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(-) Description

Title :  CRYSTAL STRUCTURE OF T.TH.HB8 BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE
 
Authors :  M. Goto, Riken Structural Genomics/Proteomics Initiative (Rsgi
Date :  27 Oct 04  (Deposition) - 18 Oct 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  A,B,C  (2x)
Biol. Unit 3:  A (1x),C (1x)
Biol. Unit 4:  A (1x),C (1x)
Biol. Unit 5:  B  (2x)
Keywords :  Hexamer, Plp-Dependent Enzyme, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Goto, I. Miyahara, K. Hirotsu
Crystal Structure Of T. Th. Hb8 Branched-Chain Amino Acid Aminotransferase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE
    Chains: A, B, C
    EC Number: 2.6.1.42
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HB8
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Synonym: ILVE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): ABC
Biological Unit 2 (2x): ABC
Biological Unit 3 (1x): A (1x) C (1x)
Biological Unit 4 (1x): A (1x) C (1x)
Biological Unit 5 (2x):  B 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2MPD5Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3PLP3Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MPD5Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3PLP3Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 2 (2, 16)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MPD10Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3PLP6Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 5 (2, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:68 , GLU C:173 , ARG C:269 , HOH C:1437BINDING SITE FOR RESIDUE CL A 420
02AC2SOFTWAREGLU A:173 , ARG B:269 , HOH B:959 , ARG C:68BINDING SITE FOR RESIDUE CL B 920
03AC3SOFTWAREARG A:269 , HOH A:1451 , ARG B:68 , GLU B:173BINDING SITE FOR RESIDUE CL A 1420
04AC4SOFTWAREARG A:59 , ARG A:148 , LYS A:159 , TYR A:164 , GLU A:193 , GLY A:196 , LEU A:216 , GLY A:218 , ILE A:219 , THR A:220 , GLY A:255 , THR A:256 , MPD A:414 , HOH A:1422 , HOH A:1452BINDING SITE FOR RESIDUE PLP A 413
05AC5SOFTWAREARG B:59 , ARG B:148 , LYS B:159 , TYR B:164 , GLU B:193 , GLY B:196 , LEU B:216 , GLY B:218 , ILE B:219 , THR B:220 , GLY B:255 , THR B:256 , MPD B:914 , HOH B:925 , HOH B:943BINDING SITE FOR RESIDUE PLP B 913
06AC6SOFTWAREARG C:59 , ARG C:148 , LYS C:159 , TYR C:164 , GLU C:193 , GLY C:196 , LEU C:216 , GLY C:218 , ILE C:219 , THR C:220 , GLY C:255 , THR C:256 , MPD C:1414 , HOH C:1416 , HOH C:1468BINDING SITE FOR RESIDUE PLP C 1413
07AC7SOFTWARETYR A:164 , GLY A:196 , ALA A:257 , PLP A:413 , HOH A:1464 , VAL C:109BINDING SITE FOR RESIDUE MPD A 414
08AC8SOFTWARELEU B:107 , GLY B:196 , PLP B:913 , MPD B:915 , HOH B:931 , HOH B:1030BINDING SITE FOR RESIDUE MPD B 914
09AC9SOFTWARETYR C:164 , GLY C:196 , PLP C:1413 , HOH C:1462BINDING SITE FOR RESIDUE MPD C 1414
10BC1SOFTWAREASP A:230 , ARG C:295 , HOH C:1518BINDING SITE FOR RESIDUE MPD A 415
11BC2SOFTWARETRP B:124 , TRP B:126 , MPD B:914 , HOH B:921BINDING SITE FOR RESIDUE MPD B 915

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Asn A:115 -Pro A:116
2Asn B:115 -Pro B:116
3Asn C:115 -Pro C:116

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WRV)

(-) 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:297
 aligned with Q5SM19_THET8 | Q5SM19 from UniProtKB/TrEMBL  Length:308

