2P7P - JenaLib

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Title :   CRYSTAL STRUCTURE OF GENOMICALLY ENCODED FOSFOMYCIN RESISTANCE PROTEIN, FOSX, FROM LISTERIA MONOCYTOGENES COMPLEXED WITH MN(II) AND SULFATE ION

Authors :   K. L. Fillgrove, S. Pakhomova, M. Schaab, M. E. Newcomer, R. N. Armstron

Date :   20 Mar 07 (Deposition) - 17 Jul 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.17

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: E,F  (1x)
Biol. Unit 4: A (1x),B (1x),C (1x),D (1x),E (1x),F (1x)

Keywords :   Fosfomycin Resistance Protein, Mn Binding, Antibiotic Resistance, Metal Binding Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. L. Fillgrove, S. Pakhomova, M. R. Schaab, M. E. Newcomer, R. N. Armstrong
Structure And Mechanism Of The Genomically Encoded Fosfomycin Resistance Protein, Fosx, From Listeria Monocytogenes.
Biochemistry V. 46 8110 2007
PubMed-ID: 17567049 | Reference-DOI: 10.1021/BI700625P

Molecule 1 - GLYOXALASE FAMILY PROTEIN
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET20B(+)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	LISTERIA MONOCYTOGENES
	Organism Taxid	:	169963
	Strain	:	EGD-E

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:					E	F
Biological Unit 4 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)	E (1x)	F (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 12)

No.	Name	Count	Type	Full Name
1	MN	6	Ligand/Ion	MANGANESE (II) ION
2	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 4 (1, 2)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:7 , SO4 A:6002 , HIS B:69 , TYR B:108 , GLU B:118	BINDING SITE FOR RESIDUE MN B 1001
02	AC2	SOFTWARE	HIS A:69 , TYR A:108 , GLU A:118 , HIS B:7 , SO4 B:6003	BINDING SITE FOR RESIDUE MN A 2001
03	AC3	SOFTWARE	HIS C:7 , SO4 C:6004 , HIS D:69 , TYR D:108 , GLU D:118	BINDING SITE FOR RESIDUE MN D 3001
04	AC4	SOFTWARE	HIS C:69 , TYR C:108 , GLU C:118 , HIS D:7 , SO4 D:6005	BINDING SITE FOR RESIDUE MN C 4001
05	AC5	SOFTWARE	HIS E:7 , SO4 E:6006 , HIS F:69 , TYR F:108 , GLU F:118	BINDING SITE FOR RESIDUE MN F 5001
06	AC6	SOFTWARE	HIS E:69 , TYR E:108 , GLU E:118 , HIS F:7 , SO4 F:6007	BINDING SITE FOR RESIDUE MN E 6001
07	AC7	SOFTWARE	HIS A:7 , THR A:9 , PHE A:46 , CYS A:55 , MN B:1001	BINDING SITE FOR RESIDUE SO4 A 6002
08	AC8	SOFTWARE	TYR A:67 , HIS A:69 , MN A:2001 , HIS B:7 , THR B:9 , GLU B:44	BINDING SITE FOR RESIDUE SO4 B 6003
09	AC9	SOFTWARE	HIS C:7 , THR C:9 , CYS C:55 , HOH C:6028 , TYR D:67 , HIS D:69 , TYR D:108 , MN D:3001	BINDING SITE FOR RESIDUE SO4 C 6004
10	BC1	SOFTWARE	HIS C:69 , MN C:4001 , HIS D:7 , THR D:9 , CYS D:55 , MET D:57	BINDING SITE FOR RESIDUE SO4 D 6005
11	BC2	SOFTWARE	HIS E:7 , THR E:9 , CYS E:55 , HIS F:69 , TYR F:108 , MN F:5001	BINDING SITE FOR RESIDUE SO4 E 6006
12	BC3	SOFTWARE	TYR E:67 , HIS E:69 , MN E:6001 , HIS F:7 , THR F:9 , GLU F:44 , CYS F:55 , MET F:57	BINDING SITE FOR RESIDUE SO4 F 6007

(no "SS Bond" information available for 2P7P)

(no "Cis Peptide Bond" information available for 2P7P)

(no "SAP(SNP)/Variant" information available for 2P7P)

Asymmetric Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VOC	PS51819	Vicinal oxygen chelate (VOC) domain profile.	FOSX_LISMO	4-122	6	A:4-122 B:4-122 C:4-122 D:4-122 E:4-122 F:4-122

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VOC	PS51819	Vicinal oxygen chelate (VOC) domain profile.	FOSX_LISMO	4-122	2	A:4-122 B:4-122 - - - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VOC	PS51819	Vicinal oxygen chelate (VOC) domain profile.	FOSX_LISMO	4-122	2	- - C:4-122 D:4-122 - -

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VOC	PS51819	Vicinal oxygen chelate (VOC) domain profile.	FOSX_LISMO	4-122	2	- - - - E:4-122 F:4-122

