2R6X - JenaLib

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Title :   STRUCTURE OF A D35N VARIANT PDUO-TYPE ATP:CO(I)RRINOID ADENOSYLTRANSFERASE FROM LACTOBACILLUS REUTERI COMPLEXED WITH ATP

Authors :   M. St Maurice, P. E. Mera, J. C. Escalante-Semerena, I. Rayment

Date :   06 Sep 07 (Deposition) - 18 Dec 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.61

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (3x)
Biol. Unit 2: B  (3x)

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

Reference :   P. E. Mera, M. St Maurice, I. Rayment, J. C. Escalante-Semerena
Structural And Functional Analyses Of The Human-Type Corrinoid Adenosyltransferase (Pduo) From Lactobacillus Reuteri.
Biochemistry V. 46 13829 2007
PubMed-ID: 17988155 | Reference-DOI: 10.1021/BI701622J
(for further references see the PDB file header)

Molecule 1 - COBALAMIN ADENOSYLTRANSFERASE PDUO-LIKE PROTEIN
	Chains	:	A, B
	EC Number	:	2.5.1.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	COBA
	Mutation	:	YES
	Organism Scientific	:	LACTOBACILLUS REUTERI
	Organism Taxid	:	1598
	Strain	:	CRL1098

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (3x)	:	A
Biological Unit 2 (3x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

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

Biological Unit 1 (1, 3)

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

Biological Unit 2 (1, 3)

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

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:3 , ASP A:160 , ATP A:995 , HOH A:1048	BINDING SITE FOR RESIDUE MG A 189
2	AC2	SOFTWARE	LYS A:23 , ASN A:156 , ATP A:995	BINDING SITE FOR RESIDUE MG A 190
3	AC3	SOFTWARE	LYS B:23 , ASN B:156 , ATP B:995 , HOH B:999	BINDING SITE FOR RESIDUE MG B 189
4	AC4	SOFTWARE	ILE B:3 , ASP B:160 , ATP B:995	BINDING SITE FOR RESIDUE MG B 190
5	AC5	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 , ARG A:132 , GLU A:135 , ARG A:136 , ASN A:156 , MG A:189 , MG A:190 , HOH A:1008	BINDING SITE FOR RESIDUE ATP A 995
6	AC6	SOFTWARE	THR B:5 , LYS B:6 , ASN B:7 , GLY B:8 , GLN B:12 , THR B:13 , ARG B:14 , LYS B:23 , VAL B:28 , TYR B:31 , GLY B:32 , ARG B:132 , GLU B:135 , ARG B:136 , ASN B:156 , ASP B:160 , MG B:189 , MG B:190 , HOH B:999 , HOH B:1022 , HOH B:1023	BINDING SITE FOR RESIDUE ATP B 995

(no "SS Bond" information available for 2R6X)

Asymmetric Unit

No.	Residues
1	Val B:109	-	Lys B:110

(no "SAP(SNP)/Variant" information available for 2R6X)

(no "PROSITE Motif" information available for 2R6X)

(no "Exon" information available for 2R6X)

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
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Chain A from PDB  Type:PROTEIN  Length:176
 aligned with Q50EJ2_LACRE | Q50EJ2 from UniProtKB/TrEMBL  Length:188

    Alignment length:180
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
         Q50EJ2_LACRE     2 KIYTKNGDKGQTRIIGKQILYKNDPRVAAYGEVDELNSWVGYTKSLINSHTQVLSNELEEIQQLLFDCGHDLATPADDERHSFKFKQEQPTVWLEEKIDNYTQVVPAVKKFILPGGTQLASALHVARTITRRAERQIVQLMREEQINQDVLIFINRLSDYFFAAARYANYLEQQPDMLYR 181
               SCOP domains d2r6xa_ A: automated matches                                                                                                                                                         SCOP domains
               CATH domains ----------2r6xA01 A:12-181  [code=1.20.1200.10, no name defined]                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eee.....eee..hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh........-....hhhhhhhhhhhhhhhhhhh.---..ee...hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh....ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2r6x A   2 KIYTKNGDKGQTRIIGKQILYKNDPRVAAYGEVNELNSWVGYTKSLINSHTQVLSNELEEIQQLLFDCGHDLATPADDERH-FKFKQEQPTVWLEEKIDNYTQVVP---KFILPGGTQLASALHVARTITRRAERQIVQLMREEQINQDVLIFINRLSDYFFAAARYANYLEQQPDMLYR 181
                                    11        21        31        41        51        61        71        81| |     91       101     | 111       121       131       141       151       161       171       181
                                                                                                           82 |                    107 111                                                                      
                                                                                                             84

Chain B from PDB  Type:PROTEIN  Length:173
 aligned with Q50EJ2_LACRE | Q50EJ2 from UniProtKB/TrEMBL  Length:188

    Alignment length:179
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172         
         Q50EJ2_LACRE     3 IYTKNGDKGQTRIIGKQILYKNDPRVAAYGEVDELNSWVGYTKSLINSHTQVLSNELEEIQQLLFDCGHDLATPADDERHSFKFKQEQPTVWLEEKIDNYTQVVPAVKKFILPGGTQLASALHVARTITRRAERQIVQLMREEQINQDVLIFINRLSDYFFAAARYANYLEQQPDMLYR 181
               SCOP domains d2r6xb_ B: aut  omated matches                                                                                                                                                      SCOP domains
               CATH domains ---------2r6xB  01 B:12-181  [code=1.20.1200.10, no name defined]                                                                                                                   CATH domains
           Pfam domains (1) Cob_adeno_tran  s-2r6xB01 B:3-170                                                                                                                                       ----------- Pfam domains (1)
           Pfam domains (2) Cob_adeno_tran  s-2r6xB02 B:3-170                                                                                                                                       ----------- Pfam domains (2)
         Sec.struct. author .........eee..--.eee..hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..----.......hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r6x B   3 IYTKNGDKGQTRII--QILYKNDPRVAAYGEVNELNSWVGYTKSLINSHTQVLSNELEEIQQLLFDCGHDLATP----RHSFKFKQEQPTVWLEEKIDNYTQVVPAVKKFILPGGTQLASALHVARTITRRAERQIVQLMREEQINQDVLIFINRLSDYFFAAARYANYLEQQPDMLYR 181
                                    12   |  | 22        32        42        52        62        72   |    82        92       102       112       122       132       142       152       162       172         
                                        16 19                                                       76   81

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 Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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)

1a	d2r6xa_	A:
1b	d2r6xb_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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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)

1a	2r6xB01	B:12-181
1b	2r6xA01	A:12-181

Asymmetric Unit

Clans(

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Families(

)

Organisms( (-)

)

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

Family: Cob_adeno_trans (11)

Lactobacillus reuteri (3)

1a	Cob_adeno_trans-2r6xB01	B:3-170
1b	Cob_adeno_trans-2r6xB02	B:3-170

Asymmetric Unit(hide GO term definitions)

Chain A,B (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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		Val B:109 - Lys B:110	[ RasMol ]

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