    Alignment length:305
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301     
         Q5SM19_THET8     2 QIKAGLIWMNGAFVPQEEAKTSVLSHALHYGTSVFEGIRAYETAKGPAIFRLKEHVKRFYNSAKVLRMEIPFAPEELEEAIKEVVRRNGYRSCYIRPLAWMGAKALGVNPLPNNPAEVMVAAWEWGAYLGEEAVRKGARLITSSWARFPANVMPGKAKVGGNYVNSALAKMEAVAAGADEALLLDEEGYVAEGSGENLFFVRDGVIYALEHSVNLEGITRDSVIRIAKDLGYEVQVVRATRDQLYMADEVFMTGTAAEVTPVSMIDWRPIGKGTAGPVALRLREVYLEAVTGRRPEYEGWLTYVN 306
               SCOP domains d1wrva_ A: automated matches                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ---1wrvA01 A:5-126  [code=3.30.470.10, no name defined]                                                                      --------1wrvA02 A:135-294 D-amino Acid Aminotransferase, subunit A, domain 2                                                                                            ------------ CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..eeee.hhh.....hhhhhhh.eee..eeee......eeehhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh....eeeeeeee.........hhhhh..eeeeeeee.--------....eeeee................hhhhhhhhhhhhhhhhhh...eeeee.....eeee...eeeeee..eeeee.......hhhhhhhhhhhhhh...eeee..hhhhhhh..eeeeee...eeeeeeee..ee......hhhhhhhhhhhhhhhh..hhhhhh.eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wrv A   2 QIKAGLIWMNGAFVPQEEAKTSVLSHALHYGTSVFEGIRAYETAKGPAIFRLKEHVKRFYNSAKVLRMEIPFAPEELEEAIKEVVRRNGYRSCYIRPLAWMGAKALGVNPLPNNPAEVMVAAWEW--------VRKGARLITSSWARFPANVMPGKAKVGGNYVNSALAKMEAVAAGADEALLLDEEGYVAEGSGENLFFVRDGVIYALEHSVNLEGITRDSVIRIAKDLGYEVQVVRATRDQLYMADEVFMTGTAAEVTPVSMIDWRPIGKGTAGPVALRLREVYLEAVTGRRPEYEGWLTYVN 306
                                    11        21        31        41        51        61        71        81        91       101       111       121    |    -   |   141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301     
                                                                                                                                                      126      135                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:305
 aligned with Q5SM19_THET8 | Q5SM19 from UniProtKB/TrEMBL  Length:308

    Alignment length:305
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301     
         Q5SM19_THET8     2 QIKAGLIWMNGAFVPQEEAKTSVLSHALHYGTSVFEGIRAYETAKGPAIFRLKEHVKRFYNSAKVLRMEIPFAPEELEEAIKEVVRRNGYRSCYIRPLAWMGAKALGVNPLPNNPAEVMVAAWEWGAYLGEEAVRKGARLITSSWARFPANVMPGKAKVGGNYVNSALAKMEAVAAGADEALLLDEEGYVAEGSGENLFFVRDGVIYALEHSVNLEGITRDSVIRIAKDLGYEVQVVRATRDQLYMADEVFMTGTAAEVTPVSMIDWRPIGKGTAGPVALRLREVYLEAVTGRRPEYEGWLTYVN 306
               SCOP domains d1wrvb_ B: automated matches                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ---1wrvB01 B:5-131  [code=3.30.470.10, no name defined]                                                                           1wrvB02 B:132-294 D-amino Acid Aminotransferase, subunit A, domain 2                                                                                               ------------ CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeehhhhh.....hhhhhhh.eee..eeeeee..eeeeehhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh....eeeeeeee.........hhhhh..eeeeeee......hhhhhhhheeeee................hhhhhhhhhhhhhhhhhh...eeeee.....eeee...eeeeee..eeeee.......hhhhhhhhhhhhhh..eeeee..hhhhhhh..eeeeee...eeeeeeee..ee......hhhhhhhhhhhhhhhh..hhhhhh.eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wrv B   2 QIKAGLIWMNGAFVPQEEAKTSVLSHALHYGTSVFEGIRAYETAKGPAIFRLKEHVKRFYNSAKVLRMEIPFAPEELEEAIKEVVRRNGYRSCYIRPLAWMGAKALGVNPLPNNPAEVMVAAWEWGAYLGEEAVRKGARLITSSWARFPANVMPGKAKVGGNYVNSALAKMEAVAAGADEALLLDEEGYVAEGSGENLFFVRDGVIYALEHSVNLEGITRDSVIRIAKDLGYEVQVVRATRDQLYMADEVFMTGTAAEVTPVSMIDWRPIGKGTAGPVALRLREVYLEAVTGRRPEYEGWLTYVN 306
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301     


