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(-) Description

Title :  CRYSTAL STRUCTURE OF N-ACETYL-GAMMA-GLUTAMYL-PHOSPHATE REDUCTASE (TM1782) FROM THERMOTOGA MARITIMA AT 1.80 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  11 Jun 04  (Deposition) - 22 Jun 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tm1782, N-Acetyl-Gamma-Glutamyl-Phosphate Reductase, Structural Genomics, Jcsg, Psi, Protein Structure Initiative, Joint Center For Structural Genomics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of N-Acetyl-Gamma-Glutamyl-Phosphate Reductase (Tm1782) From Thermotoga Maritima At 1. 80 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - N-ACETYL-GAMMA-GLUTAMYL-PHOSPHATE REDUCTASE
    Chains: A, B, C, D
    EC Number: 1.2.1.38
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ARGC, TM1782
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: AGPR, N-ACETYL-GLUTAMATE SEMIALDEHYDE DEHYDROGENASE, NAGSA DEHYDROGENASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 36)

Asymmetric/Biological Unit (1, 36)
No.NameCountTypeFull Name
1MSE36Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1VKN)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Tyr A:338 -Pro A:339
2Tyr B:338 -Pro B:339
3Tyr C:338 -Pro C:339
4Ser D:79 -Tyr D:80
5Tyr D:338 -Pro D:339

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARGCPS01224 N-acetyl-gamma-glutamyl-phosphate reductase active site.ARGC_THEMA140-156
 
 
 		  4A:140-156
B:140-156
C:140-156
D:140-156

(-) Exons   (0, 0)

(no "Exon" information available for 1VKN)

(-) Sequences/Alignments

Asymmetric/Biological 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:340
 aligned with ARGC_THEMA | Q9X2A2 from UniProtKB/Swiss-Prot  Length:339

    Alignment length:340
                             1                                                                                                                                                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339
           ARGC_THEMA     - -MIRAGIIGATGYTGLELVRLLKNHPEAKITYLSSRTYAGKKLEEIFPSTLENSILSEFDPEKVSKNCDVLFTALPAGASYDLVRELKGVKIIDLGADFRFDDPGVYREWYGKELSGYENIKRVYGLPELHREEIKNAQVVGNPGCYPTSVILALAPALKHNLVDPETILVDAKSGVSGAGRKEKVDYLFSEVNESLRPYNVAKHRHVPEMEQELGKISGKKVNVVFTPHLVPMTRGILSTIYVKTDKSLEEIHEAYLEFYKNEPFVHVLPMGIYPSTKWCYGSNHVFIGMQMEERTNTLILMSAIDNLVKGASGQAVQNMNIMFGLDETKGLEFTPIYP 339
               SCOP domains -d1vkna1 A:1-144,A:308-339 N-acetyl-gamma-glutamyl-phosphate reductase ArgC                                                                      d1vkna2 A:145-307 N-acetyl-gamma-glutamyl-phosphate reductase ArgC                                                                                                 d1vkna1 A:1-144,A:308-339        SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------------------------------------1vknA02 A:143-307 Dihydrodipicolinate Reductase; domain 2                                                                                                            -------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhh........hhhhhhhhh.eeee....hhhhhhhh.....eeee........hhhhhhhhhh....hhhhh.eee.hhhhhhhhhh...eee..hhhhhhhhhhhhhhhhh......eeeeeeeee.hhhh...hhhhhhhhhh...ee......hhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeeee...hhhhhhhhhhhhhh....eee.......hhhhhh....eeeeeeee....eeeeeeee......hhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------ARGC             --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vkn A   0 HmIRAGIIGATGYTGLELVRLLKNHPEAKITYLSSRTYAGKKLEEIFPSTLENSILSEFDPEKVSKNCDVLFTALPAGASYDLVRELKGVKIIDLGADFRFDDPGVYREWYGKELSGYENIKRVYGLPELHREEIKNAQVVGNPGCYPTSVILALAPALKHNLVDPETILVDAKSGVSGAGRKEKVDYLFSEVNESLRPYNVAKHRHVPEmEQELGKISGKKVNVVFTPHLVPmTRGILSTIYVKTDKSLEEIHEAYLEFYKNEPFVHVLPmGIYPSTKWCYGSNHVFIGmQmEERTNTLILmSAIDNLVKGASGQAVQNmNImFGLDETKGLEFTPIYP 339
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209|      219       229   |   239       249       259       269 |     279       289| |    299  |    309       319|  |   329       339
                             |                                                                                                                                                                                                              210-MSE                233-MSE                               271-MSE            290-MSE     302-MSE           320-MSE               
                             1-MSE                                                                                                                                                                                                                                                                                            292-MSE                        323-MSE            


