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(-) Description

Title :  THE CRYSTAL STRUCTURE OF NICOTINATE PHOSPHORIBOSYLTRANSFERASE FROM YERSINIA PESTIS
 
Authors :  N. Maltseva, Y. Kim, M. Gu, W. F. Anderson, A. Joachimiak, Center For S Genomics Of Infectious Diseases (Csgid)
Date :  08 Sep 10  (Deposition) - 22 Sep 10  (Release) - 22 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Tim Barrel, Cytosol, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Maltseva, Y. Kim, M. Gu, W. F. Anderson, A. Joachimiak
The Crystal Structure Of Nicotinate Phosphoribosyltransferase From Yersinia Pestis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NICOTINATE PHOSPHORIBOSYLTRANSFERASE
    Chains: A, B
    EC Number: 2.4.2.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG28
    Expression System Strain: BL21 MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PNCB, Y2757, YPO1413, YP_1180
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 214092
    Strain: CO92
    Synonym: NAPRTASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 31)

Asymmetric Unit (7, 31)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2CL5Ligand/IonCHLORIDE ION
3FMT3Ligand/IonFORMIC ACID
4GOL5Ligand/IonGLYCEROL
5MG2Ligand/IonMAGNESIUM ION
6MSE12Mod. Amino AcidSELENOMETHIONINE
7PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (5, 13)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2CL-1Ligand/IonCHLORIDE ION
3FMT2Ligand/IonFORMIC ACID
4GOL2Ligand/IonGLYCEROL
5MG-1Ligand/IonMAGNESIUM ION
6MSE6Mod. Amino AcidSELENOMETHIONINE
7PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (4, 11)
No.NameCountTypeFull Name
1ACY-1Ligand/IonACETIC ACID
2CL-1Ligand/IonCHLORIDE ION
3FMT1Ligand/IonFORMIC ACID
4GOL3Ligand/IonGLYCEROL
5MG-1Ligand/IonMAGNESIUM ION
6MSE6Mod. Amino AcidSELENOMETHIONINE
7PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:239 , ASP A:271 , HOH A:542 , HOH A:666 , HOH A:902 , HOH A:927BINDING SITE FOR RESIDUE MG A 410
02AC2SOFTWAREVAL A:216 , GLY A:217 , FMT A:414 , HOH A:676 , HOH A:878 , HOH B:652BINDING SITE FOR RESIDUE GOL A 411
03AC3SOFTWAREGLN A:3 , SER A:6 , PRO A:7 , GLU A:300 , GLY A:303 , ASP A:305 , HOH A:514 , HOH A:573 , HOH A:680 , HOH A:729 , HOH A:731BINDING SITE FOR RESIDUE PEG A 412
04AC4SOFTWAREMSE A:172 , THR A:218 , ARG A:282 , GOL A:411 , HOH A:693 , HOH A:937BINDING SITE FOR RESIDUE FMT A 414
05AC5SOFTWAREASP A:83 , ILE A:289 , GLU A:290 , GLU A:293 , HOH A:697BINDING SITE FOR RESIDUE ACY A 415
06AC6SOFTWAREGLU A:45 , LEU A:47 , LEU A:107 , HOH A:686BINDING SITE FOR RESIDUE CL A 417
07AC7SOFTWAREALA A:37 , VAL A:118 , ILE A:119 , TRP A:121 , GLU A:122 , GLU A:222 , ILE A:357 , LYS A:358 , LEU A:359 , HOH A:796BINDING SITE FOR RESIDUE GOL A 418
08AC8SOFTWAREARG A:182 , HIS A:186 , HOH A:747 , HOH A:808 , HOH A:918BINDING SITE FOR RESIDUE CL A 419
09AC9SOFTWARELYS A:153 , ASP A:318 , LEU A:319 , ILE A:339 , ARG A:342BINDING SITE FOR RESIDUE CL A 420
10BC1SOFTWAREARG A:92 , LYS A:94 , PEG A:422 , HOH A:692 , HOH A:801 , HOH A:860BINDING SITE FOR RESIDUE FMT A 421
11BC2SOFTWAREGLY A:62 , ARG A:92 , PHE A:93 , FMT A:421 , HOH A:746 , HOH A:859BINDING SITE FOR RESIDUE PEG A 422
12BC3SOFTWAREMSE B:172 , GLY B:217 , THR B:218 , ILE B:255 , ARG B:282 , HOH B:568 , HOH B:674 , HOH B:675BINDING SITE FOR RESIDUE PEG B 410
13BC4SOFTWAREGLN A:229 , PRO A:366 , GLN A:387 , ARG B:136 , HOH B:786BINDING SITE FOR RESIDUE GOL B 411
14BC5SOFTWAREGLN A:148 , HOH A:605 , HOH A:706 , GLN B:243 , PHE B:274 , ARG B:277 , HOH B:472BINDING SITE FOR RESIDUE GOL B 412
15BC6SOFTWARELEU B:47 , LYS B:106 , LEU B:107 , HOH B:687BINDING SITE FOR RESIDUE CL B 415
16BC7SOFTWAREASP A:194 , GLU B:361 , ASP B:364BINDING SITE FOR RESIDUE FMT B 416
17BC8SOFTWARELYS B:19 , VAL B:118 , ILE B:119 , TRP B:121 , GLU B:122 , GLU B:222 , ILE B:357 , LYS B:358 , LEU B:359 , HOH B:795BINDING SITE FOR RESIDUE GOL B 417
18BC9SOFTWARETYR B:30 , ARG B:31 , HIS B:32 , HOH B:797BINDING SITE FOR RESIDUE CL B 418
19CC1SOFTWARESER B:75 , HOH B:501 , HOH B:671 , HOH B:690 , HOH B:870BINDING SITE FOR RESIDUE MG B 419

