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(-) Description

Title :  CRYSTAL STRUCTURE OF C176A MUTANT OF GLUTAMINE-DEPENDENT NAD+ SYNTHETASE FROM M. TUBERCULOSIS IN APO FORM
 
Authors :  W. Chuenchor, B. Gerratana
Date :  09 Jun 11  (Deposition) - 11 Apr 12  (Release) - 11 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (8x)
Keywords :  Glutamine-Amidotransferase, Glutaminase, Glutamine-Dependent Nad+ Synthetase, Ligase, Ammonia Tunneling, Atp Binding, Nad, Nucleotide Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Chuenchor, T. I. Doukov, M. Resto, A. Chang, B. Gerratana
Regulation Of The Intersubunit Ammonia Tunnel In Mycobacterium Tuberculosis Glutamine-Dependent Nad+ Synthetase.
Biochem. J. V. 443 417 2012
PubMed-ID: 22280445  |  Reference-DOI: 10.1042/BJ20112210

(-) Compounds

Molecule 1 - GLUTAMINE-DEPENDENT NAD(+) SYNTHETASE
    Chains: A
    EC Number: 6.3.5.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSMT3
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MT2513, MTCY428.08, NADE, RV2438C
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: NAD(+) SYNTHASE [GLUTAMINE-HYDROLYZING]

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (8x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3SDB)

(-) Sites  (0, 0)

(no "Site" information available for 3SDB)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SDB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3SDB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SDB)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CN_HYDROLASEPS50263 Carbon-nitrogen hydrolase domain profile.NADE_MYCTO12-276  1A:12-276
NADE_MYCTU12-276  1A:12-276
Biological Unit 1 (1, 16)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CN_HYDROLASEPS50263 Carbon-nitrogen hydrolase domain profile.NADE_MYCTO12-276  8A:12-276
NADE_MYCTU12-276  8A:12-276

(-) Exons   (0, 0)

(no "Exon" information available for 3SDB)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:647
 aligned with NADE_MYCTO | P9WJJ2 from UniProtKB/Swiss-Prot  Length:679

