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Asym./Biol. Unit (Jmol Viewer)

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Title :   PENICILLIN-BINDING PROTEIN 2X (PBP-2X)

Authors :   E. J. Gordon, N. Mouz, E. Duee, O. Dideberg

Date :   28 Sep 99 (Deposition) - 25 May 00 (Release) - 30 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A

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

Reference :   E. J. Gordon, N. Mouz, E. Duee, O. Dideberg
The Crystal Structure Of The Penicillin-Binding Protein 2X From Streptococcus Pneumoniae And Its Acyl-Enzyme Form: Implication In Drug Resistance.
J. Mol. Biol. V. 299 477 2000
PubMed-ID: 10860753 | Reference-DOI: 10.1006/JMBI.2000.3740
(for further references see the PDB file header)

Molecule 1 - PENICILLIN-BINDING PROTEIN 2X
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX
	Expression System Strain	:	MC1061
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 49-750
	Gene	:	PBP2X
	Organism Scientific	:	STREPTOCOCCUS PNEUMONIAE
	Organism Taxid	:	1313
	Strain	:	MC1061
	Synonym	:	PBP-2X, PBP2X

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 3)

No.	Name	Count	Type	Full Name
1	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:337 , SER A:395 , SER A:548 , GLY A:549 , THR A:550 , HOH A:2358	BINDING SITE FOR RESIDUE SO4 A1001
2	AC2	SOFTWARE	ARG A:384 , TYR A:524 , HOH A:2359	BINDING SITE FOR RESIDUE SO4 A1002
3	AC3	SOFTWARE	ASN A:470 , ASP A:471 , VAL A:473 , LYS A:496 , TYR A:700	BINDING SITE FOR RESIDUE SO4 A1003

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

Asymmetric/Biological Unit

No.	Residues
1	Arg A:307	-	Pro A:308
2	Ser A:576	-	Pro A:577

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

Asymmetric/Biological Unit (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

(no "Exon" information available for 1QME)

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:558
 aligned with PBPX_STRPN | P14677 from UniProtKB/Swiss-Prot  Length:750

