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(-) Description

Title :  CRYSTAL STRUCTURE OF E.COLI NICOTINIC ACID MONONUCLEOTIDE ADENYLYLTRANSFERASE COMPLEXED TO DEAMIDO-NAD
 
Authors :  H. Zhang, T. Zhou, O. Kurnasov, S. Cheek, N. V. Grishin, A. Osterman
Date :  08 Oct 01  (Deposition) - 08 Oct 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Nucleotidyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Zhang, T. Zhou, O. Kurnasov, S. Cheek, N. V. Grishin, A. Osterman
Crystal Structures Of E. Coli Nicotinate Mononucleotide Adenylyltransferase And Its Complex With Deamido-Nad.
Structure V. 10 69 2002
PubMed-ID: 11796112  |  Reference-DOI: 10.1016/S0969-2126(01)00693-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NAMN ADENYLYLTRANSFERASE
    Chains: A, B, C
    EC Number: 2.7.7.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NADD
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1CIT3Ligand/IonCITRIC ACID
2NAD3Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:8 , GLY A:9 , GLY A:10 , THR A:11 , PHE A:12 , GLY A:18 , HIS A:19 , ASN A:40 , HIS A:45 , ARG A:46 , TYR A:84 , THR A:85 , PHE A:104 , ILE A:106 , GLY A:107 , ASP A:109 , SER A:110 , TRP A:117 , TYR A:118 , ARG A:134 , PHE A:177 , ILE A:179 , HOH A:605 , HOH A:608 , HOH A:612 , HOH A:615 , HOH A:616 , HOH A:617 , HOH A:618 , HOH A:635 , HOH A:663 , HOH A:698 , HOH A:736 , HOH A:754BINDING SITE FOR RESIDUE NAD A 601
2AC2SOFTWAREARG A:46 , ASP A:109 , ARG A:134 , SER A:180 , ALA A:181 , THR A:182 , ARG A:185 , HOH A:608 , HOH A:615 , HOH A:620 , HOH A:622 , HOH A:736 , HOH A:765BINDING SITE FOR RESIDUE CIT A 604
3AC3SOFTWAREPHE B:8 , GLY B:9 , GLY B:10 , THR B:11 , PHE B:12 , GLY B:18 , HIS B:19 , ASN B:40 , HIS B:45 , ARG B:46 , TYR B:84 , THR B:85 , PHE B:104 , ILE B:106 , GLY B:107 , ASP B:109 , SER B:110 , TRP B:117 , TYR B:118 , ARG B:133 , ARG B:134 , PHE B:177 , ILE B:179 , HOH B:607 , HOH B:608 , HOH B:611 , HOH B:614 , HOH B:627 , HOH B:640 , HOH B:644 , HOH B:663 , HOH B:697 , HOH B:710 , HOH B:749 , HOH B:766BINDING SITE FOR RESIDUE NAD B 602
4AC4SOFTWAREARG B:46 , ASP B:109 , ARG B:134 , SER B:180 , ALA B:181 , THR B:182 , ARG B:185 , HOH B:611 , HOH B:621 , HOH B:631 , HOH B:644 , HOH B:749 , HOH B:772BINDING SITE FOR RESIDUE CIT B 605
5AC5SOFTWAREPHE C:8 , GLY C:9 , GLY C:10 , THR C:11 , PHE C:12 , GLY C:18 , HIS C:19 , ASN C:40 , HIS C:45 , ARG C:46 , TYR C:84 , THR C:85 , PHE C:104 , ILE C:106 , GLY C:107 , ASP C:109 , SER C:110 , TRP C:117 , TYR C:118 , ARG C:133 , ARG C:134 , PHE C:177 , ILE C:179 , HOH C:608 , HOH C:609 , HOH C:611 , HOH C:613 , HOH C:617 , HOH C:620 , HOH C:637 , HOH C:646 , HOH C:665 , HOH C:680 , HOH C:701 , HOH C:762BINDING SITE FOR RESIDUE NAD C 603
6AC6SOFTWAREARG C:46 , ASP C:109 , ARG C:134 , SER C:180 , ALA C:181 , THR C:182 , ARG C:185 , HOH C:609 , HOH C:611 , HOH C:618 , HOH C:762BINDING SITE FOR RESIDUE CIT C 606

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K4M)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Asp A:13 -Pro A:14
2Asp B:13 -Pro B:14
3Asp C:13 -Pro C:14

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K4M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1K4M)

(-) Exons   (0, 0)

(no "Exon" information available for 1K4M)

(-) Sequences/Alignments

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:213
 aligned with NADD_ECOLI | P0A752 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   
           NADD_ECOLI     1 MKSLQALFGGTFDPVHYGHLKPVETLANLIGLTRVTIIPNNVPPHRPQPEANSVQRKHMLELAIADKPLFTLDERELKRNAPSYTAQTLKEWRQEQGPDVPLAFIIGQDSLLTFPTWYEYETILDNAHLIVCRRPGYPLEMAQPQYQQWLEDHLTHNPEDLHLQPAGKIYLAETPWFNISATIIRERLQNGESCEDLLPEPVLTYINQQGLYR 213
               SCOP domains d1k4ma_ A: Nicotinamide mononucleotide (NMN) adenylyltransferase                                                                                                                                                      SCOP domains
               CATH domains 1k4mA00 A:1-213 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.....hhhhhhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhh....eee.hhhhhh....hhhhhhhhhhhhhh....eeeeeehhhhhhhhhh.hhhhhhhhheeeee..........hhhhhhhhhhhh....hhhhhh....eeee.......hhhhhhhhhhh........hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k4m A   1 MKSLQALFGGTFDPVHYGHLKPVETLANLIGLTRVTIIPNNVPPHRPQPEANSVQRKHMLELAIADKPLFTLDERELKRNAPSYTAQTLKEWRQEQGPDVPLAFIIGQDSLLTFPTWYEYETILDNAHLIVCRRPGYPLEMAQPQYQQWLEDHLTHNPEDLHLQPAGKIYLAETPWFNISATIIRERLQNGESCEDLLPEPVLTYINQQGLYR 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   


