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(-) Description

Title :  CRYSTAL STRUCTURE OF NICOTINATE-NUCLEOTIDE PYROPHOSPHORYLASE FROM EHRLICHIA CHAFFEENSIS AT 2.05A RESOLUTION
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  09 Dec 09  (Deposition) - 22 Dec 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,C  (1x)
Biol. Unit 3:  B,D  (1x)
Keywords :  Ssgcid, Nih, Niaid, Sbri, Uw, Emerald Biostructures, Als Collaborative Crystallography, Ehrlichia Chaffeensis, Nicotinate- Nucleotide Pyrophosphorylase, Glycosyltransferase, Transferase, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Seattle Structural Genomics Center For Infectious Disease (Ssgcid), J. Abendroth, B. Sankaran, T. Arakaki, B. Staker
Crystal Structure Of Nicotinate-Nucleotide Pyrophosphorylas From Ehrlichia Chaffeensis At 2. 05A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NICOTINATE-NUCLEOTIDE PYROPHOSPHORYLASE
    Chains: A, B, C, D
    EC Number: 2.4.2.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NADC, ECH_0026
    Organism Scientific: EHRLICHIA CHAFFEENSIS
    Organism Taxid: 205920
    Strain: ARKANSAS

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (1x): A C 
Biological Unit 3 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2FMT4Ligand/IonFORMIC ACID
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2FMT4Ligand/IonFORMIC ACID
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2FMT2Ligand/IonFORMIC ACID
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2FMT2Ligand/IonFORMIC ACID

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:128 , THR A:129 , TYR A:152 , LEU A:211 , GLU A:234 , HOH A:293 , FMT A:301BINDING SITE FOR RESIDUE EDO A 300
2AC2SOFTWARESER B:128 , THR B:129 , TYR B:152 , GLU B:234 , SER B:256 , FMT B:301 , HOH B:323BINDING SITE FOR RESIDUE EDO B 300
3AC3SOFTWAREARG C:127 , SER C:128 , THR C:129 , TYR C:152 , LEU C:211 , GLU C:234 , SER C:256 , HOH C:290 , FMT C:301BINDING SITE FOR RESIDUE EDO C 300
4AC4SOFTWAREARG D:127 , SER D:128 , THR D:129 , TYR D:152 , LEU D:211 , GLU D:234 , FMT D:301 , HOH D:303BINDING SITE FOR RESIDUE EDO D 300
5AC5SOFTWAREARG A:130 , ARG A:153 , LYS A:163 , EDO A:300 , HOH A:304BINDING SITE FOR RESIDUE FMT A 301
6AC6SOFTWAREARG B:130 , ARG B:153 , LEU B:161 , LYS B:163 , HOH B:293 , EDO B:300BINDING SITE FOR RESIDUE FMT B 301
7AC7SOFTWAREARG C:130 , ARG C:153 , LEU C:161 , LYS C:163 , EDO C:300 , HOH C:347BINDING SITE FOR RESIDUE FMT C 301
8AC8SOFTWAREARG D:130 , ARG D:153 , LYS D:163 , EDO D:300 , HOH D:862BINDING SITE FOR RESIDUE FMT D 301

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1C:238 -C:259
2D:238 -D:259

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu D:274 -Tyr D:275

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L0G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3L0G)

(-) Exons   (0, 0)

(no "Exon" information available for 3L0G)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  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:272
 aligned with Q2GI74_EHRCR | Q2GI74 from UniProtKB/TrEMBL  Length:279

