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(-) Description

Title :  CRYSTAL STRUCTURE OF ARGININE BIOSYNTHESIS BIFUNCTIONAL PROTEIN ARGJ (10175521) FROM BACILLUS HALODURANS AT 2.00 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  17 Feb 05  (Deposition) - 12 Apr 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  10175521, Arginine Biosynthesis Bifunctional Protein Argj, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Arginine Biosynthesis Bifunctional Protein Argj (10175521) From Bacillus Halodurans At 2. 00 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ARGININE BIOSYNTHESIS BIFUNCTIONAL PROTEIN ARGJ
    Chains: A
    EC Number: 2.3.1.35, 2.3.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: ALPHA CHAIN, RESIDUES 1-196
    Gene: ARGJ
    Organism Scientific: BACILLUS HALODURANS
    Organism Taxid: 86665
    Other Details: BOTH CHAIN A AND CHAIN B WERE EXPRESSED FROM A SINGLE CONSTRUCT WHICH ENCODES RESIDUES 1-411 OF THE ARGJ GENE
 
Molecule 2 - ARGININE BIOSYNTHESIS BIFUNCTIONAL PROTEIN ARGJ
    Chains: B
    EC Number: 2.3.1.35, 2.3.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: BETA CHAIN, RESIDUES 197-411
    Gene: ARGJ
    Organism Scientific: BACILLUS HALODURANS
    Organism Taxid: 86665
    Other Details: BOTH CHAIN A AND CHAIN B WERE EXPRESSED FROM A SINGLE CONSTRUCT WHICH ENCODES RESIDUES 1-411 OF THE ARGJ GENE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 28)

Asymmetric Unit (4, 28)
No.NameCountTypeFull Name
1EDO16Ligand/Ion1,2-ETHANEDIOL
2MSE9Mod. Amino AcidSELENOMETHIONINE
3SO42Ligand/IonSULFATE ION
4UNL1Ligand/IonUNKNOWN LIGAND
Biological Unit 1 (4, 28)
No.NameCountTypeFull Name
1EDO16Ligand/Ion1,2-ETHANEDIOL
2MSE9Mod. Amino AcidSELENOMETHIONINE
3SO42Ligand/IonSULFATE ION
4UNL1Ligand/IonUNKNOWN LIGAND
Biological Unit 2 (4, 56)
No.NameCountTypeFull Name
1EDO32Ligand/Ion1,2-ETHANEDIOL
2MSE18Mod. Amino AcidSELENOMETHIONINE
3SO44Ligand/IonSULFATE ION
4UNL2Ligand/IonUNKNOWN LIGAND

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:123 , GLY A:124 , THR A:160 , LYS A:186 , EDO A:203 , HOH A:224 , HOH A:246 , EDO B:10 , THR B:197 , HOH B:423BINDING SITE FOR RESIDUE SO4 A 197
02AC2SOFTWAREGLU A:115 , HIS A:116 , HIS A:152 , GLU A:165 , HOH A:212 , HOH A:239BINDING SITE FOR RESIDUE SO4 A 198
03AC3SOFTWARELYS A:34 , ARG A:35 , LYS A:36 , ARG A:37 , THR A:160 , EDO A:209 , HOH A:348 , HOH A:400BINDING SITE FOR RESIDUE UNL A 199
04AC4SOFTWARELYS A:36 , LYS A:38 , GLU A:156 , EDO A:201 , EDO A:210BINDING SITE FOR RESIDUE EDO A 200
05AC5SOFTWAREVAL A:74 , GLU A:75 , GLU A:156 , EDO A:200 , HOH A:379 , HOH A:381 , HOH A:391BINDING SITE FOR RESIDUE EDO A 201
06AC6SOFTWAREALA A:108 , ILE A:113 , GLU A:165 , HOH A:239 , HOH A:242BINDING SITE FOR RESIDUE EDO A 202
07AC7SOFTWAREGLY B:284 , THR B:286 , TYR B:320 , THR B:399 , TYR B:400 , ASP B:401 , HOH B:459 , HOH B:571BINDING SITE FOR RESIDUE EDO B 7
08AC8SOFTWAREGLY A:124 , SO4 A:197 , EDO A:209BINDING SITE FOR RESIDUE EDO A 203
09AC9SOFTWAREVAL A:27 , GLY A:28 , GLU A:145 , ALA A:153 , HOH A:263BINDING SITE FOR RESIDUE EDO A 204
10BC1SOFTWARETHR A:161 , SO4 A:197 , GLU B:283 , ASN B:406 , HOH B:471BINDING SITE FOR RESIDUE EDO B 10
11BC2SOFTWAREALA B:348 , SER B:381 , ASN B:383 , HOH B:506BINDING SITE FOR RESIDUE EDO B 11
12BC3SOFTWARECYS A:45 , PHE A:111 , HOH A:256 , HOH A:367BINDING SITE FOR RESIDUE EDO A 205
13BC4SOFTWAREALA A:53 , TYR A:55 , HOH A:220 , HOH A:222 , GLN B:214BINDING SITE FOR RESIDUE EDO A 206
14BC5SOFTWARETYR A:170 , LEU B:269 , GLU B:272 , ASP B:273 , LYS B:276 , HOH B:487BINDING SITE FOR RESIDUE EDO B 14
15BC6SOFTWAREILE A:126 , HOH A:231 , ASN B:325 , TRP B:326 , GLY B:327 , HOH B:485BINDING SITE FOR RESIDUE EDO A 207
16BC7SOFTWARETHR A:7 , ALA A:8 , ILE A:173 , ASN A:175 , GLY A:176 , ASP B:259BINDING SITE FOR RESIDUE EDO A 208
17BC8SOFTWAREPRO A:48 , SER A:50 , LYS A:77 , ALA B:206 , ASN B:207 , ILE B:208 , ALA B:244 , SER B:245 , GLY B:246BINDING SITE FOR RESIDUE EDO B 17
18BC9SOFTWAREGLY A:86 , THR A:160 , UNL A:199 , EDO A:203BINDING SITE FOR RESIDUE EDO A 209
19CC1SOFTWAREILE A:29 , HIS A:30 , LYS A:38 , EDO A:200 , HOH A:263BINDING SITE FOR RESIDUE EDO A 210