Chain B from PDB  Type:PROTEIN  Length:340
 aligned with ARGC_THEMA | Q9X2A2 from UniProtKB/Swiss-Prot  Length:339

    Alignment length:340
                             1                                                                                                                                                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339
           ARGC_THEMA     - -MIRAGIIGATGYTGLELVRLLKNHPEAKITYLSSRTYAGKKLEEIFPSTLENSILSEFDPEKVSKNCDVLFTALPAGASYDLVRELKGVKIIDLGADFRFDDPGVYREWYGKELSGYENIKRVYGLPELHREEIKNAQVVGNPGCYPTSVILALAPALKHNLVDPETILVDAKSGVSGAGRKEKVDYLFSEVNESLRPYNVAKHRHVPEMEQELGKISGKKVNVVFTPHLVPMTRGILSTIYVKTDKSLEEIHEAYLEFYKNEPFVHVLPMGIYPSTKWCYGSNHVFIGMQMEERTNTLILMSAIDNLVKGASGQAVQNMNIMFGLDETKGLEFTPIYP 339
               SCOP domains -d1vknb1 B:1-144,B:308-339 N-acetyl-gamma-glutamyl-phosphate reductase ArgC                                                                      d1vknb2 B:145-307 N-acetyl-gamma-glutamyl-phosphate reductase ArgC                                                                                                 d1vknb1 B:1-144,B:308-339        SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------------------------------------1vknB02 B:143-307 Dihydrodipicolinate Reductase; domain 2                                                                                                            -------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhh........hhhhhhhhh.eeee....hhhhhhhhh....eeee........hhhhhhhhhh....hhhhh.eee.hhhhhhhhhh...eee..hhhhhhhhhhhhhhhhh......eeeeeeeee.hhhh...hhhhhhhhhh...ee......hhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeeee...hhhhhhhhhhhhh.....eee.......hhhhhh....eeeeeeee....eeeeeeee......hhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------ARGC             --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vkn B   0 HmIRAGIIGATGYTGLELVRLLKNHPEAKITYLSSRTYAGKKLEEIFPSTLENSILSEFDPEKVSKNCDVLFTALPAGASYDLVRELKGVKIIDLGADFRFDDPGVYREWYGKELSGYENIKRVYGLPELHREEIKNAQVVGNPGCYPTSVILALAPALKHNLVDPETILVDAKSGVSGAGRKEKVDYLFSEVNESLRPYNVAKHRHVPEmEQELGKISGKKVNVVFTPHLVPmTRGILSTIYVKTDKSLEEIHEAYLEFYKNEPFVHVLPmGIYPSTKWCYGSNHVFIGmQmEERTNTLILmSAIDNLVKGASGQAVQNmNImFGLDETKGLEFTPIYP 339
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209|      219       229   |   239       249       259       269 |     279       289| |    299  |    309       319|  |   329       339
                             1-MSE                                                                                                                                                                                                          210-MSE                233-MSE                               271-MSE            290-MSE     302-MSE           320-MSE               
                                                                                                                                                                                                                                                                                                                              292-MSE                        323-MSE            