Biological Unit 4 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VOC	PS51819	Vicinal oxygen chelate (VOC) domain profile.	FOSX_LISMO	4-122	6	A:4-122 B:4-122 C:4-122 D:4-122 E:4-122 F:4-122

(no "Exon" information available for 2P7P)

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:131
 aligned with FOSX_LISMO | Q8Y6I2 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
           FOSX_LISMO     1 MISGLSHITLIVKDLNKTTTFLREIFNAEEIYSSGDQTFSLSKEKFFLIAGLWICIMEGDSLQEQTYNHIAFRIQSEEVDEYIERIKSLGVEIKPERPRVEGEGRSIYFYDFDNHLFELHAGTLEERLKRY 131
               SCOP domains d2p7pa_ A: automated matches                                                                                                        SCOP domains
               CATH domains 2p7pA00 A:1-131 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.hhhhhhhhhhhhh..eeeee.hhh......eeeeee..eeeeeee..........eeeee.hhhhhhhhhhhhhhh................eeeee.....eeeee..hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---VOC  PDB: A:4-122 UniProt: 4-122                                                                                       --------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p7p A   1 MISGLSHITLIVKDLNKTTAFLQNIFNAEEIYSSGDKTFSLSKEKFFLIAGLWICIMEGDSLQERTYNHIAFQIQSEEVDEYTERIKALGVEMKPERPRVQGEGRSIYFYDFDNHLFELHAGTLEERLKRY 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain B from PDB  Type:PROTEIN  Length:122
 aligned with FOSX_LISMO | Q8Y6I2 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:129
                                    10        20        30        40        50        60        70        80        90       100       110       120         
           FOSX_LISMO     1 MISGLSHITLIVKDLNKTTTFLREIFNAEEIYSSGDQTFSLSKEKFFLIAGLWICIMEGDSLQEQTYNHIAFRIQSEEVDEYIERIKSLGVEIKPERPRVEGEGRSIYFYDFDNHLFELHAGTLEERLK 129
               SCOP domains d2p7pb_ B: automated matches                                                                                                      SCOP domains
               CATH domains 2p7pB00 B:1-129 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.hhhhhhhhhhhhhh.eeeeeeeehhhheeeeeeeee..eeeeeee..........eeeeeehhhhhhhhhhhhhh.......-------...eeeee.....eeeeee.hhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---VOC  PDB: B:4-122 UniProt: 4-122                                                                                       ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p7p B   1 MISGLSHITLIVKDLNKTTAFLQNIFNAEEIYSSGDKTFSLSKEKFFLIAGLWICIMEGDSLQERTYNHIAFQIQSEEVDEYTERIKALGVEMKP-------EGRSIYFYDFDNHLFELHAGTLEERLK 129
                                    10        20        30        40        50        60        70        80        90    |    -  |    110       120         
                                                                                                                         95     103

Chain C from PDB  Type:PROTEIN  Length:131
 aligned with FOSX_LISMO | Q8Y6I2 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
           FOSX_LISMO     1 MISGLSHITLIVKDLNKTTTFLREIFNAEEIYSSGDQTFSLSKEKFFLIAGLWICIMEGDSLQEQTYNHIAFRIQSEEVDEYIERIKSLGVEIKPERPRVEGEGRSIYFYDFDNHLFELHAGTLEERLKRY 131
               SCOP domains d2p7pc_ C: automated matches                                                                                                        SCOP domains
               CATH domains 2p7pC00 C:1-131 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.hhhhhhhhhhhhh..eeeeeeeehhhheeeeeeeee..eeeeeee..........eeeee.hhhhhhhhhhhhhhh...ee...........eeeee.....eeeee..hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---VOC  PDB: C:4-122 UniProt: 4-122                                                                                       --------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p7p C   1 MISGLSHITLIVKDLNKTTAFLQNIFNAEEIYSSGDKTFSLSKEKFFLIAGLWICIMEGDSLQERTYNHIAFQIQSEEVDEYTERIKALGVEMKPERPRVQGEGRSIYFYDFDNHLFELHAGTLEERLKRY 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain D from PDB  Type:PROTEIN  Length:125
 aligned with FOSX_LISMO | Q8Y6I2 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  
           FOSX_LISMO     1 MISGLSHITLIVKDLNKTTTFLREIFNAEEIYSSGDQTFSLSKEKFFLIAGLWICIMEGDSLQEQTYNHIAFRIQSEEVDEYIERIKSLGVEIKPERPRVEGEGRSIYFYDFDNHLFELHAGTLEERLKRYH 132
               SCOP domains d2p7pd_ D: automated matches                                                                                                         SCOP domains
               CATH domains 2p7pD00 D:1-132 2,3-Dihydroxybiphe       nyl 1,2-Dioxygenase, domain 1                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeee.hhhhhhhhhhhhhh.eeeee.-------..eeeeee..eeeeeee..........eeeeeehhhhhhhhhhhhhh....ee..........eeeeee.....eeeeee.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---VOC  PDB: D:4-122 UniProt: 4-122                                                                                       ---------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2p7p D   1 MISGLSHITLIVKDLNKTTAFLQNIFNAEEIYSS-------SKEKFFLIAGLWICIMEGDSLQERTYNHIAFQIQSEEVDEYTERIKALGVEMKPERPRVQGEGRSIYFYDFDNHLFELHAGTLEERLKRYH 132
                                    10        20        30   |     - |      50        60        70        80        90       100       110       120       130  
                                                            34      42

