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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE GMP SYNTHASE SUBUNIT A PROTEIN (TA0944M) FROM THERMOPLASMA ACIDOPHILUM AT 2.45 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  12 Jul 05  (Deposition) - 02 Aug 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of (Np_394403. 1) From Thermoplasma Acidophilum At 2. 45 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GMP SYNTHASE
    Chains: A, B, C, D
    EC Number: 6.3.5.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GUAAA
    Organism Scientific: THERMOPLASMA ACIDOPHILUM
    Organism Taxid: 2303
    Synonym: GLUTAMINE AMIDOTRANSFERASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 21)

Asymmetric Unit (4, 21)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL7Ligand/IonGLYCEROL
3MSE8Mod. Amino AcidSELENOMETHIONINE
4SCN5Ligand/IonTHIOCYANATE ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3MSE2Mod. Amino AcidSELENOMETHIONINE
4SCN1Ligand/IonTHIOCYANATE ION
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3MSE2Mod. Amino AcidSELENOMETHIONINE
4SCN1Ligand/IonTHIOCYANATE ION
Biological Unit 3 (3, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3MSE2Mod. Amino AcidSELENOMETHIONINE
4SCN2Ligand/IonTHIOCYANATE ION
Biological Unit 4 (3, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL3Ligand/IonGLYCEROL
3MSE2Mod. Amino AcidSELENOMETHIONINE
4SCN1Ligand/IonTHIOCYANATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU B:17 , HOH B:546BINDING SITE FOR RESIDUE CL B 501
02AC2SOFTWARELYS A:157 , HIS C:99BINDING SITE FOR RESIDUE SCN A 201
03AC3SOFTWARESER B:146 , HOH B:518 , HIS D:111BINDING SITE FOR RESIDUE SCN D 201
04AC4SOFTWAREHIS B:111 , LEU B:142 , SER D:108 , SER D:145 , SER D:146 , ALA D:147 , HOH D:238BINDING SITE FOR RESIDUE SCN B 502
05AC5SOFTWARELEU C:142 , LYS C:157BINDING SITE FOR RESIDUE SCN C 201
06AC6SOFTWAREHIS B:156 , LYS B:157 , THR B:158 , ARG B:159 , TYR B:162 , TRP C:13BINDING SITE FOR RESIDUE SCN C 202
07AC7SOFTWAREGLN B:12 , TRP B:13 , ASN C:114 , HIS C:156 , THR C:158 , ARG C:159 , TYR C:162 , HOH C:221BINDING SITE FOR RESIDUE GOL C 203
08AC8SOFTWAREVAL D:6 , ASP D:8 , GLN D:12 , HIS D:15 , GLU D:17 , TRP D:18 , SER D:49BINDING SITE FOR RESIDUE GOL D 202
09AC9SOFTWAREASN A:114 , HIS A:156 , ARG A:159 , TYR A:162 , HOH A:256 , GLN D:12 , TRP D:13 , GOL D:204 , HOH D:215BINDING SITE FOR RESIDUE GOL A 202
10BC1SOFTWAREGLN A:12 , TRP A:13 , ASN D:114 , HIS D:156 , LYS D:157 , THR D:158 , ARG D:159 , TYR D:162BINDING SITE FOR RESIDUE GOL D 203
11BC2SOFTWAREGLY C:11 , GLN C:12 , THR C:14 , ARG C:16 , GLU C:17 , GLU C:169BINDING SITE FOR RESIDUE GOL C 204
12BC3SOFTWAREGLN B:150 , ILE D:134 , ASN D:135 , LEU D:136 , GLN D:150BINDING SITE FOR RESIDUE GOL B 503
13BC4SOFTWAREGLU A:113 , TYR A:155 , GOL A:202 , HOH A:205 , ARG D:16 , VAL D:170 , GLU D:171 , HIS D:172BINDING SITE FOR RESIDUE GOL D 204

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2A9V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2A9V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A9V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2A9V)

(-) Exons   (0, 0)

(no "Exon" information available for 2A9V)

