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(-) Description

Title :  THE CRYSTAL STRUCTURE OF HISTIDINOL-PHOSPHATE AMINOTRANSFERASE FROM LISTERIA INNOCUA CLIP11262.
 
Authors :  K. Tan, M. Gu, A. Joachimiak, Midwest Center For Structural Genomi
Date :  03 Dec 08  (Deposition) - 23 Dec 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Apc88260, Histidinol-Phosphate Aminotransferase, Listeria Innocua Clip11262, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Amino-Acid Biosynthesis, Aminotransferase, Histidine Biosynthesis, Pyridoxal Phosphate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, M. Gu, A. Joachimiak
The Crystal Structure Of Histidinol-Phosphate Aminotransferase From Listeria Innocua Clip11262.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HISTIDINOL-PHOSPHATE AMINOTRANSFERASE
    Chains: A, B
    EC Number: 2.6.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HISC, LIN2039, LISTERIA INNOCUA
    Organism Scientific: LISTERIA INNOCUA
    Organism Taxid: 1642
    Strain: CLIP11262
    Synonym: IMIDAZOLE ACETOL-PHOSPHATE TRANSAMINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 17)

Asymmetric/Biological Unit (2, 17)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2SO49Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:89 , VAL A:90 , ASP A:91 , THR A:219 , SER A:221 , LYS A:222 , ARG A:230BINDING SITE FOR RESIDUE SO4 A 361
2AC2SOFTWARETYR A:168 , GLU A:170 , LEU A:171 , PRO A:201 , GLU A:202 , HOH A:394BINDING SITE FOR RESIDUE SO4 A 362
3AC3SOFTWAREPHE A:115 , ASN A:163 , ARG A:328 , ARG A:340 , HOH A:421BINDING SITE FOR RESIDUE SO4 A 363
4AC4SOFTWARELYS A:46 , ASP A:267 , ALA A:269 , PHE A:270 , GLU B:151 , GLU B:347BINDING SITE FOR RESIDUE SO4 A 364
5AC5SOFTWAREGLY B:89 , VAL B:90 , ASP B:91 , THR B:219 , SER B:221 , ARG B:230BINDING SITE FOR RESIDUE SO4 B 361
6AC6SOFTWAREPHE B:115 , ASN B:163 , ARG B:328 , ARG B:340 , HOH B:371 , HOH B:413BINDING SITE FOR RESIDUE SO4 B 362
7AC7SOFTWAREGLU B:80 , GLU B:83 , ARG B:209 , ASP B:237 , LYS B:238BINDING SITE FOR RESIDUE SO4 B 363
8AC8SOFTWAREASP B:267 , ALA B:269 , PHE B:270 , SO4 B:365BINDING SITE FOR RESIDUE SO4 B 364
9AC9SOFTWARESER B:44 , LYS B:45 , LYS B:46 , SO4 B:364BINDING SITE FOR RESIDUE SO4 B 365

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Thr A:112 -Pro A:113
2Asn A:160 -Pro A:161
3Asn A:163 -Pro A:164
4Thr A:198 -Pro A:199
5Thr B:112 -Pro B:113
6Asn B:160 -Pro B:161
7Asn B:163 -Pro B:164
8Thr B:198 -Pro B:199

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FFH)

