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Title :   CRYSTAL STRUCTURE OF A HISTIDINOL-PHOSPHATE AMINOTRANSFERASE FROM GEOBACTER METALLIREDUCENS

Authors :   L. Damodharan, S. K. Burley, S. Swaminathan, New York Sgx Research For Structural Genomics (Nysgxrc)

Date :   07 May 09 (Deposition) - 19 May 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.61

Chains :   Asym./Biol. Unit : A,B

Keywords :   Transferase, Psi-Ii, 11246F, Histidinol-Phosphate Aminotransferase, Structural Genomics, Protein Structure Initiative, Nysgxrc, New York Sgx Research Center For Structural Genomics, Amino-Acid Biosynthesis, Aminotransferase, Histidine Biosynthesis, Pyridoxal Phosphate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Damodhran, S. K. Burley, S. Swaminathan
Crystal Structure Of An Histidinol-Phosphate Aminotransferase From Geobacter Metallireducens
To Be Published
PubMed: search

Molecule 1 - HISTIDINOL-PHOSPHATE AMINOTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.6.1.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSGX3(BC)
	Expression System Vector Type	:	PLASMID
	Gene	:	HISC, GMET_0385
	Organism Scientific	:	GEOBACTER METALLIREDUCENS GS-15
	Organism Taxid	:	269799
	Synonym	:	IMIDAZOLE ACETOL-PHOSPHATE TRANSAMINASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 14)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:28 , GLU A:33 , ASN A:34 , PRO A:35 , GLY A:334 , GLU A:338 , HOH A:420 , HOH A:432 , HOH A:469 , HOH A:556 , ARG B:58 , ILE B:59	BINDING SITE FOR RESIDUE GOL A 359
2	AC2	SOFTWARE	GLU A:348 , HOH A:586	BINDING SITE FOR RESIDUE MG A 360

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

Asymmetric/Biological Unit

No.	Residues
1	His A:111	-	Pro A:112
2	Thr A:155	-	Pro A:156
3	Ala A:158	-	Pro A:159
4	His B:111	-	Pro B:112
5	Thr B:155	-	Pro B:156
6	Ala B:158	-	Pro B:159

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRANSFER_CLASS_2	PS00599	Aminotransferases class-II pyridoxal-phosphate attachment site.	HIS8_GEOMG	209-218	2	A:209-218 B:209-218

(no "Exon" information available for 3HDO)

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:350
 aligned with HIS8_GEOMG | Q39YP6 from UniProtKB/Swiss-Prot  Length:350

    Alignment length:350
                                                                                                                                                                                                                                                                                                                                                                                      350 
                                    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        |-
           HIS8_GEOMG     2 IPLRQNIASMKGYIPGYQPPDIASWIKLNTNENPYPPSPEVVKAILEELGPDGAALRIYPSASSQKLREVAGELYGFDPSWIIMANGSDEVLNNLIRAFAAEGEEIGYVHPSYSYYGTLAEVQGARVRTFGLTGDFRIAGFPERYEGKVFFLTTPNAPLGPSFPLEYIDELARRCAGMLVLDETYAEFAESNALELVRRHENVVVTRTLSKSYSLAGMRIGLAIARPEVIAALDKIRDHYNLDRLAQAACVAALRDQAYLSECCRRIRETREWFTTELRSIGYDVIPSQGNYLFATPPDRDGKRVYDGLYARKVLVRHFSDPLLAHGMRISIGTREEMEQTLAALKEIG-   -
               SCOP domains d3hdoa_ A: automated matches                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh...............ee..........hhhhhhhhhhhhh..hhhhhh.....hhhhhhhhhhhhh.hhh.eeee.hhhhhhhhhhhhhh....eeeee....hhhhhhhhhhh.eeeee..................eeeee..........hhhhhhhhhhhh..eeeee..hhhhh....hhhhhhh..eeeeee............eeee.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee......eeeee....hhhhhhhhhhhh.ee............eeee..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFE------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hdo A   2 IPLRQNIASmKGYIPGYQPPDIASWIKLNTNENPYPPSPEVVKAILEELGPDGAALRIYPSASSQKLREVAGELYGFDPSWIImANGSDEVLNNLIRAFAAEGEEIGYVHPSYSYYGTLAEVQGARVRTFGLTGDFRIAGFPERYEGKVFFLTTPNAPLGPSFPLEYIDELARRCAGmLVLDETYAEFAESNALELVRRHENVVVTRTLSKSYSLAGmRIGLAIARPEVIAALDKIRDHYNLDRLAQAACVAALRDQAYLSECCRRIRETREWFTTELRSIGYDVIPSQGNYLFATPPDRDGKRVYDGLYARKVLVRHFSDPLLAHGmRISIGTREEmEQTLAALKEIGE 351
                                    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
                                    11-MSE                                                                    85-MSE                                                                                       179-MSE                                 219-MSE                                                                                                       329-MSE   339-MSE

