3GLB - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE EFFECTOR BINDING DOMAIN OF A CATM VARIANT (R156H)

Authors :   O. C. Ezezika, S. H. Craven, E. L. Neidle, C. Momany

Date :   11 Mar 09 (Deposition) - 19 May 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Lttr, Benm, Catm, Transcriptional Activator, Lysr-Type Transcriptional Regulator, Activator, Aromatic Hydrocarbons Catabolism, Dna-Binding, Repressor, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. H. Craven, O. C. Ezezika, S. Haddad, R. A. Hall, C. Momany, E. L. Neidl
Inducer Responses Of Benm, A Lysr-Type Transcriptional Regulator From Acinetobacter Baylyi Adp1.
Mol. Microbiol. V. 72 881 2009
PubMed-ID: 19400783 | Reference-DOI: 10.1111/J.1365-2958.2009.06686.X

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REGULATOR CATM
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CATM, CATR, ACIAD1445
	Mutation	:	YES
	Organism Scientific	:	ACINETOBACTER SP.
	Organism Taxid	:	62977
	Strain	:	ADP1
	Synonym	:	CAT OPERON TRANSCRIPTIONAL REGULATOR

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	CCU	4	Ligand/Ion	(2Z,4Z)-HEXA-2,4-DIENEDIOIC ACID
2	GOL	5	Ligand/Ion	GLYCEROL
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 7)

No.	Name	Count	Type	Full Name
1	CCU	2	Ligand/Ion	(2Z,4Z)-HEXA-2,4-DIENEDIOIC ACID
2	GOL	2	Ligand/Ion	GLYCEROL
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	CCU	2	Ligand/Ion	(2Z,4Z)-HEXA-2,4-DIENEDIOIC ACID
2	GOL	3	Ligand/Ion	GLYCEROL
3	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	VAL A:97 , SER A:99 , THR A:128 , LEU A:147 , PRO A:196 , PHE A:203 , HOH A:341	BINDING SITE FOR RESIDUE CCU A 3
02	AC2	SOFTWARE	LEU A:100 , GLY A:103 , LEU A:104 , HIS A:160 , ILE A:269 , HOH A:330 , HOH A:350	BINDING SITE FOR RESIDUE GOL A 2
03	AC3	SOFTWARE	SO4 B:12 , VAL B:97 , SER B:99 , THR B:128 , ARG B:146 , PRO B:196 , ASN B:202 , PHE B:203	BINDING SITE FOR RESIDUE CCU B 2
04	AC4	SOFTWARE	HIS B:297	BINDING SITE FOR RESIDUE SO4 B 11
05	AC5	SOFTWARE	CCU B:2 , VAL B:97 , SER B:98 , GLU B:125 , HOH B:364 , HOH B:368	BINDING SITE FOR RESIDUE SO4 B 12
06	AC6	SOFTWARE	LYS B:253 , ASN B:254 , LEU B:255 , HOH B:316 , HOH B:353 , HOH B:355	BINDING SITE FOR RESIDUE SO4 B 13
07	AC7	SOFTWARE	LEU B:100 , GLY B:103 , LEU B:104 , GLU B:162 , SER B:246 , ILE B:269	BINDING SITE FOR RESIDUE GOL B 5
08	AC8	SOFTWARE	VAL C:97 , SER C:98 , SER C:99 , THR C:128 , PRO C:196 , ASN C:202 , PHE C:203	BINDING SITE FOR RESIDUE CCU C 1
09	AC9	SOFTWARE	LYS C:148 , THR C:150 , ASP C:151 , ILE C:154 , ARG C:155 , HIS C:156 , HOH C:379	BINDING SITE FOR RESIDUE GOL C 314
10	BC1	SOFTWARE	GOL D:3 , VAL D:97 , SER D:98 , SER D:99 , THR D:128 , TYR D:195 , PRO D:196 , ASN D:202 , PHE D:203 , ILE D:227	BINDING SITE FOR RESIDUE CCU D 4
11	BC2	SOFTWARE	CCU D:4 , SER D:98 , GLU D:125 , GLU D:226	BINDING SITE FOR RESIDUE GOL D 3
12	BC3	SOFTWARE	LEU C:233 , GLU D:122 , LEU D:123	BINDING SITE FOR RESIDUE GOL D 314