    Alignment length:272
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272  
         Q2GI74_EHRCR     3 ISFSEIIHNALKEDLGDKGDITTNSILINEKVNFAINTRENLVVCGIPILEEVFNMNKEHVKYEIHKKDGDITGKNSTLVSGEALAIYLLPIERVILNFIQHASGIASITRQFVDEVSGTKVKIRSTRKTTPGLRMLDKYSVCIGGGESYRDNLCDGVLIKDNHIASCGSITLAIQRLRKNLKNEYIAIECDNISQVEESLSNNVDMILLDNMSISEIKKAVDIVNGKSVLEVSGCVNIRNVRNIALTGVDYISIGCITNSFQNKDIGLDIE 274
               SCOP domains d3l0ga1 A:3-107 automated matches                                                                        d3l0ga2 A:108-274 automated matches                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------3l0gA02 A:111-263 Aldolase class I                                                                                                                       ----------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh...hhhhhhhh...eeeeeeee...ee..hhhhhhhhhhhh...eeeee......ee....eeeeeeeehhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.....eee........hhhhhhhhhhhh............eeehhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhh...eeeee..hhhhhhhhhhhhh...eeeee......hhhhhhh....eee.hhhh.......eeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l0g A   3 ISFSEIIHNALKEDLGDKGDITTNSILINEKVNFAINTRENLVVCGIPILEEVFNMNKEHVKYEIHKKDGDITGKNSTLVSGEALAIYLLPIERVILNFIQHASGIASITRQFVDEVSGTKVKIRSTRKTTPGLRMLDKYSVCIGGGESYRDNLCDGVLIKDNHIASCGSITLAIQRLRKNLKNEYIAIECDNISQVEESLSNNVDMILLDNMSISEIKKAVDIVNGKSVLEVSGCVNIRNVRNIALTGVDYISIGCITNSFQNKDIGLDIE 274
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272  


Chain B from PDB  Type:PROTEIN  Length:273
 aligned with Q2GI74_EHRCR | Q2GI74 from UniProtKB/TrEMBL  Length:279

    Alignment length:273
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272   
         Q2GI74_EHRCR     3 ISFSEIIHNALKEDLGDKGDITTNSILINEKVNFAINTRENLVVCGIPILEEVFNMNKEHVKYEIHKKDGDITGKNSTLVSGEALAIYLLPIERVILNFIQHASGIASITRQFVDEVSGTKVKIRSTRKTTPGLRMLDKYSVCIGGGESYRDNLCDGVLIKDNHIASCGSITLAIQRLRKNLKNEYIAIECDNISQVEESLSNNVDMILLDNMSISEIKKAVDIVNGKSVLEVSGCVNIRNVRNIALTGVDYISIGCITNSFQNKDIGLDIEY 275
               SCOP domains d3l0gb1 B:3-107 automated matches                                                                        d3l0gb2 B:108-275 automated matches                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------3l0gB02 B:111-263 Aldolase class I                                                                                                                       ------------ CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh...hhhhhhhh...eeeeeeee...ee..hhhhhhhhhhhh...eeeee......ee....eeeeeeeehhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.....eee........hhhhhhhhhhhh............eeehhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhh...eeeee..hhhhhhhhhhhhh...eeeeee.....hhhhhhh....eeee.hhh.......eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l0g B   3 ISFSEIIHNALKEDLGDKGDITTNSILINEKVNFAINTRENLVVCGIPILEEVFNMNKEHVKYEIHKKDGDITGKNSTLVSGEALAIYLLPIERVILNFIQHASGIASITRQFVDEVSGTKVKIRSTRKTTPGLRMLDKYSVCIGGGESYRDNLCDGVLIKDNHIASCGSITLAIQRLRKNLKNEYIAIECDNISQVEESLSNNVDMILLDNMSISEIKKAVDIVNGKSVLEVSGCVNIRNVRNIALTGVDYISIGCITNSFQNKDIGLDIEY 275
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272   


Chain C from PDB  Type:PROTEIN  Length:274
 aligned with Q2GI74_EHRCR | Q2GI74 from UniProtKB/TrEMBL  Length:279

    Alignment length:274
                                    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    
         Q2GI74_EHRCR     1 MKISFSEIIHNALKEDLGDKGDITTNSILINEKVNFAINTRENLVVCGIPILEEVFNMNKEHVKYEIHKKDGDITGKNSTLVSGEALAIYLLPIERVILNFIQHASGIASITRQFVDEVSGTKVKIRSTRKTTPGLRMLDKYSVCIGGGESYRDNLCDGVLIKDNHIASCGSITLAIQRLRKNLKNEYIAIECDNISQVEESLSNNVDMILLDNMSISEIKKAVDIVNGKSVLEVSGCVNIRNVRNIALTGVDYISIGCITNSFQNKDIGLDIE 274
               SCOP domains d3l0gc1 C:1-107 automated matches                                                                          d3l0gc2 C:108-274 automated matches                                                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------3l0gC02 C:111-263 Aldolase class I                                                                                                                       ----------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh...hhhhhhhh...eeeeeeee...ee..hhhhhhhhhhhh...eeeee......ee....eeeeeeeehhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.....eee........hhhhhhhhhhhh............eeehhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhh...eeeee..hhhhhhhhhhhhh...eeeee...hhhhhhhhhh....eee.hhhh.......eeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l0g C   1 MKISFSEIIHNALKEDLGDKGDITTNSILINEKVNFAINTRENLVVCGIPILEEVFNMNKEHVKYEIHKKDGDITGKNSTLVSGEALAIYLLPIERVILNFIQHASGIASITRQFVDEVSGTKVKIRSTRKTTPGLRMLDKYSVCIGGGESYRDNLCDGVLIKDNHIASCGSITLAIQRLRKNLKNEYIAIECDNISQVEESLSNNVDMILLDNMSISEIKKAVDIVNGKSVLEVSGCVNIRNVRNIALTGVDYISIGCITNSFQNKDIGLDIE 274
                                    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    


