1NPB - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE FOSFOMYCIN RESISTANCE PROTEIN FROM TRANSPOSON TN2921

Authors :   S. Pakhomova, C. L. Rife, R. N. Armstrong, M. E. Newcomer

Date :   17 Jan 03 (Deposition) - 02 Mar 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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)

Keywords :   Manganese Binding, Potassium Binding Loop, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Pakhomova, C. L. Rife, R. N. Armstrong, M. E. Newcomer
Structure Of Fosfomycin Resistance Protein Fosa From Transposon Tn2921.
Protein Sci. V. 13 1260 2004
PubMed-ID: 15075406 | Reference-DOI: 10.1110/PS.03585004

Molecule 1 - FOSFOMYCIN-RESISTANCE PROTEIN
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-20
	Expression System Strain	:	BL21-DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	TN2921
	Organism Scientific	:	SERRATIA MARCESCENS
	Organism Taxid	:	615

		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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 17)

No.	Name	Count	Type	Full Name
1	GOL	7	Ligand/Ion	GLYCEROL
2	SO4	10	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 6)

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

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:7 , HIS B:67 , SER B:97 , TYR B:103 , GLU B:113 , ARG B:122 , HOH B:550	BINDING SITE FOR RESIDUE SO4 B 401
02	AC2	SOFTWARE	GLY A:99 , HIS A:115 , ARG A:122 , ALA A:125 , HOH A:520	BINDING SITE FOR RESIDUE SO4 A 402
03	AC3	SOFTWARE	TYR A:65 , HIS A:67 , TYR A:103 , GLU A:113 , ARG A:122 , HOH A:555 , HIS B:7	BINDING SITE FOR RESIDUE SO4 A 403
04	AC4	SOFTWARE	HIS C:7 , TYR D:65 , HIS D:67 , TYR D:103 , GLU D:113 , ARG D:122 , HOH D:543	BINDING SITE FOR RESIDUE SO4 D 404
05	AC5	SOFTWARE	GLY C:99 , HIS C:115 , ARG C:122	BINDING SITE FOR RESIDUE SO4 C 405
06	AC6	SOFTWARE	HIS C:67 , TYR C:103 , GLU C:113 , ARG C:122 , HOH C:560 , HIS D:7	BINDING SITE FOR RESIDUE SO4 C 406
07	AC7	SOFTWARE	GLY D:99 , HIS D:115 , ARG D:122	BINDING SITE FOR RESIDUE SO4 D 407
08	AC8	SOFTWARE	HIS E:7 , THR E:9 , TYR F:65 , HIS F:67 , TYR F:103 , GLU F:113 , ARG F:122 , HOH F:555	BINDING SITE FOR RESIDUE SO4 F 408
09	AC9	SOFTWARE	HIS E:115 , ARG E:122 , HOH E:515	BINDING SITE FOR RESIDUE SO4 E 409
10	BC1	SOFTWARE	TYR E:65 , HIS E:67 , TYR E:103 , GLU E:113 , ARG E:122 , HIS F:7 , THR F:9	BINDING SITE FOR RESIDUE SO4 E 410
11	BC2	SOFTWARE	VAL A:58 , GLU A:62 , SER A:63 , ASP A:64 , HOH A:526 , HOH A:542 , GOL B:502	BINDING SITE FOR RESIDUE GOL A 501
12	BC3	SOFTWARE	GOL A:501 , SER B:63 , ASP B:64 , HOH B:536 , HOH B:539 , HOH B:546 , HOH B:552	BINDING SITE FOR RESIDUE GOL B 502
13	BC4	SOFTWARE	SER C:63 , ASP C:64 , HOH C:533 , HOH C:541 , ARG D:55 , GOL D:504	BINDING SITE FOR RESIDUE GOL C 503
14	BC5	SOFTWARE	GOL C:503 , GLU D:62 , SER D:63 , ASP D:64 , HOH D:526 , HOH D:527 , HOH D:545	BINDING SITE FOR RESIDUE GOL D 504
15	BC6	SOFTWARE	GLU E:62 , SER E:63 , ASP E:64 , HOH E:535 , HOH E:545 , GOL F:506 , HOH F:524	BINDING SITE FOR RESIDUE GOL E 505
16	BC7	SOFTWARE	GOL E:505 , SER F:63 , ASP F:64 , HOH F:528	BINDING SITE FOR RESIDUE GOL F 506
17	BC8	SOFTWARE	LEU F:15 , GLN F:16 , ARG F:33 , ASN F:35 , HOH F:515	BINDING SITE FOR RESIDUE GOL F 507

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

(no "Cis Peptide Bond" information available for 1NPB)

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

Asymmetric Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VOC	PS51819	Vicinal oxygen chelate (VOC) domain profile.	FOSA_SERMA	4-117	6	A:4-117 B:4-117 C:4-117 D:4-117 E:4-117 F:4-117

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.	FOSA_SERMA	4-117	2	A:4-117 B:4-117 - - - -

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.	FOSA_SERMA	4-117	2	- - C:4-117 D:4-117 - -

