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Title :   STRUCTURE OF THE AMPR EFFECTOR BINDING DOMAIN FROM CITROBACTER FREUNDII

Authors :   B. L. Mark, M. D Balcewich

Date :   13 Nov 09 (Deposition) - 26 May 10 (Release) - 28 Jul 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.83

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

Keywords :   Alpha-Beta Sandwich, Activator, Dna-Binding, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. D. Balcewich, T. M. Reeve, E. A. Orlikow, L. J. Donald, D. J. Vocadlo, B. L. Mark
Crystal Structure Of The Ampr Effector Binding Domain Provides Insight Into The Molecular Regulation Of Inducible Ampc Beta-Lactamase.
J. Mol. Biol. V. 400 998 2010
PubMed-ID: 20594961 | Reference-DOI: 10.1016/J.JMB.2010.05.040

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 16)

Sites (9, 9)

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:15 , HOH A:55 , THR A:103 , SER A:191 , SER A:221 , TYR A:264 , HOH A:355 , HOH A:391 , HOH A:401	BINDING SITE FOR RESIDUE MES A 302
2	AC2	SOFTWARE	GLN A:93 , ASP A:124 , LEU A:125 , THR A:212 , HIS A:213 , ASN A:214 , VAL A:215 , HOH A:380	BINDING SITE FOR RESIDUE MES A 303
3	AC3	SOFTWARE	GLY A:148 , GLY A:149 , GLY A:150 , ALA A:151 , TRP A:152 , HOH A:320 , HOH A:345	BINDING SITE FOR RESIDUE GOL A 1
4	AC4	SOFTWARE	HOH A:16 , LYS A:95 , ASP A:142 , ARG A:272 , THR A:275 , HOH A:314 , HOH A:379	BINDING SITE FOR RESIDUE GOL A 2
5	AC5	SOFTWARE	LEU A:184 , LYS A:185 , PHE A:186 , PRO A:187 , HIS A:213 , ASN A:214	BINDING SITE FOR RESIDUE GOL A 3
6	AC6	SOFTWARE	HIS A:130 , ASN A:131 , ARG A:133 , GLU A:139 , TYR A:192 , HOH A:362 , HOH A:374 , HOH A:397	BINDING SITE FOR RESIDUE GOL A 4
7	AC7	SOFTWARE	ILE A:106 , ASP A:135 , GLU A:226 , ALA A:230 , HIS A:244 , HOH A:336 , HOH A:371	BINDING SITE FOR RESIDUE GOL A 5
8	AC8	SOFTWARE	PHE A:255 , LEU A:256 , THR A:257	BINDING SITE FOR RESIDUE GOL A 6
9	AC9	SOFTWARE	CYS A:161 , SER A:162 , ARG A:240 , MSE A:241 , HOH A:346 , HOH A:348 , HOH A:403	BINDING SITE FOR RESIDUE GOL A 7

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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
	(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:200
 aligned with AMPR_CITFR | P12529 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:200
                                                                                                                                                                                                                                291 
                                   102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282        |-
           AMPR_CITFR    93 QEKLKIGVVGTFAIGCLFPLLSDFKRSYPHIDLHISTHNNRVDPAAEGLDYTIRYGGGAWHDTDAQYLCSALMSPLCSPTLASQIQTPADILKFPLLRSYRRDEWALWMQAAGEAPPSPTHNVMVFDSSVTMLEAAQGGMGVAIAPVRMFTHLLSSERIVQPFLTQIDLGSYWITRLQSRPETPAMREFSRWLTGVLHK-   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains LysR_substrate-3kosA01 A:93-290                                                                                                                                                                       -- Pfam domains
         Sec.struct. author .eeeeeee.hhhhh..hhhhhhhhhhhhh.eeeeeeee.....hhhh...eeeeee......eeeeeeeeeeeeeee.hhhhhhh..hhhhhh..eeee...hhhhhhhhhhh........eeeee.hhhhhhhhhhh...eeeeehhhhhhhhhh..............eeeeeee......hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kos A  93 QEKLKIGVVGTFAIGCLFPLLSDFKRSYPHIDLHISTHNNRVDPAAEGLDYTIRYGGGAWHDTDAQYLCSALmSPLCSPTLASQIQTPADILKFPLLRSYRRDEWALWmQTVGEAPPSPTHNVmVFDSSVTmLEAAQAGmGVAIAPVRmFTHLLSSERIVQPFLTQIDLGSYWITRLQSRPETPAmREFSRWLTGVLHKT 292
                                   102       112       122       132       142       152       162  |    172       182       192       202       212   |   222 |     232       242       252       262       272     | 282       292
                                                                                                  165-MSE                             201-MSE        216-MSE 224-MSE 232-MSE  241-MSE                              278-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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (5, 5)

Asymmetric Unit(hide GO term definitions)

Chain A (AMPR_CITFR | P12529)

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: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.
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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