1M8K - JenaLib

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Title :   CRYSTAL STRUCTURE OF METHANOBACTERIUM THERMOAUTOTROPHICUM NICOTINAMIDE MONONUCLEOTIDE ADENYLYLTRANSFERASE MUTANT H19A COMPLEXED WITH NAD

Authors :   V. Saridakis, E. F. Pai

Date :   25 Jul 02 (Deposition) - 15 Jul 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Nucleotidyltransferase Hxgh Active Site Motif, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Saridakis, E. F. Pai
Mutational, Structural, And Kinetic Studies Of The Atp-Binding Site Of Methanobacterium Thermoautotrophicum Nicotinamide Mononucleotide Adenylyltransferase
J. Biol. Chem. V. 278 34356 2003
PubMed-ID: 12810729 | Reference-DOI: 10.1074/JBC.M205369200

Molecule 1 - NICOTINAMIDE-NUCLEOTIDE ADENYLYLTRANSFERASE
	Chains	:	A, B, C
	EC Number	:	2.7.7.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	MTH150
	Mutation	:	YES
	Organism Scientific	:	METHANOTHERMOBACTER THERMAUTOTROPHICUS
	Organism Taxid	:	145262
	Synonym	:	NAD(+) PYROPHOSPHORYLASE, NAD(+) DIPHOSPHORYLASE, NMN ADENYLYLTRANSFERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	NAD	3	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	NAD	6	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	NAD	3	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG C:11 , SER C:131 , GLY C:132 , THR C:133 , ARG C:136 , NAD C:2004	BINDING SITE FOR RESIDUE SO4 C 1760
2	AC2	SOFTWARE	ARG A:11 , GLY A:132 , THR A:133 , ARG A:136 , NAD A:2006	BINDING SITE FOR RESIDUE SO4 A 1759
3	AC3	SOFTWARE	ARG B:11 , SER B:131 , GLY B:132 , THR B:133 , ARG B:136 , NAD B:2005	BINDING SITE FOR RESIDUE SO4 B 1761
4	AC4	SOFTWARE	VAL B:9 , ARG B:11 , GLY B:38 , SER B:39 , ASP B:80 , ILE B:81 , ASN B:84 , TRP B:87 , ASN B:105 , LEU B:107 , PRO B:122 , LEU B:124 , PHE B:125 , TYR B:126 , SO4 B:1761	BINDING SITE FOR RESIDUE NAD B 2005
5	AC5	SOFTWARE	VAL A:9 , GLY A:10 , ARG A:11 , VAL A:22 , GLY A:38 , SER A:39 , ASP A:80 , ILE A:81 , ASN A:84 , TRP A:87 , ASN A:105 , LEU A:107 , PRO A:122 , LEU A:124 , PHE A:125 , TYR A:126 , SO4 A:1759	BINDING SITE FOR RESIDUE NAD A 2006
6	AC6	SOFTWARE	VAL C:9 , GLY C:10 , ARG C:11 , VAL C:22 , GLY C:38 , SER C:39 , ASP C:80 , ILE C:81 , ASN C:84 , TRP C:87 , ASN C:105 , PRO C:122 , LEU C:124 , PHE C:125 , TYR C:126 , SO4 C:1760	BINDING SITE FOR RESIDUE NAD C 2004

(no "SS Bond" information available for 1M8K)

Asymmetric Unit

No.	Residues
1	Gln A:13	-	Pro A:14
2	Gln B:13	-	Pro B:14
3	Gln C:13	-	Pro C:14

(no "SAP(SNP)/Variant" information available for 1M8K)

(no "PROSITE Motif" information available for 1M8K)

(no "Exon" information available for 1M8K)

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:169
 aligned with NADM_METTH | O26253 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:169
                             1                                                                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159         
           NADM_METTH     - -MRGLLVGRMQPFHRGHLQVIKSILEEVDELIICIGSAQLSHSIRDPFTAGERVMMLTKALSENGIPASRYYIIPVQDIECNALWVGHIKMLTPPFDRVYSGNPLVQRLFSEDGYEVTAPPLFYRDRYSGTEVRRRMLDDGDWRSLLPESVVEVIDEINGVERIKHLAK 168
               SCOP domains d1m8ka_ A: Nicotinamide mononucleotide (NMN) adenylyltransferase                                                                                                          SCOP domains
               CATH domains 1m8kA00 A:3-171 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhh....eeeeeee............hhhhhhhhhhhhhhhh..hhh.eeeeee....hhhhhhhhhhhhh....eee..hhhhhhhhhh...eee......hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m8k A   3 TMRGLLVGRMQPFHRGALQVIKSILEEVDELIICIGSAQLSHSIRDPFTAGERVMMLTKALSENGIPASRYYIIPVQDIECNALWVGHIKMLTPPFDRVYSGNPLVQRLFSEDGYEVTAPPLFYRDRYSGTEVRRRMLDDGDWRSLLPESVVEVIDEINGVERIKHLAK 171
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162