(-) 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:199
 aligned with GUAAA_THEAC | Q9HJM3 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:199
                               1                                                                                                                                                                                                   
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187         
          GUAAA_THEAC     - ---MLKIYVVDNGGQWTHREWRVLRELGVDTKIVPNDIDSSELDGLDGLVLSGGAPNIDEELDKLGSVGKYIDDHNYPILGICVGAQFIALHFGASVVKAKHPEFGKTKVSVMHSENIFGGLPSEITVWENHNDEIINLPDDFTLAASSATCQVQGFYHKTRPIYATQFHPEVEHTQYGRDIFRNFIGICASYREIQKE 196
               SCOP domains ---d2a9va1 A:1-196 GMP synthase subunit A, GuaAA                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee......hhhhhhhhhh.....eee...hhhhhh...eeee.....hhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhh..eeeeeeeeeeeeeeeee...hhhhh....eeeeeeeeeeeee.....eeeeee.......eeee....eeee..........hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a9v A  -2 HHHmLKIYVVDNGGQWTHREWRVLRELGVDTKIVPNDIDSSELDGLDGLVLSGGAPNIDEELDKLGSVGKYIDDHNYPILGICVGAQFIALHFGASVVKAKHPEFGKTKVSVmHSENIFGGLPSEITVWENHNDEIINLPDDFTLAASSATCQVQGFYHKTRPIYATQFHPEVEHTQYGRDIFRNFIGICASYREIQKE 196
                               |     7        17        27        37        47        57        67        77        87        97       107  |    117       127       137       147       157       167       177       187         
                               |                                                                                                          110-MSE                                                                                  
                               1-MSE                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:197
 aligned with GUAAA_THEAC | Q9HJM3 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:197
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       
          GUAAA_THEAC     1 MLKIYVVDNGGQWTHREWRVLRELGVDTKIVPNDIDSSELDGLDGLVLSGGAPNIDEELDKLGSVGKYIDDHNYPILGICVGAQFIALHFGASVVKAKHPEFGKTKVSVMHSENIFGGLPSEITVWENHNDEIINLPDDFTLAASSATCQVQGFYHKTRPIYATQFHPEVEHTQYGRDIFRNFIGICASYREIQKEN 197
               SCOP domains d2a9vb_ B: GMP synthase subunit A, GuaAA                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......hhhhhhhhhh.....eee...hhhhhh...eeee.....hhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhh..eeeeeeeeeeeeeeeee...hhhhh....eeeeeeeeeeeee.....eeeeee.......eeee....eeee..........hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a9v B   1 mLKIYVVDNGGQWTHREWRVLRELGVDTKIVPNDIDSSELDGLDGLVLSGGAPNIDEELDKLGSVGKYIDDHNYPILGICVGAQFIALHFGASVVKAKHPEFGKTKVSVmHSENIFGGLPSEITVWENHNDEIINLPDDFTLAASSATCQVQGFYHKTRPIYATQFHPEVEHTQYGRDIFRNFIGICASYREIQKEN 197
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       
                            1-MSE                                                                                                      110-MSE                                                                                   


Chain C from PDB  Type:PROTEIN  Length:199
 aligned with GUAAA_THEAC | Q9HJM3 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:199
                             1                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189         
          GUAAA_THEAC     - -MLKIYVVDNGGQWTHREWRVLRELGVDTKIVPNDIDSSELDGLDGLVLSGGAPNIDEELDKLGSVGKYIDDHNYPILGICVGAQFIALHFGASVVKAKHPEFGKTKVSVMHSENIFGGLPSEITVWENHNDEIINLPDDFTLAASSATCQVQGFYHKTRPIYATQFHPEVEHTQYGRDIFRNFIGICASYREIQKENF 198
               SCOP domains d2a9vc_ C: GMP synthase subunit A, GuaAA                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee......hhhhhhhhhh.....eee...hhhhhh...eeee.....hhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhh..eeeeeeeeeeeeeeeee...hhhhh....eeeeeeeeeeeee.....eeeeee.......eeee....eeee..........hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a9v C   0 HmLKIYVVDNGGQWTHREWRVLRELGVDTKIVPNDIDSSELDGLDGLVLSGGAPNIDEELDKLGSVGKYIDDHNYPILGICVGAQFIALHFGASVVKAKHPEFGKTKVSVmHSENIFGGLPSEITVWENHNDEIINLPDDFTLAASSATCQVQGFYHKTRPIYATQFHPEVEHTQYGRDIFRNFIGICASYREIQKENF 198
                             |       9        19        29        39        49        59        69        79        89        99       109|      119       129       139       149       159       169       179       189         
                             1-MSE                                                                                                      110-MSE                                                                                    


Chain D from PDB  Type:PROTEIN  Length:201
 aligned with GUAAA_THEAC | Q9HJM3 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:201
                               1                                                                                                                                                                                                     
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197 
          GUAAA_THEAC     - ---MLKIYVVDNGGQWTHREWRVLRELGVDTKIVPNDIDSSELDGLDGLVLSGGAPNIDEELDKLGSVGKYIDDHNYPILGICVGAQFIALHFGASVVKAKHPEFGKTKVSVMHSENIFGGLPSEITVWENHNDEIINLPDDFTLAASSATCQVQGFYHKTRPIYATQFHPEVEHTQYGRDIFRNFIGICASYREIQKENF 198
               SCOP domains d2a9vd_ D: GMP synthase subunit A, GuaAA                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee......hhhhhhhhhh.....eee...hhhhhh...eeee.....hhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhh..eeeeeeeeeeeeeeeee...hhhhh....eeeeeeeeeeeee.....eeeeee.......eeee....eeee..........hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a9v D  -2 HHHmLKIYVVDNGGQWTHREWRVLRELGVDTKIVPNDIDSSELDGLDGLVLSGGAPNIDEELDKLGSVGKYIDDHNYPILGICVGAQFIALHFGASVVKAKHPEFGKTKVSVmHSENIFGGLPSEITVWENHNDEIINLPDDFTLAASSATCQVQGFYHKTRPIYATQFHPEVEHTQYGRDIFRNFIGICASYREIQKENF 198
                               |     7        17        27        37        47        57        67        77        87        97       107  |    117       127       137       147       157       167       177       187       197 
                               1-MSE                                                                                                      110-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  (1, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2A9V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A9V)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (GUAAA_THEAC | Q9HJM3)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003922    GMP synthase (glutamine-hydrolyzing) activity    Catalysis of the reaction: ATP + xanthosine 5'-phosphate + L-glutamine + H2O = AMP + diphosphate + GMP + L-glutamate.
    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:0006177    GMP biosynthetic process    The chemical reactions and pathways resulting in the formation of GMP, guanosine monophosphate.
    GO:0006541    glutamine metabolic process    The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid.
    GO:0006164    purine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

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