1RP5 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   PBP2X FROM STREPTOCOCCUS PNEUMONIAE STRAIN 5259 WITH REDUCED SUSCEPTIBILITY TO BETA-LACTAM ANTIBIOTICS

Authors :   L. Pernot, L. Chesnel, A. Legouellec, J. Croize, T. Vernet, O. Dideberg, A. Dessen

Date :   03 Dec 03 (Deposition) - 03 Feb 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Penicillin-Binding Protein, Transpeptidase, Antibiotic Resistance, Peptidoglycan Synthesis, Cell Wall, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Pernot, L. Chesnel, A. Le Gouellec, J. Croize, T. Vernet, O. Dideberg, A. Dessen
A Pbp2X From A Clinical Isolate Of Streptococcus Pneumoniae Exhibits An Alternative Mechanism For Reduction Of Susceptibility To Beta-Lactam Antibiotics.
J. Biol. Chem. V. 279 16463 2004
PubMed-ID: 14734544 | Reference-DOI: 10.1074/JBC.M313492200
(for further references see the PDB file header)

Molecule 1 - PENICILLIN-BINDING PROTEIN 2X
	Chains	:	A, B
	EC Number	:	3.4.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX
	Expression System Strain	:	MC1061
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PBP2X
	Organism Scientific	:	STREPTOCOCCUS PNEUMONIAE
	Organism Taxid	:	1313
	Strain	:	5259

		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 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER B:337 , LYS B:340 , SER B:395 , LYS B:547 , SER B:548 , THR B:550	BINDING SITE FOR RESIDUE SO4 B 751
2	AC2	SOFTWARE	SER A:337 , LYS A:340 , SER A:395 , LYS A:547 , SER A:548 , GLY A:549 , THR A:550	BINDING SITE FOR RESIDUE SO4 A 751

(no "SS Bond" information available for 1RP5)

Asymmetric Unit

No.	Residues
1	Arg A:307	-	Pro A:308
2	His A:576	-	Pro A:577
3	Arg B:307	-	Pro B:308
4	His B:576	-	Pro B:577

(no "SAP(SNP)/Variant" information available for 1RP5)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PASTA	PS51178	PASTA domain profile.	PBPX_STRPN	632-691 692-750	4	A:632-691 B:632-691 A:692-750 B:692-750

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PASTA	PS51178	PASTA domain profile.	PBPX_STRPN	632-691 692-750	2	A:632-691 - A:692-750 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PASTA	PS51178	PASTA domain profile.	PBPX_STRPN	632-691 692-750	2	- B:632-691 - B:692-750

(no "Exon" information available for 1RP5)

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:687
 aligned with PBPX_STRPN | P14677 from UniProtKB/Swiss-Prot  Length:750

    Alignment length:687
                                    73        83        93       103       113       123       133       143       153       163       173       183       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       643       653       663       673       683       693       703       713       723       733       743       
           PBPX_STRPN    64 KVHQTTRTVPAKRGTIYDRNGVPIAEDATSYNVYAVIDENYKSATGKILYVEKTQFNKVAEVFHKYLDMEESYVREQLSQPNLKQVSFGAKGNGITYANMMSIKKELEAAEVKGIDFTTSPNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGTDGIITYEKDRLGNIVPGTEQVSQRTMDGKDVYTTISSPLQSFMETQMDAFQEKVKGKYMTATLVSAKTGEILATTQRPTFDADTKEGITEDFVWRDILYQSNYEPGSTMKVMMLAAAIDNNTFPGGEVFNSSELKIADATIRDWDVNEGLTGGRTMTFSQGFAHSSNVGMTLLEQKMGDATWLDYLNRFKFGVPTRFGLTDEYAGQLPADNIVNIAQSSFGQGISVTQTQMIRAFTAIANDGVMLEPKFISAIYDPNDQTARKSQKEIVGNPVSKDAASLTRTNMVLVGTDPVYGTMYNHSTGKPTVTVPGQNVALKSGTAQIADEKNGGYLVGLTDYIFSAVSMSPAENPDFILYVTVQQPEHYSGIQLGEFANPILERASAMKDSLNLQTTAKALEQVSQQSPYPMPSVKDISPGDLAEELRRNLVQPIVVGTGTKIKNSSAEEGKNLAPNQQVLILSDKAEEVPDMYGWTKETAETLAKWLNIELEFQGSGSTVQKQDVRANTAIKDIKKITLTLGD 750
               SCOP domains d1rp5a3 A:64-263 Penicillin-binding protein 2x (pbp-2x), N-terminal domain                                                                                                                              d1rp5a4 A:264-631 Penicillin-binding protein 2x (pbp-2x), transpeptidase domain                                                                                                                                                                                                                                                                                                 d1rp5a1 A:632-692                                            d1rp5a2 A:693-750                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee......ee.....eeeee..eeeeeee..................hhhhhhhhhhhhhh.hhhhhhhhhh.....eee.hhhhh..hhhhhhhhhhhhhh.....eeeeee..ee......hhhhhh.eeeee.....eeeee.hhhhhhhhhhhhh..eeeeeeee..........eeee......eeee..hhhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeee...........................hhhhhhhhhhhhhhhhh......eee...eee..eee.hhhhhh......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhh.......hhhhhhhhhhhhhh...ee....eeeeee....eeee....eee...hhhhhhhhhhhhhhhhhh.......................eeeeeeee...............eeeeeeeee......eeeeeeee.....hhhhhhhhhhhhhhhhhhhh........hhhhhh...............hhhhhhhhhhh...eeeee.....eeee............eeeeee............hhhhhhhhhhhhh.eeeeee...eeeee............eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PASTA  PDB: A:632-691 UniProt: 632-691                      PASTA  PDB: A:692-750 UniProt: 692-750                      PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rp5 A  64 KVHQTTRTVPAKRGTIYDRNGVPIAEDATSYNVYAVIDENYKSATGKILYVEKTQFNKVAEVFHKYLDMEESYVREQLSQPNLKQVSFGAKGNGITYANMMSIKKELETAEVKGIDFTTSPNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGTDGIITYEKDRLGNIVPGTEQVSQQTVDGKDVYTTISSPLQSFMETQMDAFQEKVKGKYMTATLVSAKTGEILATTQRPTFDADTKEGITEDFVWRDILYQSNYEPGSTMKVMMLAAAIDNNTFPGGEVFNSSELKIADATIRDWDVNEGLTGGRMMTFSQGFAHSSNVGMTLLEQKMGDATWLDYLNRFKFGVPTRFGLTDEYAGQLPADNIVNIAMSAFGQGISVTQTQMLRAFTAIANDGVMLEPKFISALYDPNDQSVRKSQKEIVGNPVSKEAASVTRDHMVMVGTDPTYGTMYNHSTGKATVNVPGQNVALKSGTAEIADEKNGGYLTGSTNNIFSVVSMHPAENPDFILYVTVQQPEHYSGIQLGEFANPILERASAMKESLNLQTTAKALEQVSQQSPYPMPSVKDISPGDLAEELRRNLVQPIVVGTGTKIKNSSAEEGKNLAPNQQVLILSDKAEEVPDMYGWTKETAETFAKWLNIELEFEGSGSTVQKQDVRANTAIKDIKKIKLTLGD 750
                                    73        83        93       103       113       123       133       143       153       163       173       183       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       643       653       663       673       683       693       703       713       723       733       743

