5DJ1 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE OF THE PLP-DEPENDENT L-ARGININE HYDROXYLASE MPPP HOLOENZYME

Authors :   N. R. Silvaggi, L. Han

Date :   01 Sep 15 (Deposition) - 25 Nov 15 (Release) - 03 May 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: A,B,C,D  (1x)

Keywords :   Aminotransferase, Enduracididine, Hydroxylase, Pyridoxal 5'- Phosphate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Han, A. W. Schwabacher, G. R. Moran, N. R. Silvaggi
Streptomyces Wadayamensis Mppp Is A Pyridoxal 5'-Phosphate-Dependent L-Arginine Alpha-Deaminase, Gamma-Hydroxylase In The Enduracididine Biosynthetic Pathway.
Biochemistry V. 54 7029 2015
PubMed-ID: 26551990 | Reference-DOI: 10.1021/ACS.BIOCHEM.5B01016

Molecule 1 - PLP-DEPENDENT L-ARGININE HYDROXYLASE MPPP
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Organism Scientific	:	STREPTOMYCES WADAYAMENSIS
	Organism Taxid	:	141454

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	CL	4	Ligand/Ion	CHLORIDE ION
2	LLP	4	Mod. Amino Acid	(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC ACID
3	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	LLP	2	Mod. Amino Acid	(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC ACID
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	LLP	2	Mod. Amino Acid	(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC ACID
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (1, 4)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	LLP	4	Mod. Amino Acid	(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC ACID
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:28 , ASN A:160 , ARG A:352	binding site for residue CL A 500
02	AC2	SOFTWARE	GLY B:28 , ASN B:160 , ARG B:352	binding site for residue CL B 500
03	AC3	SOFTWARE	ASP B:116 , HOH B:609 , HOH B:790 , HOH D:632 , HOH D:648 , HOH D:756	binding site for residue MG B 501
04	AC4	SOFTWARE	GLY C:28 , ASN C:160 , ARG C:352	binding site for residue CL C 500
05	AC5	SOFTWARE	GLY D:28 , ASN D:160 , LLP D:221 , ARG D:352	binding site for residue CL D 500
06	AC6	SOFTWARE	HOH A:625 , GLY B:28 , HIS B:29 , SER B:89 , SER B:90 , SER B:91 , PHE B:115 , THR B:156 , ASN B:160 , ASP B:188 , SER B:190 , PHE B:194 , ASP B:218 , THR B:219 , LEU B:222 , TRP B:223 , LYS B:229 , HOH B:608 , HOH B:625 , HOH B:628 , HOH B:629 , HOH B:649 , HOH B:652 , HOH B:689	binding site for Di-peptide GLY B 220 and LLP B 221
07	AC7	SOFTWARE	HOH A:625 , GLY B:28 , HIS B:29 , SER B:89 , SER B:90 , SER B:91 , PHE B:115 , THR B:156 , ASN B:160 , ASP B:188 , SER B:190 , GLY B:193 , PHE B:194 , THR B:219 , GLY B:220 , TRP B:223 , LYS B:229 , LEU B:277 , HOH B:625 , HOH B:628 , HOH B:629 , HOH B:649 , HOH B:652 , HOH B:688 , HOH B:689	binding site for Di-peptide LLP B 221 and LEU B 222
08	AC8	SOFTWARE	GLY C:28 , HIS C:29 , SER C:89 , SER C:90 , SER C:91 , PHE C:115 , THR C:156 , ASN C:160 , ASP C:188 , SER C:190 , PHE C:194 , ASP C:218 , THR C:219 , LEU C:222 , TRP C:223 , LYS C:229 , HOH C:613 , HOH C:628 , HOH C:630 , HOH C:632 , HOH C:647 , HOH C:652 , HOH C:666 , HOH C:744 , HOH D:631	binding site for Di-peptide GLY C 220 and LLP C 221
09	AC9	SOFTWARE	GLY C:28 , HIS C:29 , SER C:89 , SER C:90 , SER C:91 , PHE C:115 , THR C:156 , ASN C:160 , ASP C:188 , SER C:190 , GLY C:193 , PHE C:194 , THR C:219 , GLY C:220 , TRP C:223 , LYS C:229 , LEU C:277 , HOH C:613 , HOH C:628 , HOH C:630 , HOH C:642 , HOH C:647 , HOH C:652 , HOH C:666 , HOH D:631	binding site for Di-peptide LLP C 221 and LEU C 222
10	AD1	SOFTWARE	HOH C:609 , GLY D:28 , HIS D:29 , SER D:89 , SER D:90 , SER D:91 , PHE D:115 , THR D:156 , ASN D:160 , ASP D:188 , SER D:190 , PHE D:191 , PHE D:194 , ASP D:218 , THR D:219 , LEU D:222 , TRP D:223 , LYS D:229 , CL D:500 , HOH D:606 , HOH D:610 , HOH D:614 , HOH D:618 , HOH D:630 , HOH D:642 , HOH D:703	binding site for Di-peptide GLY D 220 and LLP D 221
11	AD2	SOFTWARE	HOH C:609 , GLY D:28 , HIS D:29 , SER D:89 , SER D:90 , SER D:91 , PHE D:115 , THR D:156 , ASN D:160 , ASP D:188 , SER D:190 , PHE D:191 , GLY D:193 , PHE D:194 , THR D:219 , GLY D:220 , TRP D:223 , LYS D:229 , LEU D:277 , CL D:500 , HOH D:606 , HOH D:614 , HOH D:618 , HOH D:630 , HOH D:642 , HOH D:695 , HOH D:703	binding site for Di-peptide LLP D 221 and LEU D 222

