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(-) Description

Title :  CRYSTAL STRUCTURE OF HISTIDINOL-PHOSPHATE AMINOTRANSFERASE (YP_297314.1) FROM RALSTONIA EUTROPHA JMP134 AT 2.05 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  09 Oct 08  (Deposition) - 11 Nov 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Yp_297314. 1, Histidinol-Phosphate Aminotransferase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Amino-Acid Biosynthesis, Aminotransferase, Histidine Biosynthesis, Pyridoxal Phosphate, Transferase, Aminotransferase Class I And Ii (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Histidinol-Phosphate Aminotransferase (Yp_297314. 1) From Ralstonia Eutropha Jmp134 At 2. 05 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HISTIDINOL-PHOSPHATE AMINOTRANSFERASE 2
    Chains: A, B
    EC Number: 2.6.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YP_297314.1, HISC2, REUT_A3110
    Organism Common: ALCALIGENES EUTROPHUS
    Organism Scientific: RALSTONIA EUTROPHA JMP134
    Organism Taxid: 264198
    Synonym: IMIDAZOLE ACETOL-PHOSPHATE TRANSAMINASE 2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 52)

Asymmetric/Biological Unit (3, 52)
No.NameCountTypeFull Name
1GOL14Ligand/IonGLYCEROL
2MSE31Mod. Amino AcidSELENOMETHIONINE
3SO47Ligand/IonSULFATE ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMSE B:37 , ASN B:167 , ARG B:344 , GOL B:372 , HOH B:423 , HOH B:648BINDING SITE FOR RESIDUE SO4 B 367
02AC2SOFTWAREGLY B:0 , MSE B:1 , SER B:2 , GLY B:296 , GLY B:297 , HOH B:609 , HOH B:714BINDING SITE FOR RESIDUE SO4 B 368
03AC3SOFTWAREASN A:39 , SER A:225 , LYS A:226 , ARG A:233BINDING SITE FOR RESIDUE SO4 A 367
04AC4SOFTWAREASN B:39 , SER B:225 , LYS B:226 , LEU B:227 , GLY B:228 , ARG B:233BINDING SITE FOR RESIDUE SO4 B 369
05AC5SOFTWARETYR A:23 , MSE A:37 , ASN A:167 , LYS A:330 , ARG A:344 , HOH B:639BINDING SITE FOR RESIDUE SO4 A 368
06AC6SOFTWAREGLY B:21 , ALA B:22 , ASP B:174 , ALA B:175 , HOH B:466 , HOH B:573BINDING SITE FOR RESIDUE SO4 B 370
07AC7SOFTWAREGLY A:92 , SER A:93 , ASP A:94 , THR A:223 , ARG A:233 , HOH B:439BINDING SITE FOR RESIDUE SO4 A 369
08AC8SOFTWAREVAL B:115 , PRO B:116 , GLY B:117 , PHE B:118 , VAL B:119 , TYR B:121 , ALA B:122 , HOH B:498BINDING SITE FOR RESIDUE GOL B 371
09AC9SOFTWAREARG A:285 , SER A:286 , PHE A:301 , PRO A:302 , SER A:303 , LEU A:308 , HOH A:388 , HOH A:392 , HOH B:621 , HOH B:681BINDING SITE FOR RESIDUE GOL A 370
10BC1SOFTWAREGLY B:117 , PHE B:118 , VAL B:119 , PRO B:168 , LYS B:330 , MSE B:335 , SO4 B:367 , HOH B:498 , HOH B:624BINDING SITE FOR RESIDUE GOL B 372
11BC2SOFTWAREPRO B:6 , SER B:7 , GLU B:10 , ARG B:285 , SER B:286 , PRO B:302 , SER B:303BINDING SITE FOR RESIDUE GOL B 373
12BC3SOFTWAREASP A:320 , VAL B:78 , GLN B:80 , PHE B:203 , ALA B:204 , HOH B:579 , HOH B:724BINDING SITE FOR RESIDUE GOL B 374
13BC4SOFTWAREHIS A:24 , LYS A:33 , ASP A:35 , ALA A:36 , PRO B:253 , HOH B:655BINDING SITE FOR RESIDUE GOL A 371
14BC5SOFTWAREILE A:232 , TYR A:254 , HOH A:387 , ASP B:94 , GLU B:95 , HOH B:453BINDING SITE FOR RESIDUE GOL A 372
15BC6SOFTWAREASP A:366 , TYR B:164 , TRP B:208 , ARG B:211BINDING SITE FOR RESIDUE GOL B 375
16BC7SOFTWAREGLU A:95 , TYR A:254 , SER B:98 , MSE B:120 , SER B:124 , PHE B:127 , HOH B:469 , HOH B:663BINDING SITE FOR RESIDUE GOL A 373
17BC8SOFTWARETYR A:164 , PHE A:173 , ASP A:174 , ALA A:175 , GLU A:206 , HOH B:461BINDING SITE FOR RESIDUE GOL A 374
18BC9SOFTWARETYR A:164 , GLU A:206 , SER A:207 , ARG A:211BINDING SITE FOR RESIDUE GOL A 375
19CC1SOFTWAREARG A:14 , ASP A:15 , ASP A:16 , ARG B:106 , PRO B:107BINDING SITE FOR RESIDUE GOL A 376
20CC2SOFTWAREHIS B:295 , GLY B:296 , HOH B:654 , HOH B:729 , HOH B:730BINDING SITE FOR RESIDUE GOL B 376
21CC3SOFTWAREHIS A:295 , GLY A:296 , GLN A:365BINDING SITE FOR RESIDUE GOL A 377