(-) 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:354
 aligned with HIS8_LISIN | Q92A83 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:362
                              1                                                                                                                                                                                                                                                                                                                                                                       
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358  
           HIS8_LISIN     - --MKWKKSLAGLSSYKPGKREEEVMAELGLTKITKLSSNENPLGTSKKVAAIQANSSVETEIYPDGWASSLRKEVADFYQLEEEELIFTAGVDELIELLTRVLLDTTTNTVMATPTFVQYRQNALIEGAEVREIPLLQDGEHDLEGMLNAIDEKTTIVWICNPNNPTGNYIELADIQAFLDRVPSDVLVVLDEAYIEYVTPQPEKHEKLVRTYKNLIITRTFSKIYGLASARVGYGIADKEIIRQLNIVRPPFNTTSIGQKLAIEAIKDQAFIGECRTSNANGIKQYEAFAKRFEKVKLYPANGNFVLIDLGIEAGTIFSYLEKNGYITRSGAALGFPTAVRITIGKEEDNSAVIALLEKLL 360
               SCOP domains d3ffha_ A: aut    omated matches                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------3    ffhA01 A:12-53,A:267-360             3ffhA02     A:54-266 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                             3ffhA01 A:12-53,A:267-360 Aspartate Aminotransferase, domain 1                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh....----hhhhhhhhh......ee..........hhhhhhhhhh........----hhhhhhhhhhhhh.hhh.eeee.hhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhh.eeeeee.......hhhhhhhhh...eeeeeee..........hhhhhhhhhh......eeeee..hhhhh......hhhhhhh...eeeeee............eeeeehhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee......eeeee...hhhhhhhhhhhh.ee.ee........eeeee..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ffh A  -1 NAmKWKKSLAGLSS----KREEEVmAELGLTKITKLSSNENPLGTSKKVAAIQANSSVETEIY----ASSLRKEVADFYQLEEEELIFTAGVDELIELLTRVLLDTTTNTVmATPTFVQYRQNALIEGAEVREIPLLQDGEHDLEGmLNAIDEKTTIVWICNPNNPTGNYIELADIQAFLDRVPSDVLVVLDEAYIEYVTPQPEKHEKLVRTYKNLIITRTFSKIYGLASARVGYGIADKEIIRQLNIVRPPFNTTSIGQKLAIEAIKDQAFIGECRTSNANGIKQYEAFAKRFEKVKLYPANGNFVLIDLGIEAGTIFSYLEKNGYITRSGAALGFPTAVRITIGKEEDNSAVIALLEKLL 360
                              |      8   |    18    |   28        38        48        58  |    |68        78        88        98       108 |     118       128       138      |148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358  
                              |         12   17     |                                    61   66                                         110-MSE                            145-MSE                                                                                                                                                                                                                   
                              1-MSE                23-MSE                                                                                                                                                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:352
 aligned with HIS8_LISIN | Q92A83 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:361
                             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 
           HIS8_LISIN     - -MKWKKSLAGLSSYKPGKREEEVMAELGLTKITKLSSNENPLGTSKKVAAIQANSSVETEIYPDGWASSLRKEVADFYQLEEEELIFTAGVDELIELLTRVLLDTTTNTVMATPTFVQYRQNALIEGAEVREIPLLQDGEHDLEGMLNAIDEKTTIVWICNPNNPTGNYIELADIQAFLDRVPSDVLVVLDEAYIEYVTPQPEKHEKLVRTYKNLIITRTFSKIYGLASARVGYGIADKEIIRQLNIVRPPFNTTSIGQKLAIEAIKDQAFIGECRTSNANGIKQYEAFAKRFEKVKLYPANGNFVLIDLGIEAGTIFSYLEKNGYITRSGAALGFPTAVRITIGKEEDNSAVIALLEKLL 360
               SCOP domains d3ffhb_ B: a      utomated matches                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------      3ffhB01 B:18-53,B:267-360           3ffhB02 B   :54-266 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                              3ffhB01 B:18-53,B:267-360 Aspartate Aminotransferase, domain 1                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh...------hhhhhhhh......ee..........hhhhhhhhhh.........---hhhhhhhhhhhh..hhh.eeee.hhhhhhhhhhhhhh....eeeeee...hhhhhhhhhh..eeeeee.......hhhhhhhhh...eeeeeee..........hhhhhhhhhhhh....eeeee..hhhhh........hhhhhh..eeeeee............eeeeehhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee......eeeee...hhhhhhhhhhh..ee.ee.hhh....eeeee..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ffh B   0 AmKWKKSLAGLS------REEEVmAELGLTKITKLSSNENPLGTSKKVAAIQANSSVETEIYP---ASSLRKEVADFYQLEEEELIFTAGVDELIELLTRVLLDTTTNTVmATPTFVQYRQNALIEGAEVREIPLLQDGEHDLEGmLNAIDEKTTIVWICNPNNPTGNYIELADIQAFLDRVPSDVLVVLDEAYIEYVTPQPEKHEKLVRTYKNLIITRTFSKIYGLASARVGYGIADKEIIRQLNIVRPPFNTTSIGQKLAIEAIKDQAFIGECRTSNANGIKQYEAFAKRFEKVKLYPANGNFVLIDLGIEAGTIFSYLEKNGYITRSGAALGFPTAVRITIGKEEDNSAVIALLEKLL 360
                             |       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 
                             1-MSE    11     18    |                                     62  66                                         110-MSE                            145-MSE                                                                                                                                                                                                                   
                                                  23-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  (2, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (HIS8_LISIN | Q92A83)
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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