4BYY - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   APO GLXR

Authors :   E. Pohl, M. J. Cann, P. D. Townsend, V. A. Money

Date :   21 Jul 13 (Deposition) - 30 Jul 14 (Release) - 17 Dec 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.48

Chains :   Asym./Biol. Unit : A,B

Keywords :   Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. D. Townsend, B. Jungwirth, F. Pojer, M. Bussmann, V. A. Money, S. T. Cole, A. Puhler, A. Tauch, M. Bott, M. J. Cann, E. Pohl
The Crystal Structures Of Apo And Camp-Bound Glxr From Corynebacterium Glutamicum Reveal Structural And Dynamic Changes Upon Camp Binding In Crp/Fnr Family Transcription Factors.
Plos One V. 9 3265 2014
PubMed-ID: 25469635 | Reference-DOI: 10.1371/JOURNAL.PONE.0113265

Molecule 1 - TRANSCRIPTIONAL REGULATOR, CRP/FNR FAMILY
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	DH5[ALPHA]
	Expression System Taxid	:	668369
	Organism Scientific	:	CORYNEBACTERIUM GLUTAMICUM
	Organism Taxid	:	1718
	Synonym	:	CAMP-BINDING DOMAINS-CATABOLITE GENE ACTIVATOR AND REGULATORY SUBUNIT OF CAMP-DEPENDENT PROTEIN KINASES, GLXR

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:135 , GLY B:82 , SER B:85 , ARG B:92 , THR B:93 , HOH B:2009	BINDING SITE FOR RESIDUE PO4 B1218
2	AC2	SOFTWARE	PHE A:41 , GLY A:82 , LEU A:84 , SER A:85 , ARG A:92 , THR A:93 , HOH A:2018 , HOH A:2020	BINDING SITE FOR RESIDUE PO4 A1227
3	AC3	SOFTWARE	THR A:31 , VAL A:32 , ARG A:33 , PHE B:34 , ALA B:38 , THR B:39 , ILE B:40	BINDING SITE FOR RESIDUE GOL A1228
4	AC4	SOFTWARE	GLN B:15	BINDING SITE FOR RESIDUE GOL B1219

(no "SS Bond" information available for 4BYY)

(no "Cis Peptide Bond" information available for 4BYY)

(no "SAP(SNP)/Variant" information available for 4BYY)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CNMP_BINDING_3	PS50042	cAMP/cGMP binding motif profile.	CRPL_CORGL	13-133	2	A:13-133 B:13-133
2	HTH_CRP_2	PS51063	Crp-type HTH domain profile.	CRPL_CORGL	147-220	2	A:147-220 B:147-217

(no "Exon" information available for 4BYY)

Asymmetric/Biological 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:226
 aligned with CRPL_CORGL | Q79VI7 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
           CRPL_CORGL     1 MEGVQEILSRAGIFQGVDPTAVNNLIQDMETVRFPRGATIFDEGEPGDRLYIITSGKVKLARHAPDGRENLLTIMGPSDMFGELSIFDPGPRTSSAVCVTEVHAATMNSDMLRNWVADHPAIAEQLLRVLARRLRRTNASLADLIFTDVPGRVAKTLLQLANRFGTQEAGALRVNHDLTQEEIAQLVGASRETVNKALATFAHRGWIRLEGKSVLIVDTEHLARRA 226
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh..hhhhhhhhhhhheeeee....eee....ee..eeeeee..eeeeee.....eeeeeee....eehhhhhhh.ee...eeee...eeeeeehhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeee..eeee....hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeee.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------CNMP_BINDING_3  PDB: A:13-133 UniProt: 13-133                                                                            -------------HTH_CRP_2  PDB: A:147-220 UniProt: 147-220                                ------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4byy A   1 MEGVQEILSRAGIFQGVDPTAVNNLIQDMETVRFPRGATIFDEGEPGDRLYIITSGKVKLARHAPDGRENLLTIMGPSDMFGELSIFDPGPRTSSAVCVTEVHAATMNSDMLRNWVADHPAIAEQLLRVLARRLRRTNASLADLIFTDVPGRVAKTLLQLANRFGTQEAGALRVNHDLTQEEIAQLVGASRETVNKALATFAHRGWIRLEGKSVLIVDTEHLARRA 226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain B from PDB  Type:PROTEIN  Length:202
 aligned with CRPL_CORGL | Q79VI7 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:215
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212     
           CRPL_CORGL     3 GVQEILSRAGIFQGVDPTAVNNLIQDMETVRFPRGATIFDEGEPGDRLYIITSGKVKLARHAPDGRENLLTIMGPSDMFGELSIFDPGPRTSSAVCVTEVHAATMNSDMLRNWVADHPAIAEQLLRVLARRLRRTNASLADLIFTDVPGRVAKTLLQLANRFGTQEAGALRVNHDLTQEEIAQLVGASRETVNKALATFAHRGWIRLEGKSVLIV 217
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhhhhhh..eeeee....eee....ee.eeeeeee..eeeeee.hhh.eeeeeee....eehhhhhh..ee...eeee...eeeeeeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...-------------.hhhhhhhhhh.hhhhhhhhhhhhhhh..ee......ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------CNMP_BINDING_3  PDB: B:13-133 UniProt: 13-133                                                                            -------------HTH_CRP_2  PDB: B:147-217 UniProt: 147-220                              PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4byy B   3 GVQEILSRAGIFQGVDPTAVNNLIQDMETVRFPRGATIFDEGEPGDRLYIITSGKVKLARHAPDGRENLLTIMGPSDMFGELSIFDPGPRTSSAVCVTEVHAATMNSDMLRNWVADHPAIAEQLLRVLARRLRRTNASLADLIFTDVPGRVAKTLLQLANRF-------------LTQEEIAQLVGASRETVNKALATFAHRGWIRLEGKSVLIV 217
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162 |       -     | 182       192       202       212     
                                                                                                                                                                                           164           178

Legend:		→ Mismatch	(orange background)
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	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 4BYY)

(no "CATH Domain" information available for 4BYY)

(no "Pfam Domain" information available for 4BYY)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (CRPL_CORGL | Q79VI7)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0030552	cAMP binding	Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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: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:2000874	regulation of glyoxylate cycle	Any process that modulates the frequency, rate or extent of glyoxylate cycle.
	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/Biological Unit
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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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