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EUC)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Val A:115 -Pro A:116
2Tyr A:164 -Pro A:165
3Asn A:167 -Pro A:168
4Val B:115 -Pro B:116
5Tyr B:164 -Pro B:165
6Asn B:167 -Pro B:168

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EUC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EUC)

(-) Exons   (0, 0)

(no "Exon" information available for 3EUC)

(-) 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:365
 aligned with HIS82_CUPNJ | Q46WL3 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:365
                                    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       311       321       331       341       351       361     
          HIS82_CUPNJ     2 SVVDPSLIERIIRDDVRAMGAYHVPDSHGLVKLDAMENPYRLPPALRSELAARLGEVALNRYPVPSSEALRAKLKEVMQVPAGMEVLLGNGSDEIISMLALAAARPGAKVMAPVPGFVMYAMSAQFAGLEFVGVPLRADFTLDRGAMLAAMAEHQPAIVYLAYPNNPTGNLFDAADMEAIVRAAQGSVCRSLVVVDEAYQPFAQESWMSRLTDFGNLLVMRTVSKLGLAGIRLGYVAGDPQWLEQLDKVRPPYNVNVLTEATALFALEHVAVLDEQAAQLRAERSRVAEGMAAHGGVTVFPSAANFLLARVPDAAQTFDRLLARKVLIKNVSKMHPLLANCLRVTVSTPEENAQFLEAFAASLQD 366
               SCOP domains d3euca_ A: automated matches                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh...........ee..........hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhh.....eeeeee......hhhhhh...eeeeee.......hhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhh.......eeeee..........hhhhhhh...eeeeee..........eeeeeehhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee......eeeee..hhhhhhhhhhh..ee.ee.hhhhhhhh.eeeee..hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3euc A   2 SVVDPSLIERIIRDDVRAmGAYHVPDSHGLVKLDAmENPYRLPPALRSELAARLGEVALNRYPVPSSEALRAKLKEVmQVPAGmEVLLGNGSDEIISmLALAAARPGAKVmAPVPGFVmYAmSAQFAGLEFVGVPLRADFTLDRGAmLAAmAEHQPAIVYLAYPNNPTGNLFDAADmEAIVRAAQGSVCRSLVVVDEAYQPFAQESWmSRLTDFGNLLVmRTVSKLGLAGIRLGYVAGDPQWLEQLDKVRPPYNVNVLTEATALFALEHVAVLDEQAAQLRAERSRVAEGmAAHGGVTVFPSAANFLLARVPDAAQTFDRLLARKVLIKNVSKmHPLLANCLRVTVSTPEENAQFLEAFAASLQD 366
                                    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       311       321       331   |   341       351       361     
                                             20-MSE           37-MSE                                    79-MSE |            99-MSE      112-MSE 120-MSE                     148-MSE                       178-MSE                        209-MSE     221-MSE                                                                292-MSE                                    335-MSE                           
                                                                                                              85-MSE                               123-MSE                      152-MSE                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:357
 aligned with HIS82_CUPNJ | Q46WL3 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:366
                             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       349       359      
