNEMTSMLLDVINTGTGQSAAVSGHEMAGKTGSTQVPFDDTSGTKDQWFVGYTPNLVGAVWMGYDKTDKEHYLTTTSSAGVSSLAHYVMNSGLQYQ 641
                                   193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633

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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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (3, 3)

Asymmetric/Biological Unit(show GO term definitions)

Chain A,B (Q8Y547_LISMO | Q8Y547)

molecular function
	GO:0008658	penicillin binding
cellular component
	GO:0016021	integral component of membrane
	GO:0016020	membrane

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

3zg7	CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 4 FROM LISTERIA MONOCYTOGENES IN THE APO FORM
3zg8	CRYSTAL STRUCTURE OF PENICILLIN BINDING PROTEIN 4 FROM LISTERIA MONOCYTOGENES IN THE AMPICILLIN BOUND FORM
3zg9	CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 4 FROM LISTERIA MONOCYTOGENES IN THE CEFUROXIME BOUND FORM

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