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(-) Description

Title :  ATP PHOSPHORIBOSYLTRANSFERASE (ATP-PRTASE) FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH AMP AND HISTIDINE
 
Authors :  Y. Cho, V. Sharma, J. C. Sacchettini, Tb Structural Genomics Consor (Tbsgc)
Date :  18 Dec 02  (Deposition) - 11 Feb 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (6x)
Keywords :  Prtase, De Novo His Biosynthesis, Prpp, Transferase, Phosphoribosyltransferase, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Cho, V. Sharma, J. C. Sacchettini
Crystal Structure Of Atp Phosphoribosyltransferase From Mycobacterium Tuberculosis
J. Biol. Chem. V. 278 8333 2003
PubMed-ID: 12511575  |  Reference-DOI: 10.1074/JBC.M212124200

(-) Compounds

Molecule 1 - ATP PHOSPHORIBOSYLTRANSFERASE
    Chains: A
    EC Number: 2.4.2.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET2A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS H37RV
    Organism Taxid: 83332
    Strain: H37RV

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A
Biological Unit 2 (6x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2HIS1Mod. Amino AcidHISTIDINE
3SO43Ligand/IonSULFATE ION
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2HIS2Mod. Amino AcidHISTIDINE
3SO46Ligand/IonSULFATE ION
Biological Unit 2 (3, 30)
No.NameCountTypeFull Name
1AMP6Ligand/IonADENOSINE MONOPHOSPHATE
2HIS6Mod. Amino AcidHISTIDINE
3SO418Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:175 , ASP A:176BINDING SITE FOR RESIDUE SO4 A 285
2AC2SOFTWAREALA A:108 , GLY A:109 , MET A:110 , ASP A:150 , HOH A:3117 , HOH A:3208 , HOH A:3209BINDING SITE FOR RESIDUE SO4 A 286
3AC3SOFTWAREARG A:121 , ARG A:135 , HOH A:3093 , HOH A:3147 , HOH A:3153BINDING SITE FOR RESIDUE SO4 A 287
4AC4SOFTWAREASP A:30 , TYR A:116 , VAL A:155 , GLY A:157 , SER A:158 , GLY A:159 , ARG A:160 , THR A:161 , HOH A:3096 , HOH A:3126 , HOH A:3146BINDING SITE FOR RESIDUE AMP A 288
5AC5SOFTWARETYR A:217 , ASP A:218 , GLY A:233 , LEU A:234 , SER A:236 , THR A:238 , LEU A:242 , ARG A:251 , LEU A:253 , ALA A:273 , LEU A:275 , HOH A:3161BINDING SITE FOR RESIDUE HIS A 289

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NH8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NH8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NH8)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ATP_P_PHORIBOSYLTRPS01316 ATP phosphoribosyltransferase signature.HIS1_MYCTO141-162  1A:141-162
HIS1_MYCTU141-162  1A:141-162
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ATP_P_PHORIBOSYLTRPS01316 ATP phosphoribosyltransferase signature.HIS1_MYCTO141-162  2A:141-162
HIS1_MYCTU141-162  2A:141-162
Biological Unit 2 (1, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ATP_P_PHORIBOSYLTRPS01316 ATP phosphoribosyltransferase signature.HIS1_MYCTO141-162  6A:141-162
HIS1_MYCTU141-162  6A:141-162

(-) Exons   (0, 0)

(no "Exon" information available for 1NH8)

(-) 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:277
 aligned with HIS1_MYCTO | P9WMN0 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:285
                                                                                                                                                                                                                                                                                                                     284 
                                    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   | 
           HIS1_MYCTO     1 MLRVAVPNKGALSEPATEILAEAGYRRRTDSKDLTVIDPVNNVEFFFLRPKDIAIYVGSGELDFGITGRDLVCDSGAQVRERLALGFGSSSFRYAAPAGRNWTTADLAGMRIATAYPNLVRKDLATKGIEATVIRLDGAVEISVQLGVADAIADVVGSGRTLSQHDLVAFGEPLCDSEAVLIERAGTDGQDQTEARDQLVARVQGVVFGQQYLMLDYDCPRSALKKATAITPGLESPTIAPLADPDWVAIRALVPRRDVNGIMDELAAIGAKAILASDIRFCRF-   -
               SCOP domains d1nh8a1 A:1-210 ATP phosphoribosyltransferase (ATP-PRTase, HisG), catalytic domain                                                                                                                                d1nh8a2 A:211-284                                                         - SCOP domains
               CATH domains 1nh8A01 A:1-84,A:179-211 Periplasmic binding protein-like II                        ------1nh8A02 A:91-176 Periplasmic binding protein-like II                                  --1nh8A01         A:1-84,A:179-211 1nh8A03 A:212-278  [code=3.30.70.120, no name defined]             ------- CATH domains
               Pfam domains -----------------------------------------------HisG-1nh8A02 A:48-207                                                                                                                                           HisG_C-1nh8A01 A:208-282                                                   --- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhh...........eeee....eeeeeehhhhhhhhhhhh...eeeeehhhhhhhh..eeeeee.....eeeeeeee.....hhhhhh..eeee.hhhhhhhhhhhhh...eeee.....hhhhhh....eeeeee..hhhhhhh.eeeeeeeeeee.eeeeee.--------hhhhhhhhhhhhhhhhh.eeeeeeeee..hhhhhhhhh......eeee.....eeeeeeeee..hhhhhhhhhhhh..eeeeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------ATP_P_PHORIBOSYLTR    --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nh8 A   1 MLRVAVPNKGALSEPATEILAEAGYRRRTDSKDLTVIDPVNNVEFFFLRPKDIAIYVGSGELDFGITGRDLVCDSGAQVRERLALGFGSSSFRYAAPAGRNWTTADLAGMRIATAYPNLVRKDLATKGIEATVIRLDGAVEISVQLGVADAIADVVGSGRTLSQHDLVAFGEPLCDSEAVLIERA--------EARDQLVARVQGVVFGQQYLMLDYDCPRSALKKATAITPGLESPTIAPLADPDWVAIRALVPRRDVNGIMDELAAIGAKAILASDIRFCRFH 289
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    |    -   |   200       210       220       230       240       250       260       270       280   ||
                                                                                                                                                                                                                  185      194                                                                                       284|
                                                                                                                                                                                                                                                                                                                      289


