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Description

Title :   ATP BOUND AT THE ACTIVE SITE OF A PDUO TYPE ATP:CO(I)RRINOID ADENOSYLTRANSFERASE FROM LACTOBACILLUS REUTERI

Authors :   M. St-Maurice, P. E. Mera, M. P. Taranto, F. Sesma, J. C. Escalante-Seme I. Rayment

Date :   07 Nov 06 (Deposition) - 21 Nov 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.68

Chains :   Asym. Unit : A
Biol. Unit 1: A  (3x)

Keywords :   Atp Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. St Maurice, P. E. Mera, M. P. Taranto, F. Sesma, J. C. Escalante-Semerena, I. Rayment
Structural Characterization Of The Active Site Of The Pduo-Type Atp:Co(I)Rrinoid Adenosyltransferase From Lactobacillus Reuteri.
J. Biol. Chem. V. 282 2596 2007
PubMed-ID: 17121823 | Reference-DOI: 10.1074/JBC.M609557200

Compounds

Molecule 1 - COBALAMIN ADENOSYLTRANSFERASE
	Chains	:	A
	EC Number	:	2.5.1.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PDUO
	Organism Scientific	:	LACTOBACILLUS REUTERI
	Organism Taxid	:	1598
	Strain	:	CRL1098

Structural Features

Chains, Units

		1
Asymmetric Unit	:	A
Biological Unit 1 (3x)	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (4, 5)

Asymmetric Unit (4, 5)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	GOL	2	Ligand/Ion	GLYCEROL
3	MG	1	Ligand/Ion	MAGNESIUM ION
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 12)

No.	Name	Count	Type	Full Name
1	ATP	3	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	GOL	6	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	SO4	3	Ligand/Ion	SULFATE ION

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:156 , ATP A:999 , HOH A:1003 , HOH A:1039	BINDING SITE FOR RESIDUE MG A 998
2	AC2	SOFTWARE	TRP A:40 , ILE A:130 , HOH A:1140	BINDING SITE FOR RESIDUE SO4 A 601
3	AC3	SOFTWARE	THR A:5 , LYS A:6 , ASN A:7 , GLY A:8 , GLN A:12 , THR A:13 , ARG A:14 , LYS A:23 , VAL A:28 , TYR A:31 , GLY A:32 , ARG A:132 , GLU A:135 , ARG A:136 , ASN A:156 , GOL A:889 , MG A:998 , HOH A:1003 , HOH A:1013 , HOH A:1033 , HOH A:1039 , HOH A:1058 , HOH A:1118	BINDING SITE FOR RESIDUE ATP A 999
4	AC4	SOFTWARE	ASN A:7 , GLY A:8 , GLN A:12 , THR A:13 , ILE A:20 , ATP A:999 , HOH A:1118 , HOH A:1121 , HOH A:1139	BINDING SITE FOR RESIDUE GOL A 889
5	AC5	SOFTWARE	GLN A:19 , LEU A:21 , ARG A:27 , GLU A:145 , HOH A:1010 , HOH A:1100	BINDING SITE FOR RESIDUE GOL A 888

SS Bonds (0, 0)

(no "SS Bond" information available for 2NT8)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2NT8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 2NT8)

PROSITE Motifs (0, 0)

(no "PROSITE Motif" information available for 2NT8)

Exons (0, 0)

(no "Exon" information available for 2NT8)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

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Chain A from PDB  Type:PROTEIN  Length:181
 aligned with Q50EJ2_LACRE | Q50EJ2 from UniProtKB/TrEMBL  Length:188

    Alignment length:181
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181 
         Q50EJ2_LACRE     2 KIYTKNGDKGQTRIIGKQILYKNDPRVAAYGEVDELNSWVGYTKSLINSHTQVLSNELEEIQQLLFDCGHDLATPADDERHSFKFKQEQPTVWLEEKIDNYTQVVPAVKKFILPGGTQLASALHVARTITRRAERQIVQLMREEQINQDVLIFINRLSDYFFAAARYANYLEQQPDMLYRN 182
               SCOP domains d2nt8a_ A: automated matches                                                                                                                                                          SCOP domains
               CATH domains ----------2nt8A01 A:12-182  [code=1.20.1200.10, no name defined]                                                                                                                      CATH domains
               Pfam domains -Cob_adeno_trans-2nt8A01 A:3-170                                                                                                                                         ------------ Pfam domains
         Sec.struct. author ..........eee.....eee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhh......ee...hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh....ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nt8 A   2 KIYTKNGDKGQTRIIGKQILYKNDPRVAAYGEVDELNSWVGYTKSLINSHTQVLSNELEEIQQLLFDCGHDLATPADDERHSFKFKQEQPTVWLEEKIDNYTQVVPAVKKFILPGGTQLASALHVARTITRRAERQIVQLMREEQINQDVLIFINRLSDYFFAAARYANYLEQQPDMLYRN 182
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric 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)

Lactobacillus reuteri [TaxId: 1598] (9)

d2nt8a_

CATH Domains (1, 1)

Asymmetric 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)

Lactobacillus reuteri. Organism_taxid: 1598. Strain: crl1098. (6)

2nt8A01

A:12-182

Pfam Domains (1, 1)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Cob_adeno_trans] (11)

Family: Cob_adeno_trans (11)

Lactobacillus reuteri (3)

Cob_adeno_trans-2nt8A01

A:3-170

Gene Ontology (5, 5)

Asymmetric Unit(hide GO term definitions)

Chain A (Q50EJ2_LACRE | Q50EJ2)


GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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.

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Related Entries Specified in the PDB File

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