          HIS82_CUPNJ     - -MSVVDPSLIERIIRDDVRAMGAYHVPDSHGLVKLDAMENPYRLPPALRSELAARLGEVALNRYPVPSSEALRAKLKEVMQVPAGMEVLLGNGSDEIISMLALAAARPGAKVMAPVPGFVMYAMSAQFAGLEFVGVPLRADFTLDRGAMLAAMAEHQPAIVYLAYPNNPTGNLFDAADMEAIVRAAQGSVCRSLVVVDEAYQPFAQESWMSRLTDFGNLLVMRTVSKLGLAGIRLGYVAGDPQWLEQLDKVRPPYNVNVLTEATALFALEHVAVLDEQAAQLRAERSRVAEGMAAHGGVTVFPSAANFLLARVPDAAQTFDRLLARKVLIKNVSKMHPLLANCLRVTVSTPEENAQFLEAFAASLQ 365
               SCOP domains d3eucb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh...........eee.....-...hhhhhhhhhhhhhhh--------hhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhh.....eeeeee...hhhhhhhhhh..eeeeee.......hhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhh.......eeeee..........hhhhhhh...eeeeee..........eeeeeehhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee......eeeee..hhhhhhhhhhhh.eeeee....hhhhh.eeeee..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3euc B   0 GmSVVDPSLIERIIRDDVRAmGAYHVPDSHGLVKLDAmEN-YRLPPALRSELAARLGEV--------SSEALRAKLKEVmQVPAGmEVLLGNGSDEIISmLALAAARPGAKVmAPVPGFVmYAmSAQFAGLEFVGVPLRADFTLDRGAmLAAmAEHQPAIVYLAYPNNPTGNLFDAADmEAIVRAAQGSVCRSLVVVDEAYQPFAQESWmSRLTDFGNLLVmRTVSKLGLAGIRLGYVAGDPQWLEQLDKVRPPYNVNVLTEATALFALEHVAVLDEQAAQLRAERSRVAEGmAAHGGVTVFPSAANFLLARVPDAAQTFDRLLARKVLIKNVSKmHPLLANCLRVTVSTPEENAQFLEAFAASLQ 365
                             |       9        19|       29       |39 |      49        |-       |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       349       359      
                             1-MSE             20-MSE           37-MSE               58       67          79-MSE |            99-MSE      112-MSE 120-MSE                     148-MSE                       178-MSE                        209-MSE     221-MSE                                                                292-MSE                                    335-MSE                          
                                                                  39 |                                          85-MSE                               123-MSE                      152-MSE                                                                                                                                                                                                                 
                                                                    41
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "CATH Domain" information available for 3EUC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EUC)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (HIS82_CUPNJ | Q46WL3)
molecular function
    GO:0080130    L-phenylalanine:2-oxoglutarate aminotransferase activity    Catalysis of the reaction: L-phenylalanine + 2-oxoglutarate = phenylpyruvate + 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:0004400    histidinol-phosphate transaminase activity    Catalysis of the reaction: L-histidinol-phosphate + 2-oxoglutarate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + L-glutamate.
    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:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    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:0000105    histidine biosynthetic process    The chemical reactions and pathways resulting in the formation of histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.

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