2ZHZ - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A PDUO-TYPE ATP:COBALAMIN ADENOSYLTRANSFERASE FROM BURKHOLDERIA THAILANDENSIS

Authors :   J. H. Moon, A. K. Park, E. H. Jang, H. S. Kim, Y. M. Chi

Date :   12 Feb 08 (Deposition) - 29 Jul 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Helix Bundle, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. H. Moon, A. K. Park, E. H. Jang, H. S. Kim, Y. M. Chi
Crystal Structure Of A Pduo-Type Atp:Cobalamin Adenosyltransferase From Burkholderia Thailandensis.
Proteins V. 72 1066 2008
PubMed-ID: 18473361 | Reference-DOI: 10.1002/PROT.22084

Molecule 1
	Chains	:	A, B, C
	EC Number	:	2.5.1.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PDUO
	Organism Scientific	:	BURKHOLDERIA THAILANDENSIS
	Organism Taxid	:	57975
	Synonym	:	PDUO-TYPE ADENOSYLTRANSFERASE

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 7)

No.	Name	Count	Type	Full Name
1	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	GOL	3	Ligand/Ion	GLYCEROL
3	MG	2	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:129 , ASN A:153	BINDING SITE FOR RESIDUE MG A 203
2	AC2	SOFTWARE	ASN B:153	BINDING SITE FOR RESIDUE MG B 204
3	AC3	SOFTWARE	ARG A:129 , GLU A:132 , ARG A:133 , ASN A:153 , ASP A:157 , ARG B:11 , THR B:12 , GLY B:13 , THR B:18 , GLY B:19 , GLY B:23 , LYS B:28 , ILE B:33	BINDING SITE FOR RESIDUE ATP B 201
4	AC4	SOFTWARE	ARG B:129 , GLU B:132 , ARG B:133 , ASN B:153 , ARG C:11 , THR C:12 , GLY C:13 , THR C:18 , GLY C:19 , LYS C:28 , ILE C:33	BINDING SITE FOR RESIDUE ATP B 202
5	AC5	SOFTWARE	ALA A:34 , ASP A:38 , ARG A:130 , SER A:134 , ARG C:130 , ARG C:133	BINDING SITE FOR RESIDUE GOL A 205
6	AC6	SOFTWARE	ARG B:133 , ALA C:34 , ASP C:38 , ARG C:130 , SER C:134	BINDING SITE FOR RESIDUE GOL C 206
7	AC7	SOFTWARE	ARG A:130 , ARG A:133 , ALA B:34 , ASP B:38 , ARG B:130	BINDING SITE FOR RESIDUE GOL B 207

(no "SS Bond" information available for 2ZHZ)

(no "Cis Peptide Bond" information available for 2ZHZ)

(no "SAP(SNP)/Variant" information available for 2ZHZ)

(no "PROSITE Motif" information available for 2ZHZ)

(no "Exon" information available for 2ZHZ)

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:148
 aligned with Q2SZ09_BURTA | Q2SZ09 from UniProtKB/TrEMBL  Length:183

    Alignment length:148
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168        
         Q2SZ09_BURTA    29 DDARIAAIGDVDELNSQIGVLLAEPLPDDVRAALSAIQHDLFDLGGELCIPGHAAITDAHLARLDGWLAHYNGQLPPLEEFILPGGARGAALAHVCRTVCRRAERSIVALGASEPLNAAPRRYVNRLSDLLFVLARVLNRAAGGADVL 176
               SCOP domains d2zhza_ A: automated matches                                                                                                                         SCOP domains
               CATH domains 2zhzA00 A:29-176  [code=1.20.1200.10, no name defined]                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zhz A  29 DDARIAAIGDVDELNSQIGVLLAEPLPDDVRAALSAIQHDLFDLGGELCIPGHAAITDAHLARLDGWLAHYNGQLPPLEEFILPGGARGAALAHVCRTVCRRAERSIVALGASEPLNAAPRRYVNRLSDLLFVLARVLNRAAGGADVL 176
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168