Chain D from PDB  Type:PROTEIN  Length:274
 aligned with Q2GI74_EHRCR | Q2GI74 from UniProtKB/TrEMBL  Length:279

    Alignment length:274
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    
         Q2GI74_EHRCR     2 KISFSEIIHNALKEDLGDKGDITTNSILINEKVNFAINTRENLVVCGIPILEEVFNMNKEHVKYEIHKKDGDITGKNSTLVSGEALAIYLLPIERVILNFIQHASGIASITRQFVDEVSGTKVKIRSTRKTTPGLRMLDKYSVCIGGGESYRDNLCDGVLIKDNHIASCGSITLAIQRLRKNLKNEYIAIECDNISQVEESLSNNVDMILLDNMSISEIKKAVDIVNGKSVLEVSGCVNIRNVRNIALTGVDYISIGCITNSFQNKDIGLDIEY 275
               SCOP domains d3l0gd1 D:2-107 automated matches                                                                         d3l0gd2 D:108-275 automated matches                                                                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------3l0gD02 D:111-263 Aldolase class I                                                                                                                       ------------ CATH domains
           Pfam domains (1) ----------------QRPTase_N-3l0gD01 D:18-106                                                               -QRPTase_C-3l0gD05 D:108-272                                                                                                                                          --- Pfam domains (1)
           Pfam domains (2) ----------------QRPTase_N-3l0gD02 D:18-106                                                               -QRPTase_C-3l0gD06 D:108-272                                                                                                                                          --- Pfam domains (2)
           Pfam domains (3) ----------------QRPTase_N-3l0gD03 D:18-106                                                               -QRPTase_C-3l0gD07 D:108-272                                                                                                                                          --- Pfam domains (3)
           Pfam domains (4) ----------------QRPTase_N-3l0gD04 D:18-106                                                               -QRPTase_C-3l0gD08 D:108-272                                                                                                                                          --- Pfam domains (4)
         Sec.struct. author ...hhhhhhhhhhhhhh...hhhhhhhh...eeeeeeee...ee..hhhhhhhhhhh....eeeee......ee....eeeeeeeehhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.....eee........hhhhhhhhhhhh............eeehhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhh...eeeee..hhhhhhhhhhhhh...eeeee......hhhhhhhh...eee.hhhh.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l0g D   2 KISFSEIIHNALKEDLGDKGDITTNSILINEKVNFAINTRENLVVCGIPILEEVFNMNKEHVKYEIHKKDGDITGKNSTLVSGEALAIYLLPIERVILNFIQHASGIASITRQFVDEVSGTKVKIRSTRKTTPGLRMLDKYSVCIGGGESYRDNLCDGVLIKDNHIASCGSITLAIQRLRKNLKNEYIAIECDNISQVEESLSNNVDMILLDNMSISEIKKAVDIVNGKSVLEVSGCVNIRNVRNIALTGVDYISIGCITNSFQNKDIGLDIEY 275
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271
   Legend:   → Mismatch (orange background)
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  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  (2, 8)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (2, 8)

Asymmetric Unit
(-)
Clan: Hybrid (58)
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q2GI74_EHRCR | Q2GI74)
molecular function
    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:0004514    nicotinate-nucleotide diphosphorylase (carboxylating) activity    Catalysis of the reaction: CO(2) + diphosphate + nicotinate D-ribonucleotide = 5-phospho-alpha-D-ribose 1-diphosphate + 2 H(+) + quinolinate.
    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.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
    GO:0016763    transferase activity, transferring pentosyl groups    Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor).
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: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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