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Title :   AMIDE RECEPTOR OF THE AMIDASE OPERON OF PSEUDOMONAS AERUGINOSA (AMIC) COMPLEXED WITH THE POSITIVE REGULATOR AMIR.

Authors :   L. H. Pearl, B. P. O'Hara, S. M. Roe

Date :   26 Oct 99 (Deposition) - 23 Dec 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

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

Keywords :   Binding Protein, Gene Regulator, Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. P. O'Hara, R. A. Norman, P. T. C. Wan, S. M. Roe, T. E. Barrett, R. E. Drew, L. H. Pearl
Crystal Structure And Induction Mechanism Of Amic-Amir: A Ligand-Regulated Transcription Antitermination Complex
Embo J. V. 18 5175 1999
PubMed-ID: 10508151 | Reference-DOI: 10.1093/EMBOJ/18.19.5175
(for further references see the PDB file header)

Molecule 1 - AMIC
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	PSEUDOMONAS AERUGINOSA
	Expression System Taxid	:	287
	Fragment	:	AMIDE RECEPTOR
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287
	Other Details	:	COMPLEXED WITH BUTYRAMIDE MOLECULE
	Strain	:	PAC1

Molecule 2 - AMIR
	Chains	:	D, E
	Engineered	:	YES
	Expression System	:	PSEUDOMONAS AERUGINOSA
	Expression System Taxid	:	287
	Fragment	:	AMIDE RECEPTOR/NEGATIVE REGULATOR
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287
	Strain	:	PAC1

		1	2	3	4
Asymmetric Unit	:	A	B	D	E
Biological Unit 1 (2x)	:	A	B	D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	BMD	2	Ligand/Ion	BUTYRAMIDE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	BMD	4	Ligand/Ion	BUTYRAMIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:83 , MET A:84 , SER A:85 , TYR A:104 , PRO A:107 , TYR A:108 , TYR A:150 , TYR A:152	BINDING SITE FOR RESIDUE BMD A 400
2	AC2	SOFTWARE	TYR B:83 , MET B:84 , SER B:85 , TYR B:104 , PRO B:107 , TYR B:108 , TYR B:150 , TYR B:152	BINDING SITE FOR RESIDUE BMD B 500

(no "SS Bond" information available for 1QO0)

Asymmetric Unit

No.	Residues
1	Gln D:108	-	Pro D:109
2	Gln E:108	-	Pro E:109

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_AMIC_PSEAE_001 *	T	106	N	AMIC_PSEAE	---	---	A/B	T	106	N
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_AMIC_PSEAE_001 *	T	106	N	AMIC_PSEAE	---	---	A/B	T	106	N
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ANTAR	PS50921	ANTAR domain profile.	AMIR_PSEAE	129-190	2	D:129-190 E:129-190

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ANTAR	PS50921	ANTAR domain profile.	AMIR_PSEAE	129-190	4	D:129-190 E:129-190

(no "Exon" information available for 1QO0)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:373
 aligned with AMIC_PSEAE | P27017 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:373
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376   
           AMIC_PSEAE     7 RPLIGLLFSETGVTADIERSQRYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLIRHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDVQRAVERIYQARADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPYFSSIDTAASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGSWRVEDVQRHLYDICIDAPQGPVRVERQNNHSRLSSRIAEIDARGVFQVRWQSPEPIRPDPYVVVHNLDDWSASM 379
               SCOP domains d1qo0a_ A: Amide receptor/negative regulator of the amidase operon (AmiC)                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -1qo0A01 A:8-122,A:262-338  [code=3.40.50.2300, no name defined]                                                    1qo0A02 A:123-261,A:339-375  [code=3.40.50.2300, no name defined]                                                                          1qo0A01 A:8-122,A:262-338  [code=3.40.50.2300, no name defined]              1qo0A02 A:123-261,A:339-375          ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......hhhhhhhhhhhhhhhhhhhhhh........eeeee....hhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhh.eeee............eee...hhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh.....eeee...hhhhhh..hhhhhh..eeee.......hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...eee..eee.............eeeee.....eeeeee..............hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------N--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qo0 A   7 RPLIGLLFSETGVTADIERSQRYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLIRHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQARADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPYFSSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSRLSSRIAEIDARGVFQVRWQSPEPIRPDPYVVVHNLDDWSASM 379
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376

Chain B from PDB  Type:PROTEIN  Length:374
 aligned with AMIC_PSEAE | P27017 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:374
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376    
           AMIC_PSEAE     7 RPLIGLLFSETGVTADIERSQRYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLIRHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDVQRAVERIYQARADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPYFSSIDTAASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGSWRVEDVQRHLYDICIDAPQGPVRVERQNNHSRLSSRIAEIDARGVFQVRWQSPEPIRPDPYVVVHNLDDWSASMG 380
               SCOP domains d1qo0b_ B: Amide receptor/negative regulator of the amidase operon (AmiC)                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -1qo0B01 B:8-122,B:262-338  [code=3.40.50.2300, no name defined]                                                    1qo0B02 B:123-261,B:339-375  [code=3.40.50.2300, no name defined]                                                                          1qo0B01 B:8-122,B:262-338  [code=3.40.50.2300, no name defined]              1qo0B02 B:123-261,B:339-375          ----- CATH domains
           Pfam domains (1) --Peripla_BP_5-1qo0B01 B:9-372                                                                                                                                                                                                                                                                                                                                                -------- Pfam domains (1)
           Pfam domains (2) --Peripla_BP_5-1qo0B02 B:9-372                                                                                                                                                                                                                                                                                                                                                -------- Pfam domains (2)
         Sec.struct. author ..eeeee......hhhhhhhhhhhhhhhhhhhhhh........eeeee....hhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhh.eeee............eee...hhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhhh..eeeeeeee....hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhh......eeee...hhhhhh..hhhhhh..eeee.......hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.....eee..eee.............eeeee.....eeeeee..............hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------N---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qo0 B   7 RPLIGLLFSETGVTADIERSQRYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLIRHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQARADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPYFSSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSRLSSRIAEIDARGVFQVRWQSPEPIRPDPYVVVHNLDDWSASMG 380
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376

