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Description

Title :   CRYSTAL STRUCTURE OF A PUTATIVE 16S RIBOSOMAL RNA PROCESSING PROTEIN RIMM (PA3744) FROM PSEUDOMONAS AERUGINOSA AT 2.46 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   14 Nov 05 (Deposition) - 28 Feb 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.46

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

Keywords :   16S Rrna Processing Protein, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of 16S Rrna Processing Protein From Pseudomonas Aeruginosa At 2. 46 A Resolution
To Be Published
PubMed: search

Compounds

Molecule 1 - 16S RRNA PROCESSING PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	9949912
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287

Structural Features

Chains, Units

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 7)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
3	UNL	2	Ligand/Ion	UNKNOWN LIGAND

Biological Unit 1 (3, 14)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
3	UNL	4	Ligand/Ion	UNKNOWN LIGAND

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:31 , ALA A:130 , ASP A:132 , TYR A:152	BINDING SITE FOR RESIDUE UNL A 176
2	AC2	SOFTWARE	TYR A:27 , SER A:28 , PHE A:29 , THR A:30 , LEU A:33 , LYS A:63 , ASN A:131 , LEU A:149 , PRO A:151 , THR A:153 , GLN A:155 , GOL A:179 , HOH A:195	BINDING SITE FOR RESIDUE UNL A 177
3	AC3	SOFTWARE	LYS A:70 , GLY A:71 , GLU A:77	BINDING SITE FOR RESIDUE GOL A 178
4	AC4	SOFTWARE	LYS A:63 , GLN A:155 , TRP A:171 , ASP A:172 , UNL A:177 , HOH A:215	BINDING SITE FOR RESIDUE GOL A 179
5	AC5	SOFTWARE	PRO A:32 , ASP A:34 , ASN A:35 , ASP A:38 , TYR A:101 , SER A:159 , ILE A:160 , HOH A:202	BINDING SITE FOR RESIDUE GOL A 180

SS Bonds (0, 0)

(no "SS Bond" information available for 2F1L)

Cis Peptide Bonds (1, 1)

Asymmetric Unit

No.	Residues
1	Asp A:31	-	Pro A:32

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 2F1L)

PROSITE Motifs (0, 0)

(no "PROSITE Motif" information available for 2F1L)

Exons (0, 0)

(no "Exon" information available for 2F1L)

Sequences/Alignments

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
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Chain A from PDB  Type:PROTEIN  Length:164
 aligned with RIMM_PSEAE | Q9HXQ0 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:169
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166         
           RIMM_PSEAE     7 DLVVIGKIVSVYGIRGEVKVYSFTDPLDNLLDYRRWTLRRDGEIRQAELVRGRLHGKVLAAKLKGLDDREEARTFTGYEICIPRSELPSLEEGEYYWHQLEGLKVIDQGRQLLGVIDHLLETGANDVMVVKPCAGSLDDRERLLPYTGQCVLSIDLAAGEMRVDWDADF 175
               SCOP domains d2f1la2 A:7-95 16S rRNA processing protein RimM, N-terminal domain                       -----d2f1la1 A:101-175 16S rRNA processing protein RimM, C-terminal domain       SCOP domains
               CATH domains 2f1lA01 A:7-95 RimM N-terminal domain-like                                               -----2f1lA02 A:101-175 PRC-barrel domain                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee....eeeeee...hhhhhhhh.eeeeee..eeeeeeeeeeeee..eeeeee....hhhhhhh....eeeee.hhh..-----.hhhhhh..eeee....eeeeeeeee......eeeee..........eeee.....eeeee....eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f1l A   7 DLVVIGKIVSVYGIRGEVKVYSFTDPLDNLLDYRRWTLRRDGEIRQAELVRGRLHGKVLAAKLKGLDDREEARTFTGYEICIPRSELPS-----YYWHQLEGLKVIDQGRQLLGVIDHLLETGANDVmVVKPCAGSLDDRERLLPYTGQCVLSIDLAAGEmRVDWDADF 175
                                    16        26        36        46        56        66        76        86        |-    |  106       116       126       136       146       156       166|        
                                                                                                                   95   101                              134-MSE                          167-MSE

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 '\|'

Classification and Annotation

SCOP Domains (2, 2)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: PRC-barrel domain (113)

Superfamily: PRC-barrel domain (113)

Family: RimM C-terminal domain-like (1)

Protein domain: 16S rRNA processing protein RimM, C-terminal domain (1)

Pseudomonas aeruginosa [TaxId: 287] (1)

d2f1la1

A:101-175

Fold: Reductase/isomerase/elongation factor common domain (381)

Superfamily: Translation proteins (218)

Family: RimM N-terminal domain-like (1)

Protein domain: 16S rRNA processing protein RimM, N-terminal domain (1)

Pseudomonas aeruginosa [TaxId: 287] (1)

d2f1la2

A:7-95

CATH Domains (2, 2)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Elongation Factor Tu (Ef-tu); domain 3 (323)

Homologous Superfamily: RimM N-terminal domain-like (2)

Pseudomonas aeruginosa. Organism_taxid: 287. (1)

2f1lA01

A:7-95

Architecture: Roll (1513)

Topology: SH3 type barrels. (648)

Homologous Superfamily: PRC-barrel domain (3)

Pseudomonas aeruginosa. Organism_taxid: 287. (1)

2f1lA02

A:101-175

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 2F1L)

Gene Ontology (6, 6)

Asymmetric Unit(hide GO term definitions)

Chain A (RIMM_PSEAE | Q9HXQ0)

molecular function
	GO:0043022	ribosome binding	Interacting selectively and non-covalently with any part of a ribosome.
biological process
	GO:0006364	rRNA processing	Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
	GO:0042274	ribosomal small subunit biogenesis	A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a small ribosomal subunit; includes transport to the sites of protein synthesis.
	GO:0042254	ribosome biogenesis	A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005840	ribosome	An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

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	2f1l
		Family and Domain Information	:	ProDom \| SYSTERS
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

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Exons (0, 0)

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Gene Ontology (6, 6)

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