4Q73 - JenaLib

Title :   CRYSTAL STRUCTURE OF BRADYRHIZOBIUM JAPONICUM PROLINE UTILIZATION A (PUTA) MUTANT D778Y

Authors :   J. J. Tanner, M. Luo, T. A. Pemberton

Date :   23 Apr 14 (Deposition) - 06 Aug 14 (Release) - 10 Sep 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Proline Utilization A, Puta, Beta-Alpha Barrel, Rossmann Fold, Proline Dehydrogenase, 1-Pyrroline-5-Carboxylate Dehydrogenase, Fad Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. W. Arentson, M. Luo, T. A. Pemberton, J. J. Tanner, D. F. Becker
Kinetic And Structural Characterization Of Tunnel-Perturbin Mutants In Bradyrhizobium Japonicum Proline Utilization A.
Biochemistry V. 53 5150 2014
PubMed-ID: 25046425 | Reference-DOI: 10.1021/BI5007404

Compounds

Molecule 1 - PROLINE DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.5.99.8, 1.2.1.88
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKA8H
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BJ6T_21270, BLR7261, PUTA
	Mutation	:	YES
	Organism Scientific	:	BRADYRHIZOBIUM DIAZOEFFICIENS
	Organism Taxid	:	224911
	Strain	:	USDA 110

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 14)

Asymmetric Unit (3, 14)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	GOL	4	Ligand/Ion	GLYCEROL
3	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 28)

No.	Name	Count	Type	Full Name
1	FAD	4	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	GOL	8	Ligand/Ion	GLYCEROL
3	SO4	16	Ligand/Ion	SULFATE ION

Sites (14, 14)

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:278 , ALA A:279 , ALA A:310 , GLN A:312 , TYR A:314 , ARG A:339 , VAL A:341 , LYS A:342 , GLY A:343 , ALA A:344 , TYR A:345 , TRP A:346 , PHE A:364 , THR A:365 , ARG A:366 , LYS A:367 , THR A:370 , ALA A:393 , THR A:394 , HIS A:395 , ASN A:396 , TYR A:441 , SER A:466 , PHE A:467 , HOH A:2136 , HOH A:2137 , HOH A:2138 , HOH A:2303	BINDING SITE FOR RESIDUE FAD A 2001
02	AC2	SOFTWARE	PHE A:659 , ARG A:791 , CYS A:792 , SER A:793 , ILE A:945 , GLY A:946 , ALA A:947 , HOH A:2212	BINDING SITE FOR RESIDUE SO4 A 2002
03	AC3	SOFTWARE	GLY A:570 , ARG A:624	BINDING SITE FOR RESIDUE SO4 A 2003
04	AC4	SOFTWARE	ARG A:366 , LYS A:367 , ALA A:368 , HOH A:2141	BINDING SITE FOR RESIDUE SO4 A 2004
05	AC5	SOFTWARE	SER A:585 , ARG A:586	BINDING SITE FOR RESIDUE SO4 A 2005
06	AC6	SOFTWARE	TYR A:12 , ASP A:359 , VAL A:517 , GLU A:518 , ALA A:524	BINDING SITE FOR RESIDUE GOL A 2006
07	AC7	SOFTWARE	ARG A:356 , VAL A:517 , GLU A:518 , PHE A:519 , ASP A:603 , HOH A:2140	BINDING SITE FOR RESIDUE GOL A 2007
08	AC8	SOFTWARE	ASP B:278 , ALA B:279 , ALA B:310 , GLN B:312 , TYR B:314 , ARG B:339 , VAL B:341 , LYS B:342 , GLY B:343 , ALA B:344 , TYR B:345 , TRP B:346 , PHE B:364 , THR B:365 , ARG B:366 , LYS B:367 , THR B:370 , ALA B:393 , THR B:394 , HIS B:395 , ASN B:396 , TYR B:441 , SER B:465 , SER B:466 , PHE B:467 , HOH B:1124	BINDING SITE FOR RESIDUE FAD B 1001
09	AC9	SOFTWARE	PHE B:659 , ARG B:791 , SER B:793 , ILE B:945 , GLY B:946 , ALA B:947 , HOH B:1105	BINDING SITE FOR RESIDUE SO4 B 1002
10	BC1	SOFTWARE	GLY B:570 , ARG B:624	BINDING SITE FOR RESIDUE SO4 B 1003
11	BC2	SOFTWARE	ARG B:366 , LYS B:367 , ALA B:368 , HOH B:1141	BINDING SITE FOR RESIDUE SO4 B 1004
12	BC3	SOFTWARE	SER B:585 , ARG B:586	BINDING SITE FOR RESIDUE SO4 B 1005
13	BC4	SOFTWARE	TYR B:12 , ASP B:359 , VAL B:517 , GLU B:518 , ALA B:524	BINDING SITE FOR RESIDUE GOL B 1006
14	BC5	SOFTWARE	VAL B:517 , GLU B:518 , PHE B:519 , HOH B:1140	BINDING SITE FOR RESIDUE GOL B 1007