    Alignment length:680
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750
           PBPX_STRPN    71 TVPAKRGTIYDRNGVPIAEDATSYNVYAVIDENYKSATGKILYVEKTQFNKVAEVFHKYLDMEESYVREQLSQPNLKQVSFGAKGNGITYANMMSIKKELEAAEVKGIDFTTSPNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGTDGIITYEKDRLGNIVPGTEQVSQRTMDGKDVYTTISSPLQSFMETQMDAFQEKVKGKYMTATLVSAKTGEILATTQRPTFDADTKEGITEDFVWRDILYQSNYEPGSTMKVMMLAAAIDNNTFPGGEVFNSSELKIADATIRDWDVNEGLTGGRTMTFSQGFAHSSNVGMTLLEQKMGDATWLDYLNRFKFGVPTRFGLTDEYAGQLPADNIVNIAQSSFGQGISVTQTQMIRAFTAIANDGVMLEPKFISAIYDPNDQTARKSQKEIVGNPVSKDAASLTRTNMVLVGTDPVYGTMYNHSTGKPTVTVPGQNVALKSGTAQIADEKNGGYLVGLTDYIFSAVSMSPAENPDFILYVTVQQPEHYSGIQLGEFANPILERASAMKDSLNLQTTAKALEQVSQQSPYPMPSVKDISPGDLAEELRRNLVQPIVVGTGTKIKNSSAEEGKNLAPNQQVLILSDKAEEVPDMYGWTKETAETLAKWLNIELEFQGSGSTVQKQDVRANTAIKDIKKITLTLGD 750
               SCOP domains d1qmea3 A:71-263 Penic                                                                                          illin-binding protein 2x (pbp-2x), N-terminal doma                     in        d1qmea4 A:264-620 Penicillin-binding protein 2x (pbp-2x), transpeptidase domain                                                                                                                                                                                                                                                                                                 d1qmea1 A:632-692                                            d1qmea2 A:693-750                                          SCOP domains
               CATH domains 1qmeA01                                                                                                         1qmeA01 A:71-92,A:183-263,A:481-494 Penicillin-bin                     ding prote1qmeA02 A:264-480,A:495-632 DD-peptidase/beta-lactamase superfamily                                                                                                                                                      1qmeA01       1qmeA02 A:264-480,A:495-632 DD-peptidase/beta-lactamase superfamily                                                                       ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains PBP_dimer-1qmeA03 A:71                                                                                          -232                                                                   -----------------------------------Transpeptidase-1qmeA01 A:289-609                                                                                                                                                                                                                                                                                                 -----------           --------------------------------------------------------------PASTA-1qmeA02 A:694-750                                   Pfam domains
         Sec.struct. author ..................eee.------------------------------------------------------------------------------------------..eee......hhhhhh.eeeee.....eeeee.hhhhhhhhhhhhh...---------------------......eeee..hhhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeee...........................hhhhhhhhhhhhhhhh.......eee...eee..eee.hhhhhh......eeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhh.....hhhhhhhhhhhhhh.........eeeeee....eeee..........hhhhhhhhhhhhhhhhhh.......................eeeeeeee..hhhhh........eeeeeeeee......eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhh..-----------.............hhhhhhhhhhh...eeeee.....eeee............eeeeee............hhhhhhhhhhhhh.eeeee....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
                 1qme A  71 TVPAKRGTIYDRNGVPIAEDAT------------------------------------------------------------------------------------------SPNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGTDG---------------------RTMDGKDVYTTISSPLQSFMETQMDAFQEKVKGKYMTATLVSAKTGEILATTQRPTFDADTKEGITEDFVWRDILYQSNYEPGSTMKVMMLAAAIDNNTFPGGEVFNSSELKIADATIRDWDVNEGLTGGRMMTFSQGFAHSSNVGMTLLEQKMGDATWLDYLNRFKFGVPTRFGLTDEYAGQLPADNIVNIAQSSFGQGISVTQTQMIRAFTAIANDGVMLEPKFISAIYDPNDQTARKSQKEIVGNPVSKDAASLTRTNMVLVGTDPVYGTMYNHSTGKPTVTVPGQNVALKSGTAQIADEKNGGYLVGLTDYIFSAVSMSPAENPDFILYVTVQQPEHYSGIQLGEFANPILERASAMKDSLNL-----------QQSPYPMPSVKDISPGDLAEELRRNLVQPIVVGTGTKIKNSSAEEGKNLAPNQQVLILSDKAEEVPDMYGWTKETAETLAKWLNIELEFQGSGSTVQKQDVRANTAIKDIKKITLTLGD 750
                                    80        90 |       -         -         -         -         -         -         -         -         -  |    190       200       210       220       230 |       -         -   |   260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620         - |     640       650       660       670       680       690       700       710       720       730       740       750
                                                92                                                                                        183                                              232                   254                                                                                                                                                                                                                                                                                                                                                                           620         632

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/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Beta-lactamase (210)

Family: Transpeptidase (31)

Streptococcus pneumoniae (9)

Transpeptidase-1qmeA01

A:289-609

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

Family: PASTA (12)

Streptococcus pneumoniae (7)

PASTA-1qmeA02

A:694-750

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

Family: PBP_dimer (15)

Streptococcus pneumoniae (7)

PBP_dimer-1qmeA03

A:71-232

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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/Biological Unit
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	Cis Peptide Bonds
		Arg A:307 - Pro A:308	[ RasMol ]
		Ser A:576 - Pro A:577	[ RasMol ]

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UniProtKB/Swiss-Prot
	PBPX_STRPN \| P14677	:	1pmd 1qmf 1rp5 2z2l 2z2m 2zc3 2zc4

1pmd	PENICILLIN-BINDING PROTEIN 2X (PBP-2X)
1qmf	PENICILLIN-BINDING PROTEIN 2X (PBP-2X) ACYL-ENZYME COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

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Sequence-Structure Mapping

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