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asp B:376 -Pro B:377

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VRA)

(-) Exons   (0, 0)

(no "Exon" information available for 1VRA)

(-) 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:191
 aligned with ARGJ_BACHD | Q9K8V3 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:191
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195 
           ARGJ_BACHD     6 ETANVLKLETGSVTSAKGFSAVGIHTGVKRKRKDLGAIVCEVPASSAAVYTLNKVQAAPLKVTQESIAVEGKLQAMIVNSGIANACTGKRGLDDAYTMRAVGAETFHIPEHYVAVTSTGVIGEFLPMDVITNGIRQLKPEATIEGAHAFNEAILTTDTVEKHTCYQTIVNGKTVTVGGVAKGSGMIHPNMA 196
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee....hhhhh..eeeeee..........eeeeeeeeeeeeeeeee.....hhhhhhhhhhhhhhheeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeee.....hhhhhhhhhhh.....hhhhhhhhhhhhh.......eeeeeeee..eeeeeeeeee........ee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vra A   6 ETANVLKLETGSVTSAKGFSAVGIHTGVKRKRKDLGAIVCEVPASSAAVYTLNKVQAAPLKVTQESIAVEGKLQAmIVNSGIANACTGKRGLDDAYTmRAVGAETFHIPEHYVAVTSTGVIGEFLPmDVITNGIRQLKPEATIEGAHAFNEAILTTDTVEKHTCYQTIVNGKTVTVGGVAKGSGmIHPNmA 196
                                    15        25        35        45        55        65        75     |  85        95       105       115       125      |135       145       155       165       175       185    |  195 
                                                                                                      81-MSE               103-MSE                      132-MSE                                                   190-MSE| 
                                                                                                                                                                                                                       195-MSE


Chain B from PDB  Type:PROTEIN  Length:213
 aligned with ARGJ_BACHD | Q9K8V3 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:213
                                   206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406   
           ARGJ_BACHD   197 TMLSFVTTDANIDHGHLQGALSAITNETFNRITVDGDTSTNDMVVVMASGLAENEALTPEHPDWANFYKALQLACEDLAKQIARDGEGATKLIEVEVTGAANDQEAGMVAKQIVGSDLVKTAIYGADANWGRIICAIGYSGCEVNQETIDIAIGPIVTLKQSEPTGFSEEEATAYLKEADPVKISVNLHIGNGTGKAWGCDLTYDYVRINAGY 409
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ArgJ-1vraB01 B:197-409                                                                                                                                                                                                Pfam domains (1)
           Pfam domains (2) ArgJ-1vraB02 B:197-409                                                                                                                                                                                                Pfam domains (2)
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhhhhhhh..........eeeeee..............hhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.........eeee..eeeee..ee...hhhhhhhhhhhh..eeeeee.....eeeeeeee..hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vra B 197 TmLSFVTTDANIDHGHLQGALSAITNETFNRITVDGDTSTNDmVVVmASGLAENETLTPEHPDWANFYKALQLACEDLAKQIARDGEGATKLIEVEVTGAANDQEAGmVAKQIVGSDLVKTAIYGADANWGRIICAIGYSGCEVNQETIDIAIGPIVTLKQSEPTGFSEEEATAYLKEADPVKISVNLHIGNGTGKAWGCDLTYDYVRINAGY 409
                             |     206       216       226       236  |   |246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406   
                             |                                      239-MSE                                                          304-MSE                                                                                                     
                           198-MSE                                      243-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  (0, 0)

(no "SCOP Domain" information available for 1VRA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1VRA)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: ArgJ] (6)
(-)
Family: ArgJ (6)
(-)
Bacillus halodurans (1)
1aArgJ-1vraB01B:197-409
1bArgJ-1vraB02B:197-409

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ARGJ_BACHD | Q9K8V3)
molecular function
    GO:0004042    acetyl-CoA:L-glutamate N-acetyltransferase activity    Catalysis of the reaction: L-glutamate + acetyl-CoA = N-acetyl-L-glutamate + CoA + H(+).
    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:0004358    glutamate N-acetyltransferase activity    Catalysis of the reaction: N(2)-acetyl-L-ornithine + L-glutamate = N-acetyl-L-glutamate + L-ornithine.
    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:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
    GO:0006526    arginine biosynthetic process    The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
    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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
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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