(no "SS Bond" information available for 3GLB)

Asymmetric Unit

No.	Residues
1	Tyr A:195	-	Pro A:196
2	Lys A:200	-	Pro A:201
3	Tyr B:195	-	Pro B:196
4	Lys B:200	-	Pro B:201
5	Arg B:299	-	Pro B:300
6	Tyr C:195	-	Pro C:196
7	Lys C:200	-	Pro C:201
8	Arg C:299	-	Pro C:300
9	Ser D:89	-	Gln D:90
10	Tyr D:195	-	Pro D:196
11	Lys D:200	-	Pro D:201

(no "SAP(SNP)/Variant" information available for 3GLB)

(no "PROSITE Motif" information available for 3GLB)

(no "Exon" information available for 3GLB)

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:215
 aligned with CATM_ACIAD | P07774 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:215
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298     
           CATM_ACIAD    89 SQTLRIGYVSSLLYGLLPEIIYLFRQQNPEIHIELIECGTKDQINALKQGKIDLGFGRLKITDPAIRRIVLHKEQLKLAIHKHHHLNQFAATGVHLSQIIDEPMLLYPVSQKPNFATFIQSLFTELGLVPSKLTEIREIQLALGLVAAGEGVCIVPASAMDIGVKNLLYIPILDDDAYSPISLAVRNMDHSNYIPKILACVQEVFATHHIRPLIE 303
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhh....eeee........eeeeeeeeeeeeeeee..hhhhhhh....hhhhh....eee.......hhhhhhhhhhhhh......eee..hhhhhhhhhhhh...eeee.hhhhh....eeeee......eeeeeeeee.....hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3glb A  89 SQTLRIGYVSSLLYGLLPEIIYLFRQQNPEIHIELIECGTKDQINALKQGKIDLGFGRLKITDPAIRHIVLHKEQLKLAIHKHHHLNQFAATGVHLSQIIDEPMLLYPVSQKPNFATFIQSLFTELGLVPSKLTEIREIQLALGLVAAGEGVCIVPASAMDIGVKNLLYIPILDDDAYSPISLAVRNMDHSNYIPKILACVQEVFATHHIRPLIE 303
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298

Chain B from PDB  Type:PROTEIN  Length:212
 aligned with CATM_ACIAD | P07774 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:212
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299  
           CATM_ACIAD    90 QTLRIGYVSSLLYGLLPEIIYLFRQQNPEIHIELIECGTKDQINALKQGKIDLGFGRLKITDPAIRRIVLHKEQLKLAIHKHHHLNQFAATGVHLSQIIDEPMLLYPVSQKPNFATFIQSLFTELGLVPSKLTEIREIQLALGLVAAGEGVCIVPASAMDIGVKNLLYIPILDDDAYSPISLAVRNMDHSNYIPKILACVQEVFATHHIRPL 301
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh....eeee........eeeeeeeeeeeeeeee..hhhhhhh....hhhhh....eee.......hhhhhhhhhhhhh......eee..hhhhhhhhhhhh...eeee.hhhhh....eeeee......eeeeeeeee.....hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3glb B  90 QTLRIGYVSSLLYGLLPEIIYLFRQQNPEIHIELIECGTKDQINALKQGKIDLGFGRLKITDPAIRHIVLHKEQLKLAIHKHHHLNQFAATGVHLSQIIDEPMLLYPVSQKPNFATFIQSLFTELGLVPSKLTEIREIQLALGLVAAGEGVCIVPASAMDIGVKNLLYIPILDDDAYSPISLAVRNMDHSNYIPKILACVQEVFATHHIRPL 301
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299