Chain B from PDB  Type:PROTEIN  Length:174
 aligned with Q2SZ09_BURTA | Q2SZ09 from UniProtKB/TrEMBL  Length:183

    Alignment length:174
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174    
         Q2SZ09_BURTA     5 LSKIATRTGDDGTTGLGDGSRVRKDDARIAAIGDVDELNSQIGVLLAEPLPDDVRAALSAIQHDLFDLGGELCIPGHAAITDAHLARLDGWLAHYNGQLPPLEEFILPGGARGAALAHVCRTVCRRAERSIVALGASEPLNAAPRRYVNRLSDLLFVLARVLNRAAGGADVLWD 178
               SCOP domains d2zhzb_ B: automated matches                                                                                                                                                   SCOP domains
               CATH domains ------------2zhzB01 B:17-178  [code=1.20.1200.10, no name defined]                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............eee.....eee..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.......ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh....ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2zhz B   5 LSKIATRTGDDGTTGLGDGSRVRKDDARIAAIGDVDELNSQIGVLLAEPLPDDVRAALSAIQHDLFDLGGELCIPGHAAITDAHLARLDGWLAHYNGQLPPLEEFILPGGARGAALAHVCRTVCRRAERSIVALGASEPLNAAPRRYVNRLSDLLFVLARVLNRAAGGADVLWD 178
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174

Chain C from PDB  Type:PROTEIN  Length:172
 aligned with Q2SZ09_BURTA | Q2SZ09 from UniProtKB/TrEMBL  Length:183

    Alignment length:172
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174  
         Q2SZ09_BURTA     5 LSKIATRTGDDGTTGLGDGSRVRKDDARIAAIGDVDELNSQIGVLLAEPLPDDVRAALSAIQHDLFDLGGELCIPGHAAITDAHLARLDGWLAHYNGQLPPLEEFILPGGARGAALAHVCRTVCRRAERSIVALGASEPLNAAPRRYVNRLSDLLFVLARVLNRAAGGADVL 176
               SCOP domains d2zhzc_ C: automated matches                                                                                                                                                 SCOP domains
               CATH domains ------------2zhzC01 C:17-176  [code=1.20.1200.10, no name defined]                                                                                                           CATH domains
           Pfam domains (1) ---Cob_adeno_trans-2zhzC01 C:8-167                                                                                                                                 --------- Pfam domains (1)
           Pfam domains (2) ---Cob_adeno_trans-2zhzC02 C:8-167                                                                                                                                 --------- Pfam domains (2)
           Pfam domains (3) ---Cob_adeno_trans-2zhzC03 C:8-167                                                                                                                                 --------- Pfam domains (3)
         Sec.struct. author ............eee.....eee..hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zhz C   5 LSKIATRTGDDGTTGLGDGSRVRKDDARIAAIGDVDELNSQIGVLLAEPLPDDVRAALSAIQHDLFDLGGELCIPGHAAITDAHLARLDGWLAHYNGQLPPLEEFILPGGARGAALAHVCRTVCRRAERSIVALGASEPLNAAPRRYVNRLSDLLFVLARVLNRAAGGADVL 176
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Ferritin-like (533)

Superfamily: Cobalamin adenosyltransferase-like (21)

Family: automated matches (17)

Protein domain: automated matches (17)

Burkholderia thailandensis [TaxId: 57975] (2)

1a	d2zhza_	A:
1b	d2zhzb_	B:
1c	d2zhzc_	C:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Hypothetical Protein Ta1238; Chain: A; (20)

Homologous Superfamily: [code=1.20.1200.10, no name defined] (20)

Burkholderia thailandensis. Organism_taxid: 57975. (2)

1a	2zhzC01	C:17-176
1b	2zhzB01	B:17-178
1c	2zhzA00	A:29-176

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (Q2SZ09_BURTA | Q2SZ09)


GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2zhz)

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	2zhz
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

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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