Chain B from PDB  Type:PROTEIN  Length:349
 aligned with HIS8_GEOMG | Q39YP6 from UniProtKB/Swiss-Prot  Length:350

    Alignment length:349
                                    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         
           HIS8_GEOMG     2 IPLRQNIASMKGYIPGYQPPDIASWIKLNTNENPYPPSPEVVKAILEELGPDGAALRIYPSASSQKLREVAGELYGFDPSWIIMANGSDEVLNNLIRAFAAEGEEIGYVHPSYSYYGTLAEVQGARVRTFGLTGDFRIAGFPERYEGKVFFLTTPNAPLGPSFPLEYIDELARRCAGMLVLDETYAEFAESNALELVRRHENVVVTRTLSKSYSLAGMRIGLAIARPEVIAALDKIRDHYNLDRLAQAACVAALRDQAYLSECCRRIRETREWFTTELRSIGYDVIPSQGNYLFATPPDRDGKRVYDGLYARKVLVRHFSDPLLAHGMRISIGTREEMEQTLAALKEIG 350
               SCOP domains d3hdob_ B: automated matches                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh...............ee..........hhhhhhhhhhhhh..hhhhhh.....hhhhhhhhhhhhh.hhh.eeee.hhhhhhhhhhhhhh....eeeee....hhhhhhhhhhh.eeeee..................eeeee..........hhhhhhhhhhhh..eeeee..hhhhh....hhhhhhh..eeeeee............eeee.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee......eeeee....hhhhhhhhhhhh.ee............eeee..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFE------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hdo B   2 IPLRQNIASmKGYIPGYQPPDIASWIKLNTNENPYPPSPEVVKAILEELGPDGAALRIYPSASSQKLREVAGELYGFDPSWIImANGSDEVLNNLIRAFAAEGEEIGYVHPSYSYYGTLAEVQGARVRTFGLTGDFRIAGFPERYEGKVFFLTTPNAPLGPSFPLEYIDELARRCAGmLVLDETYAEFAESNALELVRRHENVVVTRTLSKSYSLAGmRIGLAIARPEVIAALDKIRDHYNLDRLAQAACVAALRDQAYLSECCRRIRETREWFTTELRSIGYDVIPSQGNYLFATPPDRDGKRVYDGLYARKVLVRHFSDPLLAHGmRISIGTREEmEQTLAALKEIG 350
                                    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         
                                    11-MSE                                                                    85-MSE                                                                                       179-MSE                                 219-MSE                                                                                                       329-MSE   339-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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: PLP-dependent transferase-like (627)

Superfamily: PLP-dependent transferases (625)

Family: automated matches (163)

Protein domain: automated matches (163)

Geobacter metallireducens [TaxId: 269799] (1)

1a	d3hdoa_	A:
1b	d3hdob_	B:

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (HIS8_GEOMG | Q39YP6)

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.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:158 - Pro A:159	[ RasMol ]
		Ala B:158 - Pro B:159	[ RasMol ]
		His A:111 - Pro A:112	[ RasMol ]
		His B:111 - Pro B:112	[ RasMol ]
		Thr A:155 - Pro A:156	[ RasMol ]
		Thr B:155 - Pro B:156	[ RasMol ]

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Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 14)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

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