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.	FOSA_SERMA	4-117	2	- - - - E:4-117 F:4-117

(no "Exon" information available for 1NPB)

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:140
 aligned with FOSA_SERMA | Q56415 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
           FOSA_SERMA     1 MLQSLNHLTLAVSDLQKSVTFWHELLGLTLHARWNTGAYLTCGDLWVCLSYDEARQYVPPQESDYTHYAFTVAEEDFEPLSQRLEQAGVTIWKQNKSEGASFYFLDPDGHKLELHVGSLAARLAACREKPYAGMVFTSDE 140
               SCOP domains d1npba_ A: Fosfomycin resistance protein A (FosA)                                                                                            SCOP domains
               CATH domains 1npbA00 A:1-140 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.hhhhhhhhhhh....eeeeee..eeeeee..eeeeeee.......hhhhh...eeeee....hhhhhhhhhhhh...eee......eeeeee.....eeeeee.hhhhhhhhhhhh.....ee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---VOC  PDB: A:4-117 UniProt: 4-117                                                                                  ----------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1npb A   1 MLQSLNHLTLAVSDLQKSVTFWHELLGLTLHARWNTGAYLTCGDLWVCLSYDEARQYVPPQESDYTHYAFTVAEEDFEPLSQRLEQAGVTIWKQNKSEGASFYFLDPDGHKLELHVGSLAARLAACREKPYAGMVFTSDE 140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain B from PDB  Type:PROTEIN  Length:139
 aligned with FOSA_SERMA | Q56415 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130         
           FOSA_SERMA     1 MLQSLNHLTLAVSDLQKSVTFWHELLGLTLHARWNTGAYLTCGDLWVCLSYDEARQYVPPQESDYTHYAFTVAEEDFEPLSQRLEQAGVTIWKQNKSEGASFYFLDPDGHKLELHVGSLAARLAACREKPYAGMVFTSD 139
               SCOP domains d1npbb_ B: Fosfomycin resistance protein A (FosA)                                                                                           SCOP domains
               CATH domains 1npbB00 B:1-139 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.hhhhhhhhhhh....eeeeee..eeeeee..eeeeeee...............eeeee.hhhhhhhhhhhhhhh...eee.......eeeee.....eeeee..hhhhhhhhhhhh.....ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---VOC  PDB: B:4-117 UniProt: 4-117                                                                                  ---------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1npb B   1 MLQSLNHLTLAVSDLQKSVTFWHELLGLTLHARWNTGAYLTCGDLWVCLSYDEARQYVPPQESDYTHYAFTVAEEDFEPLSQRLEQAGVTIWKQNKSEGASFYFLDPDGHKLELHVGSLAARLAACREKPYAGMVFTSD 139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain C from PDB  Type:PROTEIN  Length:138
 aligned with FOSA_SERMA | Q56415 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        
           FOSA_SERMA     1 MLQSLNHLTLAVSDLQKSVTFWHELLGLTLHARWNTGAYLTCGDLWVCLSYDEARQYVPPQESDYTHYAFTVAEEDFEPLSQRLEQAGVTIWKQNKSEGASFYFLDPDGHKLELHVGSLAARLAACREKPYAGMVFTS 138
               SCOP domains d1npbc_ C: Fosfomycin resistance protein A (FosA)                                                                                          SCOP domains
               CATH domains 1npbC00 C:1-138 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeee.hhhhhhhhhhh....eeeeee..eeeeee..eeeeeee...............eeeee....hhhhhhhhhhhhh..eee......eeeeee.....eeeeee.hhhhhhhhhhhh.....ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---VOC  PDB: C:4-117 UniProt: 4-117                                                                                  --------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1npb C   1 MLQSLNHLTLAVSDLQKSVTFWHELLGLTLHARWNTGAYLTCGDLWVCLSYDEARQYVPPQESDYTHYAFTVAEEDFEPLSQRLEQAGVTIWKQNKSEGASFYFLDPDGHKLELHVGSLAARLAACREKPYAGMVFTS 138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain D from PDB  Type:PROTEIN  Length:137
 aligned with FOSA_SERMA | Q56415 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       
           FOSA_SERMA     1 MLQSLNHLTLAVSDLQKSVTFWHELLGLTLHARWNTGAYLTCGDLWVCLSYDEARQYVPPQESDYTHYAFTVAEEDFEPLSQRLEQAGVTIWKQNKSEGASFYFLDPDGHKLELHVGSLAARLAACREKPYAGMVFT 137
               SCOP domains d1npbd_ D: Fosfomycin resistance protein A (FosA)                                                                                         SCOP domains
               CATH domains 1npbD00 D:1-137 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee.hhhhhhhhhhh....eeeeee..eeeeee..eeeeeee.......hhhhh...eeeee.hhhhhhhhhhhhhhh...eee......eeeeee.....eeeeee.hhhhhhhhhhhh.....ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---VOC  PDB: D:4-117 UniProt: 4-117                                                                                  -------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1npb D   1 MLQSLNHLTLAVSDLQKSVTFWHELLGLTLHARWNTGAYLTCGDLWVCLSYDEARQYVPPQESDYTHYAFTVAEEDFEPLSQRLEQAGVTIWKQNKSEGASFYFLDPDGHKLELHVGSLAARLAACREKPYAGMVFT 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain E from PDB  Type:PROTEIN  Length:138
