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(-) Description

Title :  CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM STREPTOMYCES AVERMITILIS
 
Authors :  Y. Patskovsky, R. Toro, J. Freeman, J. Do, J. M. Sauder, S. C. Almo, S. K. B York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  13 May 10  (Deposition) - 07 Jul 10  (Release) - 07 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ligase, Structural Genomics, Protein Structure Initiative, Psi, Nysgrc, New York Structural Genomics Research Consortium, Nysgxrc, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, R. Toro, J. Freeman, J. Do, J. M. Sauder, J. A. Gerlt, S. K. Burley, S. C. Almo
Crystal Structure Of Nh3-Dependent Nad+ Synthetase From Streptomyces Avermitilis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NH(3)-DEPENDENT NAD(+) SYNTHETASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NADE, SAV5948, SAV_5948
    Organism Scientific: STREPTOMYCES AVERMITILIS
    Organism Taxid: 33903

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:188 , THR A:197 , ARG A:198 , LEU A:201 , TYR A:215BINDING SITE FOR RESIDUE SO4 A 589
2AC2SOFTWAREARG A:65 , LEU A:68 , ARG A:69 , ASP A:91BINDING SITE FOR RESIDUE SO4 A 590
3AC3SOFTWAREARG A:4 , GLY A:35 , HIS A:37 , TYR A:289 , SER B:95BINDING SITE FOR RESIDUE SO4 A 591
4AC4SOFTWARESER B:188 , THR B:197 , ARG B:198 , LEU B:201 , TYR B:215BINDING SITE FOR RESIDUE SO4 B 589
5AC5SOFTWAREARG B:192 , ALA B:303 , ASP B:304 , VAL B:307 , SER B:462 , ARG B:465BINDING SITE FOR RESIDUE SO4 B 590
6AC6SOFTWARETRP B:469 , ARG B:470 , ARG B:477BINDING SITE FOR RESIDUE SO4 B 591

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N05)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:49 -Pro A:50
2Tyr B:49 -Pro B:50

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N05)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3N05)

(-) Exons   (0, 0)

(no "Exon" information available for 3N05)

(-) 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:568
 aligned with Q82AV7_STRAW | Q82AV7 from UniProtKB/TrEMBL  Length:584

    Alignment length:584
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580    
         Q82AV7_STRAW     1 MPQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSSFVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRVALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGAGLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGEVVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPPSAELRPGQVDTDSLPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREHS 584
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee......hhhhhhhhhhhhhhhhhh....eee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeee..............eeeeeeeee..eeeeeee..........hhhhhh....eeeeeee..eeeeeee.hhhhh..hhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhh.eeeeee.eeee..eeee...eee.....eeee......eeeeeeeee................eeeeee.....................hhhhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.ee....hhhhhhhh..................hhhhhhhhhhhhhhhhhhh......hhhhhh.----------------.hhhhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhhhhhhhhh............................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n05 A   0 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSSFVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRVALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGAGLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGEVVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITK----------------PDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 583
                                     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|        -       509       519       529       539       549       559       569       579    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    490              507                                                                            


Chain B from PDB  Type:PROTEIN  Length:563
 aligned with Q82AV7_STRAW | Q82AV7 from UniProtKB/TrEMBL  Length:584

    Alignment length:584
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580    
         Q82AV7_STRAW     1 MPQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSSFVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRVALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGAGLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGEVVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPPSAELRPGQVDTDSLPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREHS 584
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----CN_hydrolase-3n05B03 B:4-185                                                                                                                                                          -------------------------------------------------------------------------------------------------------------------------NAD_synthase-3n05B01 B:307-556                                                                                                                                                                                                                            --------------------------- Pfam domains (1)
           Pfam domains (2) ----CN_hydrolase-3n05B04 B:4-185                                                                                                                                                          -------------------------------------------------------------------------------------------------------------------------NAD_synthase-3n05B02 B:307-556                                                                                                                                                                                                                            --------------------------- Pfam domains (2)
         Sec.struct. author ....eeeeee......hhhhhhhhhhhhhhhhhh....eee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeee..............eeeeeeeee..eeeeeee..........hhhhhh....eeeeeee..eeeeeee.hhhhh..hhhhhhhh....eeeeee.........hhhhhhhhhhhhhhh.eeeeee.eeee..eeee...eee.....eeee......eeeeee...................eeeeee.....................hhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.ee....hhhhhhhh..-----...........hhhhhhhhhhhhhhhhhh.......hhhhhh.----------------.hhhhhhhhhhhhh....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh............................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n05 B   0 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSSFVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRVALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGAGLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGEVVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYS-----SVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITK----------------PDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 583
                                     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|        -       509       519       529       539       549       559       569       579    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    442   448                                       490              507
   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 3N05)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N05)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: HUP (230)
(-)
Clan: no clan defined [family: CN_hydrolase] (9)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q82AV7_STRAW | Q82AV7)
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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  3n05
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 Related Entries

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