Chain C from PDB  Type:PROTEIN  Length:336
 aligned with ARGC_THEMA | Q9X2A2 from UniProtKB/Swiss-Prot  Length:339

    Alignment length:339
                                    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       290       300       310       320       330         
           ARGC_THEMA     1 MIRAGIIGATGYTGLELVRLLKNHPEAKITYLSSRTYAGKKLEEIFPSTLENSILSEFDPEKVSKNCDVLFTALPAGASYDLVRELKGVKIIDLGADFRFDDPGVYREWYGKELSGYENIKRVYGLPELHREEIKNAQVVGNPGCYPTSVILALAPALKHNLVDPETILVDAKSGVSGAGRKEKVDYLFSEVNESLRPYNVAKHRHVPEMEQELGKISGKKVNVVFTPHLVPMTRGILSTIYVKTDKSLEEIHEAYLEFYKNEPFVHVLPMGIYPSTKWCYGSNHVFIGMQMEERTNTLILMSAIDNLVKGASGQAVQNMNIMFGLDETKGLEFTPIYP 339
               SCOP domains d1vknc1 C:1-144,C:308-339 N-acetyl-gamma-glutamyl-phosphate reductase ArgC                                                                      d1vknc2 C:145-307 N-acetyl-gamma-gl   utamyl-phosphate reductase ArgC                                                                                              d1vknc1 C:1-144,C:308-339        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------1vknC02 C:143-307 Dihydrodipicolinate    Reductase; domain 2                                                                                                         -------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhh........hhhhhhhhh.eeee....hhhhhhhhhh...eeee........hhhhhhhhhh....hhhhh.eee.hhhhhhhhhh...eee..hhhhhhhhhhhhhhhhh......eeeeeeeee.hhh---.hhhhhhhhhh...ee......hhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeeee...hhhhhhhhhhhhhh....eee.......hhhhhh....eeeeeeee....eeeeeeee......hhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------ARGC             --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vkn C   1 mIRAGIIGATGYTGLELVRLLKNHPEAKITYLSSRTYAGKKLEEIFPSTLENSILSEFDPEKVSKNCDVLFTALPAGASYDLVRELKGVKIIDLGADFRFDDPGVYREWYGKELSGYENIKRVYGLPELHREEIKNAQVVGNPGCYPTSVILALAPALKHNLVDPETILVDAKSGVSGA---EKVDYLFSEVNESLRPYNVAKHRHVPEmEQELGKISGKKVNVVFTPHLVPmTRGILSTIYVKTDKSLEEIHEAYLEFYKNEPFVHVLPmGIYPSTKWCYGSNHVFIGmQmEERTNTLILmSAIDNLVKGASGQAVQNmNImFGLDETKGLEFTPIYP 339
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170        |-  |    190       200       210       220       230  |    240       250       260       270|      280       290 |     300 |     310       320  |    330         
                            1-MSE                                                                                                                                                                           179 183                        210-MSE                233-MSE                               271-MSE            290-MSE     302-MSE           320-MSE               
                                                                                                                                                                                                                                                                                                                             292-MSE                        323-MSE            


Chain D from PDB  Type:PROTEIN  Length:335
 aligned with ARGC_THEMA | Q9X2A2 from UniProtKB/Swiss-Prot  Length:339