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Asymmetric Unit

No.	Residues
1	Leu A:228	-	Pro A:229
2	Arg A:385	-	Pro A:386
3	Ala A:508	-	Pro A:509
4	Gly A:963	-	Pro A:964
5	Leu B:228	-	Pro B:229
6	Arg B:385	-	Pro B:386
7	Ala B:508	-	Pro B:509
8	Gly B:963	-	Pro B:964

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:971
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.hhhhhhhhh........eeee......hhhhhhhhhhhhhhhhhhhhh...........eeeehhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhh....eeeeeeeee..hhhhhhhhhhhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhhh......hhhhh..............hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee......eeeeeeeee..eeeee......hhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh.hhh.eee...hhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhh......eeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhheeeee...........eeee..hhhhh.......eeeeeeehhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhh...eeee................hhhhh.........hhhh.eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q73 A   3 NIPPPFTAPYAPDDAEIAARLLPASHLSPPQEARIHRTATRLIEAIRKRLGGVEDMLREFALSTKEGLALMVLAEALLRVPDARTADQFIEDKLGEGDFIHHETKSTAFLVNASAWARVIQPGETPDGTIGRLVKRLGAPAVRTATRQAMRLMGNHFVLGETIEQALERGKPGQKTRYSFDMLGEGARTAADARRYFDAYASAIETIGKAAGNHALPDRPGISVKLSALHPRFEAISRARVMVELVPQLLDLAQRAKAHDLNFTVDAEEADRLELSLDVIAATLADPSLKGWDGFGLAIQAYQKRASAVIDYVDALARAHDRKLMVRLVKGAYWDTEIKRAQERGLDGYPVFTRKAMTDLNYVACASKLLALRPRIFPQFATHNALTVATVLEMAEGSSGFEFQRLHGMGEALYEQLAKDHADIAYRTYAPVGSHRDLLAYLVRRLLENGANSSFVAQAADYRVPVPALLQRPADAIVRPQAAAHPRIPLPCDLFAPERRNSRGVEFGARTALDQLLTDVKAEIADATPDQAHAAVAAARAGFAGWSRTPAGIRAAALEQAAHLLESRSAHFIALLQREGGKTLDDALSELREAADFCRYYAAQGRKLFGSETAMPGPTGESNALTMRGRGVFVAISPWNFPLAIFLGQVTAALMAGNSVVAKPAEQTPRIAREAVALLHEAGIPKSALYLVTGDGRIGAALTAHPDIAGVVFTGSTEVARSINRALAAKDGPIVPLIAETGGINAMIADATALPEQVAYDVVTSAFRSAGQRCSALRLLFVQEDVADRMIEMVAGAARELKIGDPSDVATHVGPVIDVEAKQRLDAHIARMKTEARLHFAGPAPEGCFVAPHIFELTEAGQLTEEVFGPILHVVRYRPENLERVLRAIERTGYGLTLGVHSRIDDSIEAIIDRVQVGNIYVNRNMIGAVVGVQPFGGNGLSGTGPKAGGPHYLARFATEQTVTINTAAAG 989
                                    12        22        32        42        55        65        75        85        95       105       115      |130       140       150       160       170       180 ||    192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532  ||   548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988 
                                                                           51|                                                                122|                                                   182|                                                                                                                                                                                                                                                                                                                                                           535|                                                                                                                                                                                                                                                                                                                                                                                                                                                               
                                                                            55                                                                 128                                                    185                                                                                                                                                                                                                                                                                                                                                            542