    Alignment length:680
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679
           NADE_MYCTO     - -MNFYSAYQHGFVRVAACTHHTTIGDPAANAASVLDMARACHDDGAALAVFPELTLSGYSIEDVLLQDSLLDAVEDALLDLVTESADLLPVLVVGAPLRHRHRIYNTAVVIHRGAVLGVVPKSYLPTYREFYERRQMAPGDGERGTIRIGGADVAFGTDLLFAASDLPGFVLHVEICEDMFVPMPPSAEAALAGATVLANLSGSPITIGRAEDRRLLARSASARCLAAYVYAAAGEGESTTDLAWDGQTMIWENGALLAESERFPKGVRRSVADVDTELLRSERLRMGTFDDNRRHHRELTESFRRIDFALDPPAGDIGLLREVERFPFVPADPQRLQQDCYEAYNIQVSGLEQRLRALDYPKVVIGVSGGLDSTHALIVATHAMDREGRPRSDILAFALPGFATGEHTKNNAIKLARALGVTFSEIDIGDTARLMLHTIGHPYSVGEKVYDVTFENVQAGLRTDYLFRIANQRGGIVLGTGDLSELALGWSTYGVGDQMSHYNVNAGVPKTLIQHLIRWVISAGEFGEKVGEVLQSVLDTEITPELIPTGEEELQSSEAKVGPFALQDFSLFQVLRYGFRPSKIAFLAWHAWNDAERGNWPPGFPKSERPSYSLAEIRHWLQIFVQRFYSFSQFKRSALPNGPKVSHGGALSPRGDWRAPSDMSARIWLDQIDREVPKG 679
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhh.eeeeeeee......hhhhhhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeee..eeeeeeeeee..eeeeeee.....ee..ee....ee.......eeee..eeee....eeeee......eeeeee.hhhhh..hhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhh..eeeee................eeeee..eeeee........eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.......................hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhh..hhh.eeeee...--------hhhhhhhhhhh.eeee..hhhhhhhhhhhh------------hhhhhhhhhhhhhhhhhhhhhhheeeee..hhhhhhhh............ee.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh-------------hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...........hhhhh...hhhhhhhhhhhhhhhhhh.hhhhhh...........................hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------CN_HYDROLASE  PDB: A:12-276 UniProt: 12-276                                                                                                                                                                                                                              ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sdb A   0 SMNFYSAYQHGFVRVAACTHHTTIGDPAANAASVLDMARACHDDGAALAVFPELTLSGYSIEDVLLQDSLLDAVEDALLDLVTESADLLPVLVVGAPLRHRHRIYNTAVVIHRGAVLGVVPKSYLPTYREFYERRQMAPGDGERGTIRIGGADVAFGTDLLFAASDLPGFVLHVEIAEDMFVPMPPSAEAALAGATVLANLSGSPITIGRAEDRRLLARSASARCLAAYVYAAAGEGESTTDLAWDGQTMIWENGALLAESERFPKGVRRSVADVDTELLRSERLRMGTFDDNRRHHRELTESFRRIDFALDPPAGDIGLLREVERFPFVPADPQRLQQDCYEAYNIQVSGLEQRLRALDYPKVVIGVSGGLDSTHALIVATHAMDREGRPRSDILAFALPG--------NNAIKLARALGVTFSEIDIGDTARLMLHTI------------VTFENVQAGLRTDYLFRIANQRGGIVLGTGDLSELALGWSTYGVGDQMSHYNVNAGVPKTLIQHLIRWVISAGEFGEKVGEVLQSVLDTEIT-------------SEAKVGPFALQDFSLFQVLRYGFRPSKIAFLAWHAWNDAERGNWPPGFPKSERPSYSLAEIRHWLQIFVQRFYSFSQFKRSALPNGPKVSHGGALSPRGDWRAPSDMSARIWLDQIDREVPKG 679
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399 |       -|      419       429       439         -  |    459       469       479       489       499       509       519       529       539   |     -       559       569       579       589       599       609       619       629       639       649       659       669       679
                                                                                                                                                                                                                                                                                                                                                                                                                                           401      410                          439          452                                                                                        543           557                                                                                                                          


Chain A from PDB  Type:PROTEIN  Length:647
 aligned with NADE_MYCTU | P9WJJ3 from UniProtKB/Swiss-Prot  Length:679