Chain A from PDB  Type:PROTEIN  Length:277
 aligned with HIS1_MYCTU | P9WMN1 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:285
                                                                                                                                                                                                                                                                                                                     284 
                                    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   | 
           HIS1_MYCTU     1 MLRVAVPNKGALSEPATEILAEAGYRRRTDSKDLTVIDPVNNVEFFFLRPKDIAIYVGSGELDFGITGRDLVCDSGAQVRERLALGFGSSSFRYAAPAGRNWTTADLAGMRIATAYPNLVRKDLATKGIEATVIRLDGAVEISVQLGVADAIADVVGSGRTLSQHDLVAFGEPLCDSEAVLIERAGTDGQDQTEARDQLVARVQGVVFGQQYLMLDYDCPRSALKKATAITPGLESPTIAPLADPDWVAIRALVPRRDVNGIMDELAAIGAKAILASDIRFCRF-   -
               SCOP domains d1nh8a1 A:1-210 ATP phosphoribosyltransferase (ATP-PRTase, HisG), catalytic domain                                                                                                                                d1nh8a2 A:211-284                                                         - SCOP domains
               CATH domains 1nh8A01 A:1-84,A:179-211 Periplasmic binding protein-like II                        ------1nh8A02 A:91-176 Periplasmic binding protein-like II                                  --1nh8A01         A:1-84,A:179-211 1nh8A03 A:212-278  [code=3.30.70.120, no name defined]             ------- CATH domains
               Pfam domains -----------------------------------------------HisG-1nh8A02 A:48-207                                                                                                                                           HisG_C-1nh8A01 A:208-282                                                   --- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhh...........eeee....eeeeeehhhhhhhhhhhh...eeeeehhhhhhhh..eeeeee.....eeeeeeee.....hhhhhh..eeee.hhhhhhhhhhhhh...eeee.....hhhhhh....eeeeee..hhhhhhh.eeeeeeeeeee.eeeeee.--------hhhhhhhhhhhhhhhhh.eeeeeeeee..hhhhhhhhh......eeee.....eeeeeeeee..hhhhhhhhhhhh..eeeeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------ATP_P_PHORIBOSYLTR    --------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nh8 A   1 MLRVAVPNKGALSEPATEILAEAGYRRRTDSKDLTVIDPVNNVEFFFLRPKDIAIYVGSGELDFGITGRDLVCDSGAQVRERLALGFGSSSFRYAAPAGRNWTTADLAGMRIATAYPNLVRKDLATKGIEATVIRLDGAVEISVQLGVADAIADVVGSGRTLSQHDLVAFGEPLCDSEAVLIERA--------EARDQLVARVQGVVFGQQYLMLDYDCPRSALKKATAITPGLESPTIAPLADPDWVAIRALVPRRDVNGIMDELAAIGAKAILASDIRFCRFH 289
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    |    -   |   200       210       220       230       240       250       260       270       280   ||
                                                                                                                                                                                                                  185      194                                                                                       284|
                                                                                                                                                                                                                                                                                                                      289
   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, 2)

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

(-) CATH Domains  (2, 3)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: GlnB-like (50)
(-)
Clan: PBP (391)

(-) Gene Ontology  (14, 24)

Asymmetric Unit(hide GO term definitions)
Chain A   (HIS1_MYCTU | P9WMN1)
molecular function
    GO:0016208    AMP binding    Interacting selectively and non-covalently with AMP, adenosine monophosphate.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003879    ATP phosphoribosyltransferase activity    Catalysis of the reaction: 1-(5-phospho-D-ribosyl)-ATP + diphosphate = ATP + 5-phospho-alpha-D-ribose 1-diphosphate.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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).
biological process
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:0000105    histidine biosynthetic process    The chemical reactions and pathways resulting in the formation of histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.
cellular component
    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   (HIS1_MYCTO | P9WMN0)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003879    ATP phosphoribosyltransferase activity    Catalysis of the reaction: 1-(5-phospho-D-ribosyl)-ATP + diphosphate = ATP + 5-phospho-alpha-D-ribose 1-diphosphate.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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).
biological process
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0000105    histidine biosynthetic process    The chemical reactions and pathways resulting in the formation of histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  1nh8
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 Related Entries

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

UniProtKB/Swiss-Prot
        HIS1_MYCTO | P9WMN0: 1nh7
        HIS1_MYCTU | P9WMN1: 1nh7 5lht 5lhu

(-) Related Entries Specified in the PDB File

1nh7 RELATED ID: RV2121C RELATED DB: TARGETDB