Chain B from PDB  Type:PROTEIN  Length:970
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.hhhhhhhhh.......eeee......hhhhhhhhhhhhhhhhhhhhh...........eeeehhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhh....eeeeeeeee..hhhhhhhhhhhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhhh......hhhhh..............hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee......eeeeeeeee..eeeee......hhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh.....eee...hhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhh......eeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhh..eeeee...........eeee..hhhhh.......eeeeeeehhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhh...eeee................hhhhh.........hhhh.eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q73 B   3 NIPPPFTAPYAPDDAEIAARLLPASHLSPPQEARIHRTATRLIEAIRKRLGGVEDMLREFALSTKEGLALMVLAEALLRVPDARTADQFIEDKLGEGDFIHHETKSTAFLVNASAWARVIQPGETPDGTIGRLVKRLGAPAVRTATRQAMRLMGNHFVLGETIEQALERGKPQKTRYSFDMLGEGARTAADARRYFDAYASAIETIGKAAGNHALPDRPGISVKLSALHPRFEAISRARVMVELVPQLLDLAQRAKAHDLNFTVDAEEADRLELSLDVIAATLADPSLKGWDGFGLAIQAYQKRASAVIDYVDALARAHDRKLMVRLVKGAYWDTEIKRAQERGLDGYPVFTRKAMTDLNYVACASKLLALRPRIFPQFATHNALTVATVLEMAEGSSGFEFQRLHGMGEALYEQLAKDHADIAYRTYAPVGSHRDLLAYLVRRLLENGANSSFVAQAADYRVPVPALLQRPADAIVRPQAAAHPRIPLPCDLFAPERRNSRGVEFGARTALDQLLTDVKAEIADATPDQAHAAVAAARAGFAGWSRTPAGIRAAALEQAAHLLESRSAHFIALLQREGGKTLDDALSELREAADFCRYYAAQGRKLFGSETAMPGPTGESNALTMRGRGVFVAISPWNFPLAIFLGQVTAALMAGNSVVAKPAEQTPRIAREAVALLHEAGIPKSALYLVTGDGRIGAALTAHPDIAGVVFTGSTEVARSINRALAAKDGPIVPLIAETGGINAMIADATALPEQVAYDVVTSAFRSAGQRCSALRLLFVQEDVADRMIEMVAGAARELKIGDPSDVATHVGPVIDVEAKQRLDAHIARMKTEARLHFAGPAPEGCFVAPHIFELTEAGQLTEEVFGPILHVVRYRPENLERVLRAIERTGYGLTLGVHSRIDDSIEAIIDRVQVGNIYVNRNMIGAVVGVQPFGGNGLSGTGPKAGGPHYLARFATEQTVTINTAAAG 989
                                    12        22        32        42        55        65        75        85        95       105       115      |130       140       150       160       170       180 ||    193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533 ||    549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909       919       929       939       949       959       969       979       989
                                                                           51|                                                                122|                                                   182|                                                                                                                                                                                                                                                                                                                                                          535|                                                                                                                                                                                                                                                                                                                                                                                                                                                               
                                                                            55                                                                 128                                                    186                                                                                                                                                                                                                                                                                                                                                           542

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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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	Cis Peptide Bonds
		Ala A:508 - Pro A:509	[ RasMol ]
		Ala B:508 - Pro B:509	[ RasMol ]
		Arg A:385 - Pro A:386	[ RasMol ]
		Arg B:385 - Pro B:386	[ RasMol ]
		Gly A:963 - Pro A:964	[ RasMol ]
		Gly B:963 - Pro B:964	[ RasMol ]
		Leu A:228 - Pro A:229	[ RasMol ]
		Leu B:228 - Pro B:229	[ RasMol ]

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Description