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(-) Description

Title :  CRYSTAL STRUCTURE OF ACETYLORNITHINE AMINOTRANSFERASE (EC 2.6.1.11) (ACOAT) (TM1785) FROM THERMOTOGA MARITIMA AT 1.40 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  02 Feb 07  (Deposition) - 13 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tm1785, Acetylornithine Aminotransferase (Ec 2. 6. 1. 11) (Acoat), Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Acetylornithine Aminotransferase (Ec 2. 6. 1. 11) (Acoat) (Tm1785) From Thermotoga Maritima At 1. 40 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ACETYLORNITHINE AMINOTRANSFERASE
    Atcc: 43589
    Chains: A, B
    EC Number: 2.6.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ARGD, TM1785
    Organism Scientific: THERMOTOGA MARITIMA MSB8
    Organism Taxid: 243274
    Strain: MSB8, DSM 3109, JCM 10099
    Synonym: ACOAT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 37)

Asymmetric/Biological Unit (3, 37)
No.NameCountTypeFull Name
1GOL17Ligand/IonGLYCEROL
2MSE18Mod. Amino AcidSELENOMETHIONINE
3PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:94 , THR A:95 , PHE A:126 , HIS A:127 , GLU A:178 , ASP A:211 , GLN A:214 , LYS A:240 , HOH A:432 , HOH A:438 , HOH A:441 , HOH A:446 , HOH A:458 , HOH A:480 , HOH A:732 , THR B:268BINDING SITE FOR RESIDUE PLP A 401
02AC2SOFTWARETHR A:268 , HOH A:431 , GLY B:94 , THR B:95 , ASN B:98 , PHE B:126 , HIS B:127 , GLU B:178 , ASP B:211 , VAL B:213 , GLN B:214 , LYS B:240 , HOH B:444 , HOH B:452 , HOH B:453 , HOH B:469 , HOH B:471BINDING SITE FOR RESIDUE PLP B 401
03AC3SOFTWAREPHE A:291 , LYS A:298 , LEU A:364 , THR A:365 , GOL A:410 , HOH A:467 , HOH A:619 , HOH B:588BINDING SITE FOR RESIDUE GOL A 402
04AC4SOFTWAREASN A:258 , LEU A:260 , HOH A:502 , HOH A:579 , HOH A:697BINDING SITE FOR RESIDUE GOL A 403
05AC5SOFTWAREHIS A:-5 , HIS A:-4 , ALA A:12 , THR A:13 , ASP A:24 , GLU A:25 , HOH A:607 , HOH A:612BINDING SITE FOR RESIDUE GOL A 404
06AC6SOFTWARETYR A:16 , TYR A:23 , HOH A:493 , HOH A:660 , GLU B:376BINDING SITE FOR RESIDUE GOL A 405
07AC7SOFTWARESER A:8 , ARG A:337 , THR A:341 , HOH A:722 , HOH A:744BINDING SITE FOR RESIDUE GOL A 406
08AC8SOFTWARETRP A:21 , ASN A:346 , LYS A:347 , THR A:377 , GOL A:408 , HOH A:680 , HOH A:710 , GOL B:406BINDING SITE FOR RESIDUE GOL A 407
09AC9SOFTWAREGOL A:407 , HOH A:710 , LYS B:347 , HOH B:577 , HOH B:668BINDING SITE FOR RESIDUE GOL A 408
10BC1SOFTWAREGLU A:312 , TYR A:313 , HOH A:553 , HOH A:724BINDING SITE FOR RESIDUE GOL A 409
11BC2SOFTWAREGLU A:289 , PHE A:291 , GOL A:402 , HOH A:765 , GLU B:289 , GOL B:402 , HOH B:468BINDING SITE FOR RESIDUE GOL A 410
12BC3SOFTWARELYS A:110 , GLU A:114 , TYR A:117 , HOH A:750 , GLU B:147BINDING SITE FOR RESIDUE GOL A 411
13BC4SOFTWARELYS A:228 , HOH A:716BINDING SITE FOR RESIDUE GOL A 412
14BC5SOFTWAREGOL A:410 , HOH A:619 , PHE B:291 , LYS B:298 , LEU B:364 , THR B:365 , HOH B:450BINDING SITE FOR RESIDUE GOL B 402
15BC6SOFTWARETRP A:68 , HIS B:0 , LEU B:3 , ASN B:5 , HOH B:474 , HOH B:524BINDING SITE FOR RESIDUE GOL B 403
16BC7SOFTWARESER B:8 , PHE B:10 , ARG B:337 , HOH B:580 , HOH B:615BINDING SITE FOR RESIDUE GOL B 404
17BC8SOFTWAREGLU A:376 , TYR B:16 , TYR B:23 , GLY B:27 , HOH B:528 , HOH B:689BINDING SITE FOR RESIDUE GOL B 405
18BC9SOFTWAREGLU A:376 , THR A:377 , GOL A:407 , HOH A:707 , GLY B:27 , HOH B:508 , HOH B:689BINDING SITE FOR RESIDUE GOL B 406
19CC1SOFTWAREMSE A:1 , TYR A:2 , SER B:80 , GLY B:85 , GLY B:86 , LYS B:87 , HOH B:522 , HOH B:703BINDING SITE FOR RESIDUE GOL B 407