(no "SS Bond" information available for 5DJ1)

Asymmetric Unit

No.	Residues
1	His A:112	-	Pro A:113
2	Thr A:157	-	Pro A:158
3	Asn A:160	-	Pro A:161
4	His B:112	-	Pro B:113
5	Thr B:157	-	Pro B:158
6	Asn B:160	-	Pro B:161
7	His C:112	-	Pro C:113
8	Thr C:157	-	Pro C:158
9	Asn C:160	-	Pro C:161
10	His D:112	-	Pro D:113
11	Thr D:157	-	Pro D:158
12	Asn D:160	-	Pro D:161

(no "SAP(SNP)/Variant" information available for 5DJ1)

(no "PROSITE Motif" information available for 5DJ1)

(no "Exon" information available for 5DJ1)

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:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeee.hhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhh..eeeeeehhhhhhh..hhhhhh...eeeee..........hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhh.hhhhhhhhhh.eeeeeee............eeeee......hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............eeeee....hhhhhhhhhhhh....ee.hhhh..hhhhhh.eeeee...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dj1 A  23 LNIADGHARQALSPGQQKIVNELPVLWAESEQRPVQQIESEAHQAYFTLLGQHGYPAEPGRVLSCYSSSVSMEILARSLSASVDRVALVHPTFDNIADLLRGNGLDLVPVEEDALHGADLSAELLSSVGCVFVTTPNNPTGRVLAEERLRRLAEQCAEHGTVLALDTSFRGFDAAAHYDHYAVLQEAGCRWVVIEDTGkLWPTLDLKAGLLVFSEDIGLPVEKIYSDILLGVSPLILALIREFSRDAADGGLADLHAFILHNRSVVRRALAGVEGVSFPDPESRSSVERVAFAGRTGTEVWEELQRHHVFALPCRQFHWAEPSDGDHMVRIALSRSTEPLEKSVQVLRTVL 373
                                    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 
                                                                                                                                                                                                                                221-LLP

Chain B from PDB  Type:PROTEIN  Length:353
                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeee.hhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhh..eeeeeehhhhhhh..hhhhhh...eeeee..........hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhh.hhhhhhhhhh.eeeeeee............eeeee......hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.........eeeeee...hhhhhhhhhhhh....ee.hhhh..hhhhhh.eeeee...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dj1 B  23 LNIADGHARQALSPGQQKIVNELPVLWAESEQRPVQQIESEAHQAYFTLLGQHGYPAEPGRVLSCYSSSVSMEILARSLSASVDRVALVHPTFDNIADLLRGNGLDLVPVEEDALHGADLSAELLSSVGCVFVTTPNNPTGRVLAEERLRRLAEQCAEHGTVLALDTSFRGFDAAAHYDHYAVLQEAGCRWVVIEDTGkLWPTLDLKAGLLVFSEDIGLPVEKIYSDILLGVSPLILALIREFSRDAADGGLADLHAFILHNRSVVRRALAGVEGVSFPDPESRSSVERVAFAGRTGTEVWEELQRHHVFALPCRQFHWAEPSDGDHMVRIALSRSTEPLEKSVQVLRTVLET 375
                                    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   
                                                                                                                                                                                                                                221-LLP

