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Biological Unit 1 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF DIPHTHERIA TOXIN MUTANT CRM197

Authors :   E. Malito, G. Spraggon

Date :   04 Jan 12 (Deposition) - 28 Mar 12 (Release) - 18 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

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

Reference :   E. Malito, B. Bursulaya, C. Chen, P. L. Surdo, M. Picchianti, E. Balducci, M. Biancucci, A. Brock, F. Berti, M. J. Bottomley, M. Nissum, P. Costantino, R. Rappuoli, G. Spraggon
Structural Basis For Lack Of Toxicity Of The Diphtheria Toxin Mutant Crm197.
Proc. Natl. Acad. Sci. Usa V. 109 5229 2012
PubMed-ID: 22431623 | Reference-DOI: 10.1073/PNAS.1201964109

Molecule 1 - DIPHTHERIA TOXIN
	Chains	:	A
	EC Number	:	2.4.2.36
	Mutation	:	YES
	Organism Scientific	:	CORYNEBACTERIUM DIPHTHERIAE
	Organism Taxid	:	1717
	Synonym	:	DT, NAD(+)--DIPHTHAMIDE ADP-RIBOSYLTRANSFERASE, DIPHTHERIA TOXIN FRAGMENT A, DIPHTHERIA TOXIN FRAGMENT B, CRM197

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 4AE0)

(no "Site" information available for 4AE0)

Asymmetric Unit

No.	Residues
1	A:186	-	A:201
2	A:461	-	A:471

(no "Cis Peptide Bond" information available for 4AE0)

(no "SAP(SNP)/Variant" information available for 4AE0)

(no "PROSITE Motif" information available for 4AE0)

(no "Exon" information available for 4AE0)

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:499
 aligned with DTX_CORBE | P00588 from UniProtKB/Swiss-Prot  Length:567

    Alignment length:531
                                    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       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566 
            DTX_CORBE    37 VVDSSKSFVMENFSSYHGTKPGYVDSIQKGIQKPKSGTQGNYDDDWKGFYSTDNKYDAAGYSVDNENPLSGKAGGVVKVTYPGLTKVLALKVDNAETIKKELGLSLTEPLMEQVGTEEFIKRFGDGASRVVLSLPFAEGSSSVEYINNWEQAKALSVELEINFETRGKRGQDAMYEYMAQACAGNRVRRSVGSSLSCINLDWDVIRDKTKTKIESLKEHGPIKNKMSESPNKTVSEEKAKQYLEEFHQTALEHPELSELKTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKTTAALSILPGIGSVMGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVGELVDIGFAAYNFVESIINLFQVVHNSYNRPAYSPGHKTQPFLHDGYAVSWNTVEDSIIRTGFQGESGHDIKITAENTPLPIAGVLLPTIPGKLDVNKSKTHISVNGRKIRMRCRAIDGDVTFCRPKSPVYVGNGVHANLHVAFHRSSSEKIHSNEISSDSIGVLGYQKTVDHTKVNSKLSLFFEIKS 567
               SCOP domains d4ae0a1 A:5-187 automated matches                                                                                                                                                                   d4ae0a2 A:201-380 automated matches                                                                                                                                                 d4ae0a3 A:381-535 automated matches                                                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhheeee..eeeeee...hhhhhh.....------------...eeee.hhhhhhh..............eeeeee...eeeeee....hhhhhhhhh......hhhhhhhhhhhhhhhh....eeeeeee.......eeeee..hhhhhheeeeeee.hhhh...hhhhhhhhhhhhh-------------....hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhee..ee...hhhhhhhhhhhhhhhhhhhhhhhh----hhhhhhhhhhhhhhhhhhhhhhhhh...........eee..eeeee..hhh.eee....eeeeeeeeeee....ee..eeeee......ee.....eeee..eeeeeeeeee...eeeeee....ee.....eeeeeeeee..............eeeeeeeee---...eeeeeeee.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ae0 A   5 VVDSSKSFVMENFSSYHGTKPGYVDSIQKGIQK------------WKEFYSTDNKYDAAGYSVDNENPLSGKAGGVVKVTYPGLTKVLALKVDNAETIKKELGLSLTEPLMEQVGTEEFIKRFGDGASRVVLSLPFAEGSSSVEYINNWEQAKALSVELEINFETRGKRGQDAMYEYMAQACA-------------CINLDWDVIRDKTKTKIESLKEHGPIKNKMSESPNKTVSEEKAKQYLEEFHQTALEHPELSELKTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKTTAALSILPGIGSVMGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVG----IGFAAYNFVESIINLFQVVHNSYNRPAYSPGHKTQPFLHDGYAVSWNTVEDSIIRTGFQGESGHDIKITAENTPLPIAGVLLPTIPGKLDVNKSKTHISVNGRKIRMRCRAIDGDVTFCRPKSPVYVGNGVHANLHVAFHRSSSEKIHSNEISSDSIGVLGYQK---HTKVNSKLSLFFEIKS 535
                                    14        24        34  |      -     |  54        64        74        84        94       104       114       124       134       144       154       164       174       184  |      -      |204       214       224       234       244       254       264       274       284       294       304       314       324       334       344   |   354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514 |   | 524       534 
                                                           37           50                                                                                                                                      187           201                                                                                                                                                348  353                                                                                                                                                                516 520

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 "CATH Domain" information available for 4AE0)

(no "Pfam Domain" information available for 4AE0)

Asymmetric Unit(hide GO term definitions)

Chain A (DTX_CORBE | P00588)

molecular function
	GO:0047286	NAD+-diphthamide ADP-ribosyltransferase activity	Catalysis of the reaction: peptide diphthamide + NAD+ = peptide N-(ADP-D-ribosyl)diphthamide + niacinamide.
	GO:0008320	protein transmembrane transporter activity	Enables the transfer of a protein from one side of a membrane to the other.
	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.
	GO:0016757	transferase activity, transferring glycosyl groups	Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	GO:0071806	protein transmembrane transport	The directed movement of a protein across a membrane by means of some agent such as a transporter or pore.
cellular component
	GO:0030669	clathrin-coated endocytic vesicle membrane	The lipid bilayer surrounding a clathrin-coated endocytic vesicle.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0030666	endocytic vesicle membrane	The lipid bilayer surrounding an endocytic vesicle.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4ae0)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	4ae0
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
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	2.4.2.36
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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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UniProtKB/Swiss-Prot
	DTX_CORBE \| P00588	:	1ddt 1dtp 1f0l 1mdt 1sgk 1tox 1xdt 4ae1

1ddt	DIPHTHERIA TOXIN (DIMERIC)
1dtp	DIPHTHERIA TOXIN CATALYTIC DOMAIN (RESIDUES 1 - 190) COMPLEXED WITH ADENYLYL(3'->5')URIDINE 3'-MONOPHOSPHATE (APUP)
1f0l	1.55 ANGSTROM CRYSTAL STRUCTURE OF WILD TYPE DIPHTHERIA TOXIN
1mdt	MONOMERIC DIPHTHERIA TOXIN
1sgk	NUCLEOTIDE-FREE DIPHTHERIA TOXIN
1tox	DIPHTHERIA TOXIN DIMER COMPLEXED WITH NAD
1xdt	COMPLEX OF DIPHTHERIA TOXIN AND HEPARIN-BINDING EPIDERMAL GROWTH FACTOR
4ae1	CRYSTAL STRUCTURE OF DIPHTHERIA TOXIN MUTANT CRM197 IN COMPLEX WITH NICOTINAMIDE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

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