Chain C from PDB  Type:PROTEIN  Length:212
 aligned with CATM_ACIAD | P07774 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:212
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298  
           CATM_ACIAD    89 SQTLRIGYVSSLLYGLLPEIIYLFRQQNPEIHIELIECGTKDQINALKQGKIDLGFGRLKITDPAIRRIVLHKEQLKLAIHKHHHLNQFAATGVHLSQIIDEPMLLYPVSQKPNFATFIQSLFTELGLVPSKLTEIREIQLALGLVAAGEGVCIVPASAMDIGVKNLLYIPILDDDAYSPISLAVRNMDHSNYIPKILACVQEVFATHHIRP 300
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhh....eeee........eeeeeeeeeeeeeeee..hhhhhhh....hhhhh....eee.......hhhhhhhhhhhh.......eee..hhhhhhhhhhhh...eeee.hhhhh....eeeee......eeeeeeeee.....hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3glb C  89 SQTLRIGYVSSLLYGLLPEIIYLFRQQNPEIHIELIECGTKDQINALKQGKIDLGFGRLKITDPAIRHIVLHKEQLKLAIHKHHHLNQFAATGVHLSQIIDEPMLLYPVSQKPNFATFIQSLFTELGLVPSKLTEIREIQLALGLVAAGEGVCIVPASAMDIGVKNLLYIPILDDDAYSPISLAVRNMDHSNYIPKILACVQEVFATHHIRP 300
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298

Chain D from PDB  Type:PROTEIN  Length:219
 aligned with CATM_ACIAD | P07774 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:219
                                                                                                                                                                                                                                                303    
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298    |    
           CATM_ACIAD    89 SQTLRIGYVSSLLYGLLPEIIYLFRQQNPEIHIELIECGTKDQINALKQGKIDLGFGRLKITDPAIRRIVLHKEQLKLAIHKHHHLNQFAATGVHLSQIIDEPMLLYPVSQKPNFATFIQSLFTELGLVPSKLTEIREIQLALGLVAAGEGVCIVPASAMDIGVKNLLYIPILDDDAYSPISLAVRNMDHSNYIPKILACVQEVFATHHIRPLIE----   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh....eeee........eeeeeeeeeeeeeeee....hhhhh.............eee.......hhhhhhhhhhhh.......eee..hhhhhhhhhhhh...eeee.hhhhh....eeeee......eeeeeeeee.....hhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3glb D  89 SQTLRIGYVSSLLYGLLPEIIYLFRQQNPEIHIELIECGTKDQINALKQGKIDLGFGRLKITDPAIRHIVLHKEQLKLAIHKHHHLNQFAATGVHLSQIIDEPMLLYPVSQKPNFATFIQSLFTELGLVPSKLTEIREIQLALGLVAAGEGVCIVPASAMDIGVKNLLYIPILDDDAYSPISLAVRNMDHSNYIPKILACVQEVFATHHIRPLIESILE 307
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298

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 '\|'

(no "SCOP Domain" information available for 3GLB)

(no "CATH Domain" information available for 3GLB)

(no "Pfam Domain" information available for 3GLB)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (CATM_ACIAD | P07774)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	GO:0019439	aromatic compound catabolic process	The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

Asymmetric Unit
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	Cis Peptide Bonds
		Arg B:299 - Pro B:300	[ RasMol ]
		Arg C:299 - Pro C:300	[ RasMol ]
		Lys A:200 - Pro A:201	[ RasMol ]
		Lys B:200 - Pro B:201	[ RasMol ]
		Lys C:200 - Pro C:201	[ RasMol ]
		Lys D:200 - Pro D:201	[ RasMol ]
		Ser D:89 - Gln D:90	[ RasMol ]
		Tyr A:195 - Pro A:196	[ RasMol ]
		Tyr B:195 - Pro B:196	[ RasMol ]
		Tyr C:195 - Pro C:196	[ RasMol ]
		Tyr D:195 - Pro D:196	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	3glb
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	CATM_ACIAD \| P07774
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	CATM_ACIAD \| P07774
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UniProtKB/Swiss-Prot
	CATM_ACIAD \| P07774	:	2f7b 2f7c 2h98

2f7a	BENM-EBD AND CCM
2f7b	CATM-EFFECTOR BINDING DOMAIN
2f7c	CATM-EBD AND CCM
2h98	CATM(V158M)-EFFECTOR BINDING DOMAIN
2h99	BENM(R156H/T157S)-EFFECTOR BINDING DOMAIN
2h9b	BENM(R156H/T157S)-EFFECTOR BINDING DOMAIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (11, 11)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (0, 0)

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Gene Ontology (5, 5)

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