Chain B from PDB  Type:PROTEIN  Length:680
 aligned with PBPX_STRPN | P14677 from UniProtKB/Swiss-Prot  Length:750

    Alignment length:687
                                    73        83        93       103       113       123       133       143       153       163       173       183       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       643       653       663       673       683       693       703       713       723       733       743       
           PBPX_STRPN    64 KVHQTTRTVPAKRGTIYDRNGVPIAEDATSYNVYAVIDENYKSATGKILYVEKTQFNKVAEVFHKYLDMEESYVREQLSQPNLKQVSFGAKGNGITYANMMSIKKELEAAEVKGIDFTTSPNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGTDGIITYEKDRLGNIVPGTEQVSQRTMDGKDVYTTISSPLQSFMETQMDAFQEKVKGKYMTATLVSAKTGEILATTQRPTFDADTKEGITEDFVWRDILYQSNYEPGSTMKVMMLAAAIDNNTFPGGEVFNSSELKIADATIRDWDVNEGLTGGRTMTFSQGFAHSSNVGMTLLEQKMGDATWLDYLNRFKFGVPTRFGLTDEYAGQLPADNIVNIAQSSFGQGISVTQTQMIRAFTAIANDGVMLEPKFISAIYDPNDQTARKSQKEIVGNPVSKDAASLTRTNMVLVGTDPVYGTMYNHSTGKPTVTVPGQNVALKSGTAQIADEKNGGYLVGLTDYIFSAVSMSPAENPDFILYVTVQQPEHYSGIQLGEFANPILERASAMKDSLNLQTTAKALEQVSQQSPYPMPSVKDISPGDLAEELRRNLVQPIVVGTGTKIKNSSAEEGKNLAPNQQVLILSDKAEEVPDMYGWTKETAETLAKWLNIELEFQGSGSTVQKQDVRANTAIKDIKKITLTLGD 750
               SCOP domains d1rp5b3 B:64-263 Penicillin-binding protein 2x (pbp-2x), N-terminal domain                                                                                                                              d1rp5b4 B:264-631 Penicillin-binding protein 2x (pbp-2x), transpeptidase domain                                                                                                                                                                                                                                                                                                 d1rp5b1 B:632-692                                            d1rp5b2 B:693-750                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------PBP_dimer-1rp5B05 B:71-249                                                                                                                                                         ---------------------------------------Transpeptidase-1rp5B01 B:289-609                                                                                                                                                                                                                                                                                                 ------------------------------------------------------------------------------------PASTA-1rp5B03 B:694-750                                   Pfam domains (1)
           Pfam domains (2) -------PBP_dimer-1rp5B06 B:71-249                                                                                                                                                         ---------------------------------------Transpeptidase-1rp5B02 B:289-609                                                                                                                                                                                                                                                                                                 ------------------------------------------------------------------------------------PASTA-1rp5B04 B:694-750                                   Pfam domains (2)
         Sec.struct. author .eeeeeeee......ee.....eeeee..eeeeeee.....ee...ee......hhhhhhhhhhhhhh.hhhhhhhhhh.....eee.hhhhh..hhhhhhhhhhhhhhh....eeeeee..ee......hhhhhheeeeee.....eeeeeeehhhhhhhhhhhh..eeeeeeee..........eeee......eeee..hhhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeee...........................hhhhhhhhhhhhhhhhh......eee...eee..eee.....