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:147 -Pro A:148
2Glu B:147 -Pro B:148

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_3PS00600 Aminotransferases class-III pyridoxal-phosphate attachment site.ARGD_THEMA208-245
 		  2A:208-245
B:208-245

(-) Exons   (0, 0)

(no "Exon" information available for 2ORD)

(-) 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:393
 aligned with ARGD_THEMA | Q9X2A5 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:393
                                    1                                                                                                                                                                                                                                                                                                                                                                                                
                                    |2        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   
           ARGD_THEMA     - --------MYLMNTYSRFPATFVYGKGSWIYDEKGNAYLDFTSGIAVNVLGHSHPRLVEAIKDQAEKLIHCSNLFWNRPQMELAELLSKNTFGGKVFFANTGTEANEAAIKIARKYGKKKSEKKYRILSAHNSFHGRTLGSLTATGQPKYQKPFEPLVPGFEYFEFNNVEDLRRKMSEDVCAVFLEPIQGESGIVPATKEFLEEARKLCDEYDALLVFDEVQCGMGRTGKLFAYQKYGVVPDVLTTAKGLGGGVPIGAVIVNERANVLEPGDHGTTFGGNPLACRAGVTVIKELTKEGFLEEVEEKGNYLMKKLQEMKEEYDVVADVRGMGLMIGIQFREEVSNREVATKCFENKLLVVPAGNNTIRFLPPLTVEYGEIDLAVETLKKVLQGI 385
               SCOP domains d2orda_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -----------------------------------------------------2ordA02 A:46-289 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh.........eeeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhhhh.......eehhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhhh....eeeee.......hhhhhhhh.hhhhhhhhh.....eeee...hhhhhhhhh...eeeeee..ee.....ee.hhhhhhhhhhhhhhhh.eeeee............hhhhhhh....eeeehhhhhh....eeeee..................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeee....hhhhhhhhhhhh.ee.eee...eeee......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_3  PDB: A:208-245   -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ord A  -7 KIHHHHHHmYLmNTYSRFPATFVYGKGSWIYDEKGNAYLDFTSGIAVNVLGHSHPRLVEAIKDQAEKLIHCSNLFWNRPQmELAELLSKNTFGGKVFFANTGTEANEAAIKIARKYGKKKSEKKYRILSAHNSFHGRTLGSLTATGQPKYQKPFEPLVPGFEYFEFNNVEDLRRKmSEDVCAVFLEPIQGESGIVPATKEFLEEARKLCDEYDALLVFDEVQCGmGRTGKLFAYQKYGVVPDVLTTAKGLGGGVPIGAVIVNERANVLEPGDHGTTFGGNPLACRAGVTVIKELTKEGFLEEVEEKGNYLmKKLQEmKEEYDVVADVRGmGLmIGIQFREEVSNREVATKCFENKLLVVPAGNNTIRFLPPLTVEYGEIDLAVETLKKVLQGI 385
                                    |2 |      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   
                                    1-MSE                                                                  73-MSE                                                                                        168-MSE                                          217-MSE                                                                               303-MSE |          322-MSE                                                           
                                       4-MSE                                                                                                                                                                                                                                                                                                          309-MSE         325-MSE                                                        