    Alignment length:339
                                    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       290       300       310       320       330         
           ARGC_THEMA     1 MIRAGIIGATGYTGLELVRLLKNHPEAKITYLSSRTYAGKKLEEIFPSTLENSILSEFDPEKVSKNCDVLFTALPAGASYDLVRELKGVKIIDLGADFRFDDPGVYREWYGKELSGYENIKRVYGLPELHREEIKNAQVVGNPGCYPTSVILALAPALKHNLVDPETILVDAKSGVSGAGRKEKVDYLFSEVNESLRPYNVAKHRHVPEMEQELGKISGKKVNVVFTPHLVPMTRGILSTIYVKTDKSLEEIHEAYLEFYKNEPFVHVLPMGIYPSTKWCYGSNHVFIGMQMEERTNTLILMSAIDNLVKGASGQAVQNMNIMFGLDETKGLEFTPIYP 339
               SCOP domains d1vknd1 D:1-144,D:308-339 N-acetyl-gamma-glutamyl-phosphate reductase ArgC                                                                      d1vknd2 D:145-307 N-acetyl-gamma-g    lutamyl-phosphate reductase ArgC                                                                                             d1vknd1 D:1-144,D:308-339        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------1vknD02 D:143-307 Dihydrodipicolinat    e Reductase; domain 2                                                                                                        -------------------------------- CATH domains
           Pfam domains (1) --Semialdhyde_dh-1vknD05 D:3-137                                                                                                         ----------------Semialdhyde_dhC-1vknD01 D    :154-310                                                                                                                        ----------------------------- Pfam domains (1)
           Pfam domains (2) --Semialdhyde_dh-1vknD06 D:3-137                                                                                                         ----------------Semialdhyde_dhC-1vknD02 D    :154-310                                                                                                                        ----------------------------- Pfam domains (2)
           Pfam domains (3) --Semialdhyde_dh-1vknD07 D:3-137                                                                                                         ----------------Semialdhyde_dhC-1vknD03 D    :154-310                                                                                                                        ----------------------------- Pfam domains (3)
           Pfam domains (4) --Semialdhyde_dh-1vknD08 D:3-137                                                                                                         ----------------Semialdhyde_dhC-1vknD04 D    :154-310                                                                                                                        ----------------------------- Pfam domains (4)
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhh........hhhhhhhhh.eeee....hhhhhhhhh....eeee........hhhhhhhhhh....hhhhh.eee.hhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhh......eeeeeeeee...----.hhhhhhhhhh...ee......hhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeeee...hhhhhhhhhhhhh.....eee.......hhhhhh....eeeeeeee....eeeeeeee......hhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------ARGC             --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vkn D   1 mIRAGIIGATGYTGLELVRLLKNHPEAKITYLSSRTYAGKKLEEIFPSTLENSILSEFDPEKVSKNCDVLFTALPAGASYDLVRELKGVKIIDLGADFRFDDPGVYREWYGKELSGYENIKRVYGLPELHREEIKNAQVVGNPGCYPTSVILALAPALKHNLVDPETILVDAKSGVSG----EKVDYLFSEVNESLRPYNVAKHRHVPEmEQELGKISGKKVNVVFTPHLVPmTRGILSTIYVKTDKSLEEIHEAYLEFYKNEPFVHVLPmGIYPSTKWCYGSNHVFIGmQmEERTNTLILmSAIDNLVKGASGQAVQNmNImFGLDETKGLEFTPIYP 339
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       | -  |    190       200       210       220       230  |    240       250       260       270|      280       290 |     300 |     310       320  |    330         
                            1-MSE                                                                                                                                                                          178  183                        210-MSE                233-MSE                               271-MSE            290-MSE     302-MSE           320-MSE               
                                                                                                                                                                                                                                                                                                                             292-MSE                        323-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, 8)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Clan: GADPH_aa-bio_dh (59)
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (ARGC_THEMA | Q9X2A2)
molecular function
    GO:0003942    N-acetyl-gamma-glutamyl-phosphate reductase activity    Catalysis of the reaction: N-acetyl-L-glutamate 5-semialdehyde + NADP+ + phosphate = N-acetyl-5-glutamyl phosphate + NADPH + H+.
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016620    oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
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:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
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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  Cis Peptide Bonds
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    Tyr A:338 - Pro A:339   [ RasMol ]  
    Tyr B:338 - Pro B:339   [ RasMol ]  
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  1.2.1.38
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 Related Entries

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