Chain B from PDB  Type:PROTEIN  Length:213
 aligned with NADD_ECOLI | P0A752 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   
           NADD_ECOLI     1 MKSLQALFGGTFDPVHYGHLKPVETLANLIGLTRVTIIPNNVPPHRPQPEANSVQRKHMLELAIADKPLFTLDERELKRNAPSYTAQTLKEWRQEQGPDVPLAFIIGQDSLLTFPTWYEYETILDNAHLIVCRRPGYPLEMAQPQYQQWLEDHLTHNPEDLHLQPAGKIYLAETPWFNISATIIRERLQNGESCEDLLPEPVLTYINQQGLYR 213
               SCOP domains d1k4mb_ B: Nicotinamide mononucleotide (NMN) adenylyltransferase                                                                                                                                                      SCOP domains
               CATH domains 1k4mB00 B:1-213 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.....hhhhhhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhh....eee...........hhhhhhhhhhhhhh....eeeeeehhhhhhhhhh.hhhhhhhhheeeee..........hhhhhhhhhhhh....hhhhhh....eeee.......hhhhhhhhhhh........hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k4m B   1 MKSLQALFGGTFDPVHYGHLKPVETLANLIGLTRVTIIPNNVPPHRPQPEANSVQRKHMLELAIADKPLFTLDERELKRNAPSYTAQTLKEWRQEQGPDVPLAFIIGQDSLLTFPTWYEYETILDNAHLIVCRRPGYPLEMAQPQYQQWLEDHLTHNPEDLHLQPAGKIYLAETPWFNISATIIRERLQNGESCEDLLPEPVLTYINQQGLYR 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   


Chain C from PDB  Type:PROTEIN  Length:213
 aligned with NADD_ECOLI | P0A752 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   
           NADD_ECOLI     1 MKSLQALFGGTFDPVHYGHLKPVETLANLIGLTRVTIIPNNVPPHRPQPEANSVQRKHMLELAIADKPLFTLDERELKRNAPSYTAQTLKEWRQEQGPDVPLAFIIGQDSLLTFPTWYEYETILDNAHLIVCRRPGYPLEMAQPQYQQWLEDHLTHNPEDLHLQPAGKIYLAETPWFNISATIIRERLQNGESCEDLLPEPVLTYINQQGLYR 213
               SCOP domains d1k4mc_ C: Nicotinamide mononucleotide (NMN) adenylyltransferase                                                                                                                                                      SCOP domains
               CATH domains 1k4mC00 C:1-213 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                 CATH domains
           Pfam domains (1) ------CTP_transf_2-1k4mC01 C:7-187                                                                                                                                                         -------------------------- Pfam domains (1)
           Pfam domains (2) ------CTP_transf_2-1k4mC02 C:7-187                                                                                                                                                         -------------------------- Pfam domains (2)
           Pfam domains (3) ------CTP_transf_2-1k4mC03 C:7-187                                                                                                                                                         -------------------------- Pfam domains (3)
         Sec.struct. author ....eeeeee.....hhhhhhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhh....eee.hhhhhh....hhhhhhhhhhhhhh....eeeeeehhhhhhhhhh.hhhhhhhhheeeee..........hhhhhhhhhhhh....hhhhhh....eee........hhhhhhhhhhh........hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k4m C   1 MKSLQALFGGTFDPVHYGHLKPVETLANLIGLTRVTIIPNNVPPHRPQPEANSVQRKHMLELAIADKPLFTLDERELKRNAPSYTAQTLKEWRQEQGPDVPLAFIIGQDSLLTFPTWYEYETILDNAHLIVCRRPGYPLEMAQPQYQQWLEDHLTHNPEDLHLQPAGKIYLAETPWFNISATIIRERLQNGESCEDLLPEPVLTYINQQGLYR 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (NADD_ECOLI | P0A752)
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:0004515    nicotinate-nucleotide adenylyltransferase activity    Catalysis of the reaction: ATP + nicotinate ribonucleotide = diphosphate + deamido-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:0034628    'de novo' NAD biosynthetic process from aspartate    The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD), beginning with the synthesis of aspartate from simpler precursors; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH.
    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:0034355    NAD salvage    Any process that generates nicotinamide adenine dinucleotide (NAD) from derivatives of it, without de novo synthesis; salvage is usually from the degradation products nicotinic acid (Na) and nicotinamide (Nam).
    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.

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 Related Entries

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UniProtKB/Swiss-Prot
        NADD_ECOLI | P0A752: 1k4k

(-) Related Entries Specified in the PDB File

1k4k CRYSTAL STRUCTURE OF E. COLI NICOTINIC ACID MONONUCLEOTIDE ADENYLYLTRANSFERASE