Chain B from PDB  Type:PROTEIN  Length:393
 aligned with ARGD_THEMA | Q9X2A5 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:393
                                    1                                                                                                                                                                                                                                                                                                                                                                                                
                                    |2        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   
           ARGD_THEMA     - --------MYLMNTYSRFPATFVYGKGSWIYDEKGNAYLDFTSGIAVNVLGHSHPRLVEAIKDQAEKLIHCSNLFWNRPQMELAELLSKNTFGGKVFFANTGTEANEAAIKIARKYGKKKSEKKYRILSAHNSFHGRTLGSLTATGQPKYQKPFEPLVPGFEYFEFNNVEDLRRKMSEDVCAVFLEPIQGESGIVPATKEFLEEARKLCDEYDALLVFDEVQCGMGRTGKLFAYQKYGVVPDVLTTAKGLGGGVPIGAVIVNERANVLEPGDHGTTFGGNPLACRAGVTVIKELTKEGFLEEVEEKGNYLMKKLQEMKEEYDVVADVRGMGLMIGIQFREEVSNREVATKCFENKLLVVPAGNNTIRFLPPLTVEYGEIDLAVETLKKVLQGI 385
               SCOP domains d2ordb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -----------------------------------------------------2ordB02 B:46-289 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                ------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --------------------Aminotran_3-2ordB01 B:13-332                                                                                                                                                                                                                                                                                                    ----------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------Aminotran_3-2ordB02 B:13-332                                                                                                                                                                                                                                                                                                    ----------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhh.........eeeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhhhh.......eehhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhhh....eeeee.......hhhhhhhh.hhhhhhhhh.....eeee...hhhhhhhhh...eeeeee..ee.....ee.hhhhhhhhhhhhhhhh.eeeee............hhhhhhh....eeeehhhhhh....eeeee..................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeee....hhhhhhhhhhhh.ee.eee...eeee......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_3  PDB: B:208-245   -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ord B  -7 KIHHHHHHmYLmNTYSRFPATFVYGKGSWIYDEKGNAYLDFTSGIAVNVLGHSHPRLVEAIKDQAEKLIHCSNLFWNRPQmELAELLSKNTFGGKVFFANTGTEANEAAIKIARKYGKKKSEKKYRILSAHNSFHGRTLGSLTATGQPKYQKPFEPLVPGFEYFEFNNVEDLRRKmSEDVCAVFLEPIQGESGIVPATKEFLEEARKLCDEYDALLVFDEVQCGmGRTGKLFAYQKYGVVPDVLTTAKGLGGGVPIGAVIVNERANVLEPGDHGTTFGGNPLACRAGVTVIKELTKEGFLEEVEEKGNYLmKKLQEmKEEYDVVADVRGmGLmIGIQFREEVSNREVATKCFENKLLVVPAGNNTIRFLPPLTVEYGEIDLAVETLKKVLQGI 385
                                    |2 |      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   
                                    1-MSE                                                                  73-MSE                                                                                        168-MSE                                          217-MSE                                                                               303-MSE |          322-MSE                                                           
                                       4-MSE                                                                                                                                                                                                                                                                                                          309-MSE         325-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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PLP_aminotran (240)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ARGD_THEMA | Q9X2A5)
molecular function
    GO:0003992    N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity    Catalysis of the reaction: 2-oxoglutarate + N(2)-acetyl-L-ornithine = N-acetyl-L-glutamate 5-semialdehyde + L-glutamate.
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0008483    transaminase activity    Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
    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:0006526    arginine biosynthetic process    The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
    GO:0006525    arginine metabolic process    The chemical reactions and pathways involving 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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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        ARGD_THEMA | Q9X2A5: 2e54

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