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OS4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OS4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OS4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OS4)

(-) Exons   (0, 0)

(no "Exon" information available for 3OS4)

(-) Sequences/Alignments

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:393
 aligned with PNCB_YERPE | Q8ZG93 from UniProtKB/Swiss-Prot  Length:401

    Alignment length:393
                                    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       282       292       302       312       322       332       342       352       362       372       382       392   
           PNCB_YERPE     3 QDASPILTSLLDTDAYKLHMQQAVFHHYRHITVAAEFRCRSDELLGVYADEIRHQVTLMGQLALTSDEFIYLSSLPFFQDDYLHWLRDFRFKPEQVSVAVHDGKLDIRIAGLWCEVIMWEVPLLAVISEIVHRRRSTQVTTDQAVQQLRTKLEQFNALSADIDITHFKLMDFGTRRRFSREIQHTVVSTLKDEFPYLVGTSNYDLARTLALAPVGTQAHEWFQAHQQISPTLANSQRVALQVWLDEYPNQLGIALTDCITMDAFLRDFDLAFANRYQGLRHDSGDPIEWGEKAIAHYEKLGIDPMKKVLVFSDNLDLEKALFLYRHFYQRIKLVFGIGTRLTCDIPDVKPLNIVIKLVECNDKPVAKLSDSPGKTICQDPAFVDQLRKAFALP 395
               SCOP domains d3os4a1 A:3-140 automated matches                                                                                                         d3os4a2 A:141-395 automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhh...eeeeeeee.....hhhhhhhhhhhhhhhh....hhhhhhhhhh....hhhhhhhhhhh..hhh.eeeeee..eeeeeeeeehhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.........eee.......hhhhhhhhhhhhhhhh..eeee.hhhhhhhhh.......hhhhhhhhh....hhhhhhhhhhhhhhhhh.....eee....hhhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhh..hhhh.eeee....hhhhhhhhhhhhh...eeeeeehhhhhh.........eeeeeeee..ee..............hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3os4 A   3 QDASPILTSLLDTDAYKLHmQQAVFHHYRHITVAAEFRCRSDELLGVYADEIRHQVTLmGQLALTSDEFIYLSSLPFFQDDYLHWLRDFRFKPEQVSVAVHDGKLDIRIAGLWCEVImWEVPLLAVISEIVHRRRSTQVTTDQAVQQLRTKLEQFNALSADIDITHFKLmDFGTRRRFSREIQHTVVSTLKDEFPYLVGTSNYDLARTLALAPVGTQAHEWFQAHQQISPTLANSQRVALQVWLDEYPNQLGIALTDCITmDAFLRDFDLAFANRYQGLRHDSGDPIEWGEKAIAHYEKLGIDPmKKVLVFSDNLDLEKALFLYRHFYQRIKLVFGIGTRLTCDIPDVKPLNIVIKLVECNDKPVAKLSDSPGKTICQDPAFVDQLRKAFALP 395
                                    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       282       292       302    |  312       322       332       342       352       362       372       382       392   
                                              22-MSE                                 61-MSE                                                    120-MSE                                             172-MSE                                                                                    263-MSE                                     307-MSE                                                                                    