Chain B from PDB  Type:PROTEIN  Length:169
 aligned with NADM_METTH | O26253 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:169
                             1                                                                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159         
           NADM_METTH     - -MRGLLVGRMQPFHRGHLQVIKSILEEVDELIICIGSAQLSHSIRDPFTAGERVMMLTKALSENGIPASRYYIIPVQDIECNALWVGHIKMLTPPFDRVYSGNPLVQRLFSEDGYEVTAPPLFYRDRYSGTEVRRRMLDDGDWRSLLPESVVEVIDEINGVERIKHLAK 168
               SCOP domains d1m8kb_ B: Nicotinamide mononucleotide (NMN) adenylyltransferase                                                                                                          SCOP domains
               CATH domains 1m8kB00 B:3-171 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhh...eeeeee..............hhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhh.....eee..hhhhhhhhhhh..eee..........hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m8k B   3 TMRGLLVGRMQPFHRGALQVIKSILEEVDELIICIGSAQLSHSIRDPFTAGERVMMLTKALSENGIPASRYYIIPVQDIECNALWVGHIKMLTPPFDRVYSGNPLVQRLFSEDGYEVTAPPLFYRDRYSGTEVRRRMLDDGDWRSLLPESVVEVIDEINGVERIKHLAK 171
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162

Chain C from PDB  Type:PROTEIN  Length:169
 aligned with NADM_METTH | O26253 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:169
                             1                                                                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159         
           NADM_METTH     - -MRGLLVGRMQPFHRGHLQVIKSILEEVDELIICIGSAQLSHSIRDPFTAGERVMMLTKALSENGIPASRYYIIPVQDIECNALWVGHIKMLTPPFDRVYSGNPLVQRLFSEDGYEVTAPPLFYRDRYSGTEVRRRMLDDGDWRSLLPESVVEVIDEINGVERIKHLAK 168
               SCOP domains d1m8kc_ C: Nicotinamide mononucleotide (NMN) adenylyltransferase                                                                                                          SCOP domains
               CATH domains 1m8kC00 C:3-171 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                     CATH domains
           Pfam domains (1) ----CTP_transf_2-1m8kC01 C:7-138                                                                                                        --------------------------------- Pfam domains (1)
           Pfam domains (2) ----CTP_transf_2-1m8kC02 C:7-138                                                                                                        --------------------------------- Pfam domains (2)
           Pfam domains (3) ----CTP_transf_2-1m8kC03 C:7-138                                                                                                        --------------------------------- Pfam domains (3)
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhh....eeeeee.............hhhhhhhhhhhhhhhh..hhh.eeeee.....hhhhhhhhhhhh.....eee..hhhhhhhhhhh..eee......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m8k C   3 TMRGLLVGRMQPFHRGALQVIKSILEEVDELIICIGSAQLSHSIRDPFTAGERVMMLTKALSENGIPASRYYIIPVQDIECNALWVGHIKMLTPPFDRVYSGNPLVQRLFSEDGYEVTAPPLFYRDRYSGTEVRRRMLDDGDWRSLLPESVVEVIDEINGVERIKHLAK 171
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Adenine nucleotide alpha hydrolase-like (440)

Superfamily: Nucleotidylyl transferase (325)

Family: Adenylyltransferase (56)

Protein domain: Nicotinamide mononucleotide (NMN) adenylyltransferase (22)

Methanobacterium thermoautotrophicum [TaxId: 145262] (6)

1a	d1m8ka_	A:
1b	d1m8kb_	B:
1c	d1m8kc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1 (328)

Methanothermobacter thermautotrophicus. Organism_taxid: 145262. (4)

1a	1m8kA00	A:3-171
1b	1m8kB00	B:3-171
1c	1m8kC00	C:3-171

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HUP (230)

Family: CTP_transf_2 (36)

Methanobacterium thermoautotrophicum (strain Delta H) (3)

1a	CTP_transf_2-1m8kC01	C:7-138
1b	CTP_transf_2-1m8kC02	C:7-138
1c	CTP_transf_2-1m8kC03	C:7-138

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (NADM_METTH | O26253)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0000309	nicotinamide-nucleotide adenylyltransferase activity	Catalysis of the reaction: ATP + nicotinamide nucleotide = diphosphate + NAD+.
	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:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	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.
biological process
	GO:0009435	NAD biosynthetic process	The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide, a coenzyme present in most living cells and derived from the B vitamin nicotinic acid; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH.
	GO:0009058	biosynthetic process	The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
	GO:0019363	pyridine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
		Gln A:13 - Pro A:14	[ RasMol ]
		Gln B:13 - Pro B:14	[ RasMol ]
		Gln C:13 - Pro C:14	[ RasMol ]

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	2.7.7.1
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UniProtKB/Swiss-Prot
	NADM_METTH \| O26253	:	1ej2 1hyb 1m8f 1m8g 1m8j 4yp5 4yp6 4yp7

1m8f	NICOTINAMIDE MONONUCLEOTIDE ADENYLYLTRANSFERASE MUTANT R11A COMPLEXED WITH NAD
1m8g	NICOTINAMIDE MONONUCLEOTIDE ADENYLYLTRANSFERASE MUTANT R11K COMPLEXED WITH NAD
1m8j	NICOTINAMIDE MONONUCLEOTIDE ADENYLYLTRANSFERASE MUTANT R136A COMPLEXED WITH NAD

Description

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