 aligned with FOSA_SERMA | Q56415 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        
           FOSA_SERMA     1 MLQSLNHLTLAVSDLQKSVTFWHELLGLTLHARWNTGAYLTCGDLWVCLSYDEARQYVPPQESDYTHYAFTVAEEDFEPLSQRLEQAGVTIWKQNKSEGASFYFLDPDGHKLELHVGSLAARLAACREKPYAGMVFTS 138
               SCOP domains d1npbe_ E: Fosfomycin resistance protein A (FosA)                                                                                          SCOP domains
               CATH domains 1npbE00 E:1-138 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeee.hhhhhhhhhhh....eeeeee..eeeeee..eeeeeee.......hhhhh...eeeee.hhhhhhhhhhhhhhh...eee......eeeeee.....eeeeee.hhhhhhhhhhhh.....ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---VOC  PDB: E:4-117 UniProt: 4-117                                                                                  --------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1npb E   1 MLQSLNHLTLAVSDLQKSVTFWHELLGLTLHARWNTGAYLTCGDLWVCLSYDEARQYVPPQESDYTHYAFTVAEEDFEPLSQRLEQAGVTIWKQNKSEGASFYFLDPDGHKLELHVGSLAARLAACREKPYAGMVFTS 138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain F from PDB  Type:PROTEIN  Length:138
 aligned with FOSA_SERMA | Q56415 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        
           FOSA_SERMA     1 MLQSLNHLTLAVSDLQKSVTFWHELLGLTLHARWNTGAYLTCGDLWVCLSYDEARQYVPPQESDYTHYAFTVAEEDFEPLSQRLEQAGVTIWKQNKSEGASFYFLDPDGHKLELHVGSLAARLAACREKPYAGMVFTS 138
               SCOP domains d1npbf_ F: Fosfomycin resistance protein A (FosA)                                                                                          SCOP domains
               CATH domains 1npbF00 F:1-138 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                            CATH domains
           Pfam domains (1) ---Glyoxalase-1npbF01 F:4-114                                                                                     ------------------------ Pfam domains (1)
           Pfam domains (2) ---Glyoxalase-1npbF02 F:4-114                                                                                     ------------------------ Pfam domains (2)
           Pfam domains (3) ---Glyoxalase-1npbF03 F:4-114                                                                                     ------------------------ Pfam domains (3)
           Pfam domains (4) ---Glyoxalase-1npbF04 F:4-114                                                                                     ------------------------ Pfam domains (4)
           Pfam domains (5) ---Glyoxalase-1npbF05 F:4-114                                                                                     ------------------------ Pfam domains (5)
           Pfam domains (6) ---Glyoxalase-1npbF06 F:4-114                                                                                     ------------------------ Pfam domains (6)
         Sec.struct. author ...eeeeeeeee.hhhhhhhhhhh....eeeeee..eeeeee..eeeeeee...............eeeee.hhhhhhhhhhhhhhh...eee.......eeeee.....eeeee..hhhhhhhhhhhh.....ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---VOC  PDB: F:4-117 UniProt: 4-117                                                                                  --------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1npb F   1 MLQSLNHLTLAVSDLQKSVTFWHELLGLTLHARWNTGAYLTCGDLWVCLSYDEARQYVPPQESDYTHYAFTVAEEDFEPLSQRLEQAGVTIWKQNKSEGASFYFLDPDGHKLELHVGSLAARLAACREKPYAGMVFTS 138
                                    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)

Serratia marcescens. Organism_taxid: 615. (1)

1a	1npbA00	A:1-140
1b	1npbB00	B:1-139
1c	1npbC00	C:1-138
1d	1npbE00	E:1-138
1e	1npbF00	F:1-138
1f	1npbD00	D:1-137

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Glyoxalase (58)

Family: Glyoxalase (34)

Serratia marcescens (1)

1a	Glyoxalase-1npbF01	F:4-114
1b	Glyoxalase-1npbF02	F:4-114
1c	Glyoxalase-1npbF03	F:4-114
1d	Glyoxalase-1npbF04	F:4-114
1e	Glyoxalase-1npbF05	F:4-114
1f	Glyoxalase-1npbF06	F:4-114

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (FOSA_SERMA | Q56415)

molecular function
	GO:0004364	glutathione transferase activity	Catalysis of the reaction: R-X + glutathione = H-X + R-S-glutathione. R may be an aliphatic, aromatic or heterocyclic group; X may be a sulfate, nitrile or halide group.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
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.

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 17)

Sites (17, 17)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 6)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 6)

CATH Domains (1, 6)

Pfam Domains (1, 6)

Gene Ontology (5, 5)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File