Chain E from PDB  Type:PROTEIN  Length:131
 aligned with FOSX_LISMO | Q8Y6I2 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
           FOSX_LISMO     1 MISGLSHITLIVKDLNKTTTFLREIFNAEEIYSSGDQTFSLSKEKFFLIAGLWICIMEGDSLQEQTYNHIAFRIQSEEVDEYIERIKSLGVEIKPERPRVEGEGRSIYFYDFDNHLFELHAGTLEERLKRY 131
               SCOP domains d2p7pe_ E: automated matches                                                                                                        SCOP domains
               CATH domains 2p7pE00 E:1-131 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.hhhhhhhhhhhhhh.eeeeeeeehhhheeeeeeeee..eeeeeee..........eeeee....hhhhhhhhhhhhh...............eeeee.....eeeee..hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---VOC  PDB: E:4-122 UniProt: 4-122                                                                                       --------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p7p E   1 MISGLSHITLIVKDLNKTTAFLQNIFNAEEIYSSGDKTFSLSKEKFFLIAGLWICIMEGDSLQERTYNHIAFQIQSEEVDEYTERIKALGVEMKPERPRVQGEGRSIYFYDFDNHLFELHAGTLEERLKRY 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain F from PDB  Type:PROTEIN  Length:131
 aligned with FOSX_LISMO | Q8Y6I2 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
           FOSX_LISMO     1 MISGLSHITLIVKDLNKTTTFLREIFNAEEIYSSGDQTFSLSKEKFFLIAGLWICIMEGDSLQEQTYNHIAFRIQSEEVDEYIERIKSLGVEIKPERPRVEGEGRSIYFYDFDNHLFELHAGTLEERLKRY 131
               SCOP domains d2p7pf_ F: automated matches                                                                                                        SCOP domains
               CATH domains 2p7pF00 F:1-131 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.hhhhhhhhhhhhhh.eeeeeeeehhhheeeeeeeee..eeeeeee..........eeeeee...hhhhhhhhhhhh...............eeeeee.....eeeeee.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---VOC  PDB: F:4-122 UniProt: 4-122                                                                                       --------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p7p F   1 MISGLSHITLIVKDLNKTTAFLQNIFNAEEIYSSGDKTFSLSKEKFFLIAGLWICIMEGDSLQERTYNHIAFQIQSEEVDEYTERIKALGVEMKPERPRVQGEGRSIYFYDFDNHLFELHAGTLEERLKRY 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

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

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 (113)

Homologous Superfamily: 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 (106)

Listeria monocytogenes egd-e. Organism_taxid: 169963. Strain: egd-e. (6)

1a	2p7pA00	A:1-131
1b	2p7pE00	E:1-131
1c	2p7pF00	F:1-131
1d	2p7pD00	D:1-132
1e	2p7pB00	B:1-129
1f	2p7pC00	C:1-131

(no "Pfam Domain" information available for 2P7P)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (FOSX_LISMO | Q8Y6I2)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2p7p)

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	2p7p
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UniProtKB/Swiss-Prot
	FOSX_LISMO \| Q8Y6I2	:	2p7k 2p7l 2p7m 2p7o

2p7k	CRYSTAL STRUCTURE OF GENOMICALLY ENCODED FOSFOMYCIN RESISTANCE PROTEIN, FOSX, FROM LISTERIA MONOCYTOGENES (HEXAGONAL FORM)
2p7l	CRYSTAL STRUCTURE OF GENOMICALLY ENCODED FOSFOMYCIN RESISTANCE PROTEIN, FOSX, FROM LISTERIA MONOCYTOGENES (MONOCLINIC FORM GROWN AT PH 5.75)
2p7m	CRYSTAL STRUCTURE OF GENOMICALLY ENCODED FOSFOMYCIN RESISTANCE PROTEIN, FOSX, FROM LISTERIA MONOCYTOGENES (MONOCLINIC FORM GROWN AT PH 6.5)
2p7o	CRYSTAL STRUCTURE OF GENOMICALLY ENCODED FOSFOMYCIN RESISTANCE PROTEIN, FOSX, FROM LISTERIA MONOCYTOGENES (TETRAGONAL FORM)
2p7q	CRYSTAL STRUCTURE OF E126Q MUTANT OF GENOMICALLY ENCODED FOSFOMYCIN RESISTANCE PROTEIN, FOSX, FROM LISTERIA MONOCYTOGENES COMPLEXED WITH MN(II) AND 1S,2S- DIHYDROXYPROPYLPHOSPHONIC ACID

Description

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Ligands, Modified Residues, Ions (2, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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PROSITE Motifs (1, 6)

Exons (0, 0)

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SCOP Domains (1, 6)

CATH Domains (1, 6)

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