Chain D from PDB  Type:PROTEIN  Length:189
 aligned with AMIR_PSEAE | P10932 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:189
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181         
           AMIR_PSEAE     2 SANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPESFDVPVDVVFTSIFQNRHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQERIAGQARINQAKALLMQRHGWDEREAHQYLSREAMKRREPILKIAQELL 190
               SCOP domains d1qo0d_ D: Positive regulator of the amidase operon AmiR                                                                                                                                      SCOP domains
               CATH domains 1qo0D01 D:2-128  [code=3.40.50.2300, no name defined]                                                                          ----------------1qo0D02 D:145-190                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhh.eeeee............eeeee....hhhhhhhhhhhhh....eeeeee...hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------ANTAR  PDB: D:129-190 UniProt: 129-190                         PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qo0 D   2 SANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSIFQNRHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDEREAHQHLSREAMKRREPILKIAQELL 190
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181

Chain E from PDB  Type:PROTEIN  Length:194
 aligned with AMIR_PSEAE | P10932 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:194
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191    
           AMIR_PSEAE     2 SANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPESFDVPVDVVFTSIFQNRHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQERIAGQARINQAKALLMQRHGWDEREAHQYLSREAMKRREPILKIAQELLGNEPS 195
               SCOP domains d1qo0e_ E: Positive regulator of the amidase operon AmiR                                                                                                                                           SCOP domains
               CATH domains 1qo0E01 E:2-128  [code=3.40.50.2300, no name defined]                                                                          ----------------1qo0E02 E:145-189                            ------ CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------ANTAR-1qo0E01 E:135-190                                 ----- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------ANTAR-1qo0E02 E:135-190                                 ----- Pfam domains (2)
         Sec.struct. author hhhhhhhhh...eeeee...hhhhhhhhhhhhhhh.eeeee............eeeee....hhhhhhhhhhhhh....eeeeee...hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------ANTAR  PDB: E:129-190 UniProt: 129-190                        ----- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qo0 E   2 SANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSIFQNRHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDEREAHQHLSREAMKRREPILKIAQELLGNEPS 195
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

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: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.2300, no name defined] (308)

Pseudomonas aeruginosa. Organism_taxid: 287. Strain: pac1. (3)

1a	1qo0D01	D:2-128
1b	1qo0E01	E:2-128
1c	1qo0A02	A:123-261,A:339-375
1d	1qo0B02	B:123-261,B:339-375
1e	1qo0A01	A:8-122,A:262-338
1f	1qo0B01	B:8-122,B:262-338

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: 'winged helix' repressor DNA binding domain (507)

Pseudomonas aeruginosa. Organism_taxid: 287. Strain: pac1. (1)

2a	1qo0D02	D:145-190
2b	1qo0E02	E:145-189

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Periplas_BP (97)

Family: Peripla_BP_5 (3)

Pseudomonas aeruginosa (3)

1a	Peripla_BP_5-1qo0B01	B:9-372
1b	Peripla_BP_5-1qo0B02	B:9-372

Clan: no clan defined [family: ANTAR] (3)

Family: ANTAR (3)

Pseudomonas aeruginosa (1)

2a	ANTAR-1qo0E01	E:135-190
2b	ANTAR-1qo0E02	E:135-190

Asymmetric Unit(hide GO term definitions)

Chain A,B (AMIC_PSEAE | P27017)

molecular function
	GO:0033218	amide binding	Interacting selectively and non-covalently with an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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:0006865	amino acid transport	The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0051346	negative regulation of hydrolase activity	Any process that stops or reduces the rate of hydrolase activity, the catalysis of the hydrolysis of various bonds.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0034251	regulation of cellular amide catabolic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides.

Chain D,E (AMIR_PSEAE | P10932)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
biological process
	GO:0015976	carbon utilization	A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary carbon sources and then activates genes to scavenge the last traces of the primary carbon source and to transport and metabolize alternative carbon sources such as carbon dioxide or carbonic acid. The utilization process begins when the cell or organism detects carbon levels, includes the activation of genes whose products detect, transport or metabolize carbon-containing substances, and ends when carbon is incorporated into the cell or organism's metabolism.
	GO:0044248	cellular catabolic process	The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.
	GO:0051345	positive regulation of hydrolase activity	Any process that activates or increases the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds.
	GO:0034251	regulation of cellular amide catabolic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0031564	transcription antitermination	Regulation of transcription by a mechanism that allows RNA polymerase to continue transcription beyond termination site(s).
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

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UniProtKB/Swiss-Prot
	AMIC_PSEAE \| P27017	:	1pea 1qnl

1pea	AMIDE RECEPTOR/NEGATIVE REGULATOR OF THE AMIDASE OPERON OF PSEUDOMONAS AERUGINOSA (AMIC) COMPLEXED WITH ACETAMIDE
1qnl	AMIDE RECEPTOR/NEGATIVE REGULATOR OF THE AMIDASE OPERON OF PSEUDOMONAS AERUGINOSA (AMIC) COMPLEXED WITH BUTYRAMIDE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

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