Chain B from PDB  Type:PROTEIN  Length:365
 aligned with PNCB_YERPE | Q8ZG93 from UniProtKB/Swiss-Prot  Length:401

    Alignment length:365
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363     
           PNCB_YERPE     4 DASPILTSLLDTDAYKLHMQQAVFHHYRHITVAAEFRCRSDELLGVYADEIRHQVTLMGQLALTSDEFIYLSSLPFFQDDYLHWLRDFRFKPEQVSVAVHDGKLDIRIAGLWCEVIMWEVPLLAVISEIVHRRRSTQVTTDQAVQQLRTKLEQFNALSADIDITHFKLMDFGTRRRFSREIQHTVVSTLKDEFPYLVGTSNYDLARTLALAPVGTQAHEWFQAHQQISPTLANSQRVALQVWLDEYPNQLGIALTDCITMDAFLRDFDLAFANRYQGLRHDSGDPIEWGEKAIAHYEKLGIDPMKKVLVFSDNLDLEKALFLYRHFYQRIKLVFGIGTRLTCDIPDVKPLNIVIKLVECNDKPVA 368
               SCOP domains d3os4b1 B:4-140 automated matches                                                                                                        d3os4b2 B:141-368 automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------NAPRTase-3os4B01 B:169-368                                                                                                                                                                               Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------NAPRTase-3os4B02 B:169-368                                                                                                                                                                               Pfam domains (2)
         Sec.struct. author ............hhhhhhhhhhhhhhh...eeeeeeee.....hhhhhhhhhhhhhhhh....hhhhhhhhhh....hhhhhhhhhh...hhh.eeeeee..eeeeeeeeehhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh........eee.......hhhhhhhhhhhhhhhh..eeee.hhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhhhh.....eee....hhhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhh.hhhh.eeee....hhhhhhhhhhhhh...eeeeeehhhhhh.........eeeeeeee..ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3os4 B   4 DASPILTSLLDTDAYKLHmQQAVFHHYRHITVAAEFRCRSDELLGVYADEIRHQVTLmGQLALTSDEFIYLSSLPFFQDDYLHWLRDFRFKPEQVSVAVHDGKLDIRIAGLWCEVImWEVPLLAVISEIVHRRRSTQVTTDQAVQQLRTKLEQFNALSADIDITHFKLmDFGTRRRFSREIQHTVVSTLKDEFPYLVGTSNYDLARTLALAPVGTQAHEWFQAHQQISPTLANSQRVALQVWLDEYPNQLGIALTDCITmDAFLRDFDLAFANRYQGLRHDSGDPIEWGEKAIAHYEKLGIDPmKKVLVFSDNLDLEKALFLYRHFYQRIKLVFGIGTRLTCDIPDVKPLNIVIKLVECNDKPVA 368
                                    13        23        33        43        53       |63        73        83        93       103       113      |123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303   |   313       323       333       343       353       363     
                                             22-MSE                                 61-MSE                                                    120-MSE                                             172-MSE                                                                                    263-MSE                                     307-MSE
   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  (2, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OS4)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PNCB_YERPE | Q8ZG93)
molecular function
    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:0004516    nicotinate phosphoribosyltransferase activity    Catalysis of the reaction: diphosphate + nicotinate D-ribonucleotide = 5-phospho-alpha-D-ribose 1-diphosphate + H(+) + nicotinate.
    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.
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:0019357    nicotinate nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of nicotinamide nucleotides, any nucleotide that contains combined nicotinate (pyridine 3-carboxylic acid).
    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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