Chain C from PDB  Type:PROTEIN  Length:295
 aligned with Q5SM19_THET8 | Q5SM19 from UniProtKB/TrEMBL  Length:308

    Alignment length:305
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301     
         Q5SM19_THET8     2 QIKAGLIWMNGAFVPQEEAKTSVLSHALHYGTSVFEGIRAYETAKGPAIFRLKEHVKRFYNSAKVLRMEIPFAPEELEEAIKEVVRRNGYRSCYIRPLAWMGAKALGVNPLPNNPAEVMVAAWEWGAYLGEEAVRKGARLITSSWARFPANVMPGKAKVGGNYVNSALAKMEAVAAGADEALLLDEEGYVAEGSGENLFFVRDGVIYALEHSVNLEGITRDSVIRIAKDLGYEVQVVRATRDQLYMADEVFMTGTAAEVTPVSMIDWRPIGKGTAGPVALRLREVYLEAVTGRRPEYEGWLTYVN 306
               SCOP domains d1wrvc_ C: automated matches                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ---1wrvC01 C:5-126  [code=3.30.470.10, no name defined]                                                                      ----------1wrvC02 C:137-294 D-amino Acid Aminotransferase, subunit A, domain 2                                                                                          ------------ CATH domains
           Pfam domains (1) -------------------------------------------------Aminotran_4-1wrvC01 C:51-287                                                                                                                                                                                                                 ------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------Aminotran_4-1wrvC02 C:51-287                                                                                                                                                                                                                 ------------------- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------Aminotran_4-1wrvC03 C:51-287                                                                                                                                                                                                                 ------------------- Pfam domains (3)
         Sec.struct. author ......eee..eeehhhhh.....hhhhhhh.eee..eeeeee..eeeeehhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhh..eeeeeeee.----------..eeeee................hhhhhhhhhhhhhhhhhh...eeeee.....eeee...eeeeee..eeeee.......hhhhhhhhhhhhhhh..eeee..hhhhhhh..eeeeee...eeeeeeee..ee......hhhhhhhhhhhhhhhh..hhhhhh.eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wrv C   2 QIKAGLIWMNGAFVPQEEAKTSVLSHALHYGTSVFEGIRAYETAKGPAIFRLKEHVKRFYNSAKVLRMEIPFAPEELEEAIKEVVRRNGYRSCYIRPLAWMGAKALGVNPLPNNPAEVMVAAWEW----------KGARLITSSWARFPANVMPGKAKVGGNYVNSALAKMEAVAAGADEALLLDEEGYVAEGSGENLFFVRDGVIYALEHSVNLEGITRDSVIRIAKDLGYEVQVVRATRDQLYMADEVFMTGTAAEVTPVSMIDWRPIGKGTAGPVALRLREVYLEAVTGRRPEYEGWLTYVN 306
                                    11        21        31        41        51        61        71        81        91       101       111       121    |    -     | 141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301     
                                                                                                                                                      126        137
   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, 3)

Asymmetric Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: Aminotran_4] (8)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q5SM19_THET8 | Q5SM19)
molecular function
    GO:0004084    branched-chain-amino-acid transaminase activity    Catalysis of the reaction: a branched-chain amino acid + 2-oxoglutarate = L-glutamate + a 2-oxocarboxylate derived from the branched-chain amino acid.
    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: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:0009081    branched-chain amino acid metabolic process    The chemical reactions and pathways involving amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
    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.

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  1wrv
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 Related Entries

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

UniProtKB/TrEMBL
        Q5SM19_THET8 | Q5SM19: 2eiy 2ej0 2ej2 2ej3

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1WRV)