    Alignment length:680
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679
           NADE_MYCTU     - -MNFYSAYQHGFVRVAACTHHTTIGDPAANAASVLDMARACHDDGAALAVFPELTLSGYSIEDVLLQDSLLDAVEDALLDLVTESADLLPVLVVGAPLRHRHRIYNTAVVIHRGAVLGVVPKSYLPTYREFYERRQMAPGDGERGTIRIGGADVAFGTDLLFAASDLPGFVLHVEICEDMFVPMPPSAEAALAGATVLANLSGSPITIGRAEDRRLLARSASARCLAAYVYAAAGEGESTTDLAWDGQTMIWENGALLAESERFPKGVRRSVADVDTELLRSERLRMGTFDDNRRHHRELTESFRRIDFALDPPAGDIGLLREVERFPFVPADPQRLQQDCYEAYNIQVSGLEQRLRALDYPKVVIGVSGGLDSTHALIVATHAMDREGRPRSDILAFALPGFATGEHTKNNAIKLARALGVTFSEIDIGDTARLMLHTIGHPYSVGEKVYDVTFENVQAGLRTDYLFRIANQRGGIVLGTGDLSELALGWSTYGVGDQMSHYNVNAGVPKTLIQHLIRWVISAGEFGEKVGEVLQSVLDTEITPELIPTGEEELQSSEAKVGPFALQDFSLFQVLRYGFRPSKIAFLAWHAWNDAERGNWPPGFPKSERPSYSLAEIRHWLQIFVQRFYSFSQFKRSALPNGPKVSHGGALSPRGDWRAPSDMSARIWLDQIDREVPKG 679
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhh.eeeeeeee......hhhhhhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeee..eeeeeeeeee..eeeeeee.....ee..ee....ee.......eeee..eeee....eeeee......eeeeee.hhhhh..hhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhh..eeeee................eeeee..eeeee........eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.......................hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhh..hhh.eeeee...--------hhhhhhhhhhh.eeee..hhhhhhhhhhhh------------hhhhhhhhhhhhhhhhhhhhhhheeeee..hhhhhhhh............ee.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh-------------hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...........hhhhh...hhhhhhhhhhhhhhhhhh.hhhhhh...........................hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------CN_HYDROLASE  PDB: A:12-276 UniProt: 12-276                                                                                                                                                                                                                              ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sdb A   0 SMNFYSAYQHGFVRVAACTHHTTIGDPAANAASVLDMARACHDDGAALAVFPELTLSGYSIEDVLLQDSLLDAVEDALLDLVTESADLLPVLVVGAPLRHRHRIYNTAVVIHRGAVLGVVPKSYLPTYREFYERRQMAPGDGERGTIRIGGADVAFGTDLLFAASDLPGFVLHVEIAEDMFVPMPPSAEAALAGATVLANLSGSPITIGRAEDRRLLARSASARCLAAYVYAAAGEGESTTDLAWDGQTMIWENGALLAESERFPKGVRRSVADVDTELLRSERLRMGTFDDNRRHHRELTESFRRIDFALDPPAGDIGLLREVERFPFVPADPQRLQQDCYEAYNIQVSGLEQRLRALDYPKVVIGVSGGLDSTHALIVATHAMDREGRPRSDILAFALPG--------NNAIKLARALGVTFSEIDIGDTARLMLHTI------------VTFENVQAGLRTDYLFRIANQRGGIVLGTGDLSELALGWSTYGVGDQMSHYNVNAGVPKTLIQHLIRWVISAGEFGEKVGEVLQSVLDTEIT-------------SEAKVGPFALQDFSLFQVLRYGFRPSKIAFLAWHAWNDAERGNWPPGFPKSERPSYSLAEIRHWLQIFVQRFYSFSQFKRSALPNGPKVSHGGALSPRGDWRAPSDMSARIWLDQIDREVPKG 679
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399 |       -|      419       429       439         -  |    459       469       479       489       499       509       519       529       539   |     -       559       569       579       589       599       609       619       629       639       649       659       669       679
                                                                                                                                                                                                                                                                                                                                                                                                                                           401      410                          439          452                                                                                        543           557
   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  (0, 0)

(no "SCOP Domain" information available for 3SDB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SDB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SDB)

(-) Gene Ontology  (12, 19)

Asymmetric Unit(hide GO term definitions)
Chain A   (NADE_MYCTU | P9WJJ3)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003952    NAD+ synthase (glutamine-hydrolyzing) activity    Catalysis of the reaction: ATP + deamido-NAD+ + L-glutamine + H2O = AMP + diphosphate + NAD+ + L-glutamate.
    GO:0008795    NAD+ synthase activity    Catalysis of the reaction: ATP + deamido-NAD+ + NH3 = AMP + diphosphate + NAD+.
    GO:0016810    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds    Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    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.
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:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:0006807    nitrogen compound metabolic process    The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A   (NADE_MYCTO | P9WJJ2)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003952    NAD+ synthase (glutamine-hydrolyzing) activity    Catalysis of the reaction: ATP + deamido-NAD+ + L-glutamine + H2O = AMP + diphosphate + NAD+ + L-glutamate.
    GO:0016810    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds    Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    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.
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:0006807    nitrogen compound metabolic process    The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NADE_MYCTO | P9WJJ2: 3dla 3seq 3sez 3syt 3szg
        NADE_MYCTU | P9WJJ3: 3dla 3seq 3sez 3syt 3szg

(-) Related Entries Specified in the PDB File

3dla THE WILD TYPE PROTEIN BOUND TO DON AND NAAD+
3seq THE C176A MUTANT PROTEIN BOUND TO AMPCPP AND NAAD+
3sez THE C176A MUTANT PROTEIN BOUND TO ATP AND NAAD+