Chain C from PDB  Type:PROTEIN  Length:353
                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeee.hhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhh..eeeeeehhhhhhh..hhhhhhh..eeeee..........hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhh.hhhhhhhhhh..eeeeee............eeeee......hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............eeeee....hhhhhhhhhhhh....ee.hhhh..hhhhhh.eeeee...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dj1 C  23 LNIADGHARQALSPGQQKIVNELPVLWAESEQRPVQQIESEAHQAYFTLLGQHGYPAEPGRVLSCYSSSVSMEILARSLSASVDRVALVHPTFDNIADLLRGNGLDLVPVEEDALHGADLSAELLSSVGCVFVTTPNNPTGRVLAEERLRRLAEQCAEHGTVLALDTSFRGFDAAAHYDHYAVLQEAGCRWVVIEDTGkLWPTLDLKAGLLVFSEDIGLPVEKIYSDILLGVSPLILALIREFSRDAADGGLADLHAFILHNRSVVRRALAGVEGVSFPDPESRSSVERVAFAGRTGTEVWEELQRHHVFALPCRQFHWAEPSDGDHMVRIALSRSTEPLEKSVQVLRTVLET 375
                                    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   
                                                                                                                                                                                                                                221-LLP

Chain D from PDB  Type:PROTEIN  Length:364
                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.ee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeee.hhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhh..eeeeeehhhhhhh..hhhhhhhh.eeeee..........hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhh.hhhhhhhhhh.eeeeeee............eeeee......hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............eeeee....hhhhhhhhhhhh.ee.ee.hhhh..hhhhhh.eeeee...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dj1 D  11 LTQWEYLALNSELNIADGHARQALSPGQQKIVNELPVLWAESEQRPVQQIESEAHQAYFTLLGQHGYPAEPGRVLSCYSSSVSMEILARSLSASVDRVALVHPTFDNIADLLRGNGLDLVPVEEDALHGADLSAELLSSVGCVFVTTPNNPTGRVLAEERLRRLAEQCAEHGTVLALDTSFRGFDAAAHYDHYAVLQEAGCRWVVIEDTGkLWPTLDLKAGLLVFSEDIGLPVEKIYSDILLGVSPLILALIREFSRDAADGGLADLHAFILHNRSVVRRALAGVEGVSFPDPESRSSVERVAFAGRTGTEVWEELQRHHVFALPCRQFHWAEPSDGDHMVRIALSRSTEPLEKSVQVLRTVLE 374
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220|      230       240       250       260       270       280       290       300       310       320       330       340       350       360       370    
                                                                                                                                                                                                                                            221-LLP

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 '\|'

(no "SCOP Domain" information available for 5DJ1)

(no "CATH Domain" information available for 5DJ1)

(no "Pfam Domain" information available for 5DJ1)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 5DJ1)

Asymmetric Unit
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	Cis Peptide Bonds
		Asn A:160 - Pro A:161	[ RasMol ]
		Asn B:160 - Pro B:161	[ RasMol ]
		Asn C:160 - Pro C:161	[ RasMol ]
		Asn D:160 - Pro D:161	[ RasMol ]
		His A:112 - Pro A:113	[ RasMol ]
		His B:112 - Pro B:113	[ RasMol ]
		His C:112 - Pro C:113	[ RasMol ]
		His D:112 - Pro D:113	[ RasMol ]
		Thr A:157 - Pro A:158	[ RasMol ]
		Thr B:157 - Pro B:158	[ RasMol ]
		Thr C:157 - Pro C:158	[ RasMol ]
		Thr D:157 - Pro D:158	[ RasMol ]

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		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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	5dj1
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	A0A0X1KHF5_9 \| A0A0X1KHF5	:	5dj3

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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