-------.eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhh.....hhhhhhhhhhhhhh...ee....eeeeee....eeee....eee...hhhhhhhhhhhhhhhhhh.......................eeeeeeee...............eeeeeeeee......eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh....hhhhh................hhhhhhhhhhh...eeeee.....eeee............eeeeee............hhhhhhhhhhhhh.eeeee....eeeee............eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PASTA  PDB: B:632-691 UniProt: 632-691                      PASTA  PDB: B:692-750 UniProt: 692-750                      PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rp5 B  64 KVHQTTRTVPAKRGTIYDRNGVPIAEDATSYNVYAVIDENYKSATGKILYVEKTQFNKVAEVFHKYLDMEESYVREQLSQPNLKQVSFGAKGNGITYANMMSIKKELETAEVKGIDFTTSPNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGTDGIITYEKDRLGNIVPGTEQVSQQTVDGKDVYTTISSPLQSFMETQMDAFQEKVKGKYMTATLVSAKTGEILATTQRPTFDADTKEGITEDFVWRDILYQSNYEPGSTMKVMMLAAAIDNNTFPGGEVFNSSELKIADATIRDWDV-------RMMTFSQGFAHSSNVGMTLLEQKMGDATWLDYLNRFKFGVPTRFGLTDEYAGQLPADNIVNIAMSAFGQGISVTQTQMLRAFTAIANDGVMLEPKFISALYDPNDQSVRKSQKEIVGNPVSKEAASVTRDHMVMVGTDPTYGTMYNHSTGKATVNVPGQNVALKSGTAEIADEKNGGYLTGSTNNIFSVVSMHPAENPDFILYVTVQQPEHYSGIQLGEFANPILERASAMKESLNLQTTAKALEQVSQQSPYPMPSVKDISPGDLAEELRRNLVQPIVVGTGTKIKNSSAEEGKNLAPNQQVLILSDKAEEVPDMYGWTKETAETFAKWLNIELEFEGSGSTVQKQDVRANTAIKDIKKIKLTLGD 750
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373  |      -|      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       643       653       663       673       683       693       703       713       723       733       743       
                                                                                                                                                                                                                                                                                                                                                  376     384

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 '\|'

(no "CATH Domain" information available for 1RP5)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Beta-lactamase (210)

Family: Transpeptidase (31)

Streptococcus pneumoniae (9)

1a	Transpeptidase-1rp5B01	B:289-609
1b	Transpeptidase-1rp5B02	B:289-609

Clan: no clan defined [family: PASTA] (12)

Family: PASTA (12)

Streptococcus pneumoniae (7)

2a	PASTA-1rp5B03	B:694-750
2b	PASTA-1rp5B04	B:694-750

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

Family: PBP_dimer (15)

Streptococcus pneumoniae (7)

3a	PBP_dimer-1rp5B05	B:71-249
3b	PBP_dimer-1rp5B06	B:71-249

Asymmetric Unit(hide GO term definitions)

Chain A,B (PBPX_STRPN | P14677)

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:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0051301	cell division	The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
	GO:0071555	cell wall organization	A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
	GO:0009252	peptidoglycan biosynthetic process	The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
	GO:0008360	regulation of cell shape	Any process that modulates the surface configuration of a cell.
	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.
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.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric Unit
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	Cis Peptide Bonds
		Arg A:307 - Pro A:308	[ RasMol ]
		Arg B:307 - Pro B:308	[ RasMol ]
		His A:576 - Pro A:577	[ RasMol ]
		His B:576 - Pro B:577	[ RasMol ]

Biological Units
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	1rp5
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	PBPX_STRPN \| P14677
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	3.4.-.-
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UniProtKB/Swiss-Prot
	PBPX_STRPN \| P14677	:	1pmd 1qme 1qmf 2z2l 2z2m 2zc3 2zc4

1k25	PBP2X FROM STREPTOCOCCUS PNEUMONIAE STRAIN SP328
1pmd	PBP2X FROM STREPTOCOCCUS PNEUMONIAE STRAIN R6 AT 3.5 A
1pyy	DOUBLE MUTANT T338A-M339F PBP2X FROM STREPTOCOCCUS PNEUMONIAE STRAIN R6
1qme	PBP2X FROM STREPTOCOCCUS PNEUMONIAE STRAIN R6 AT 2.4 A
1qmf	PBP2X FROM STREPTOCOCCUS PNEUMONIAE STRAIN R6 COMPLEXED WITH CEFUROXIME

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

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SCOP Domains (3, 8)

CATH Domains (0, 0)

Pfam Domains (3, 6)

Gene Ontology (10, 10)

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