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Title :   CRYSTAL STRUCTURE OF URONATE DEHYDROGENASE FROM AGROBACTERIUM TUMEFACIENS COMPLEXED WITH NADH AND PRODUCT

Authors :   T. Parkkinen, J. Rouvinen

Date :   07 Apr 11 (Deposition) - 15 Jun 11 (Release) - 17 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Ternary Complex, Rossmann Fold, Nad Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Parkkinen, H. Boer, J. Janis, M. Andberg, M. Penttila, A. Koivula, J. Rouvinen
Crystal Structure Of Uronate Dehydrogenase From Agrobacterium Tumefaciens.
J. Biol. Chem. V. 286 27294 2011
PubMed-ID: 21676870 | Reference-DOI: 10.1074/JBC.M111.254854

Molecule 1 - URONATE DEHYDROGENASE
	Chains	:	A, B, C
	EC Number	:	1.1.1.203
	Engineered	:	YES
	Expression System	:	SACCHAROMYCES CEREVISIAE
	Expression System Taxid	:	4932
	Gene	:	UDH, AGR_L_3333, ATU3143
	Organism Scientific	:	AGROBACTERIUM TUMEFACIENS
	Organism Taxid	:	176299
	Strain	:	C58 / ATCC 33970

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 14)

No.	Name	Count	Type	Full Name
1	15L	3	Ligand/Ion	GALACTARO-1,5-LACTONE
2	NAI	3	Ligand/Ion	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
3	PO4	8	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 28)

No.	Name	Count	Type	Full Name
1	15L	6	Ligand/Ion	GALACTARO-1,5-LACTONE
2	NAI	6	Ligand/Ion	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
3	PO4	16	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:10 , ALA A:12 , GLY A:13 , GLN A:14 , LEU A:15 , ASP A:34 , LEU A:35 , SER A:36 , CYS A:50 , ASP A:51 , LEU A:52 , LEU A:71 , GLY A:72 , GLY A:73 , SER A:75 , GLY A:86 , ALA A:109 , SER A:110 , SER A:111 , TYR A:136 , LYS A:140 , ILE A:163 , GLY A:164 , SER A:165 , CYS A:166 , HOH A:295 , HOH A:296 , HOH A:369 , HOH A:376 , HOH A:381 , 15L A:401 , HOH A:499 , HOH A:737 , HOH A:757	BINDING SITE FOR RESIDUE NAI A 400
02	AC2	SOFTWARE	SER A:75 , SER A:111 , ASN A:112 , HIS A:113 , TYR A:136 , GLY A:164 , SER A:165 , ARG A:174 , PHE A:258 , HOH A:292 , HOH A:376 , NAI A:400 , HOH A:415	BINDING SITE FOR RESIDUE 15L A 401
03	AC3	SOFTWARE	GLY A:64 , ALA A:100 , HIS A:101 , HOH A:620 , GLU C:28 , ASN C:44 , HOH C:748	BINDING SITE FOR RESIDUE PO4 A 268
04	AC4	SOFTWARE	ARG A:22 , HIS A:182 , HOH A:318 , HOH A:708	BINDING SITE FOR RESIDUE PO4 A 269
05	AC5	SOFTWARE	ARG A:123 , GLY A:125 , ASP A:215 , HOH A:321 , HOH A:470 , HOH C:353	BINDING SITE FOR RESIDUE PO4 A 270
06	AC6	SOFTWARE	PRO A:119 , ARG A:131 , HOH A:298 , HOH A:437	BINDING SITE FOR RESIDUE PO4 A 271
07	AC7	SOFTWARE	GLY B:10 , ALA B:12 , GLY B:13 , GLN B:14 , LEU B:15 , ASP B:34 , LEU B:35 , SER B:36 , CYS B:50 , ASP B:51 , LEU B:52 , LEU B:71 , GLY B:72 , GLY B:73 , SER B:75 , GLY B:86 , ALA B:109 , SER B:110 , SER B:111 , TYR B:136 , LYS B:140 , ILE B:163 , GLY B:164 , SER B:165 , CYS B:166 , HOH B:282 , HOH B:297 , HOH B:341 , HOH B:371 , HOH B:388 , 15L B:401 , HOH B:613	BINDING SITE FOR RESIDUE NAI B 400
08	AC8	SOFTWARE	SER B:75 , SER B:111 , ASN B:112 , HIS B:113 , TYR B:136 , GLY B:164 , SER B:165 , ARG B:174 , PHE B:258 , NAI B:400 , HOH B:473	BINDING SITE FOR RESIDUE 15L B 401
09	AC9	SOFTWARE	ALA B:63 , GLY B:64 , HIS B:101	BINDING SITE FOR RESIDUE PO4 B 268
10	BC1	SOFTWARE	LYS B:265 , GLN B:266 , HOH B:360 , HOH B:593 , TYR C:92	BINDING SITE FOR RESIDUE PO4 B 269
11	BC2	SOFTWARE	GLY C:10 , ALA C:12 , GLY C:13 , GLN C:14 , LEU C:15 , ASP C:34 , LEU C:35 , SER C:36 , CYS C:50 , ASP C:51 , LEU C:52 , LEU C:71 , GLY C:72 , GLY C:73 , SER C:75 , GLY C:86 , ALA C:109 , SER C:110 , SER C:111 , TYR C:136 , LYS C:140 , ILE C:163 , GLY C:164 , SER C:165 , CYS C:166 , HOH C:277 , HOH C:286 , HOH C:287 , HOH C:361 , HOH C:378 , 15L C:401 , HOH C:458 , HOH C:533 , HOH C:545 , HOH C:706	BINDING SITE FOR RESIDUE NAI C 400
12	BC3	SOFTWARE	SER C:75 , SER C:111 , ASN C:112 , HIS C:113 , TYR C:136 , GLY C:164 , SER C:165 , ARG C:174 , PHE C:258 , NAI C:400 , HOH C:458 , HOH C:608 , HOH C:628	BINDING SITE FOR RESIDUE 15L C 401
13	BC4	SOFTWARE	ALA C:63 , GLY C:64 , HIS C:101 , HOH C:625 , HOH C:760 , HOH C:763	BINDING SITE FOR RESIDUE PO4 C 268
14	BC5	SOFTWARE	ARG C:22 , HIS C:182 , HOH C:343 , HOH C:622	BINDING SITE FOR RESIDUE PO4 C 269

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

(no "Cis Peptide Bond" information available for 3RFV)

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

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

(no "Exon" information available for 3RFV)

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:265
 aligned with URODH_AGRFC | Q7CRQ0 from UniProtKB/Swiss-Prot  Length:265

    Alignment length:265
                             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     
          URODH_AGRFC     - -MKRLLVTGAAGQLGRVMRERLAPMAEILRLADLSPLDPAGPNEECVQCDLADANAVNAMVAGCDGIVHLGGISVEKPFEQILQGNIIGLYNLYEAARAHGQPRIVFASSNHTIGYYPQTERLGPDVPARPDGLYGVSKCFGENLARMYFDKFGQETALVRIGSCTPEPNNYRMLSTWFSHDDFVSLIEAVFRAPVLGCPVVWGASANDAGWWDNSHLGFLGWKPKDNAEAFRRHITETTPPPDPNDALVRFQGGTFVDNPIFKQ 264
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhh...eeeeeeee..........eeeee....hhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhh.................hhhhhhhhhhhhhhhhhhhhhh..eeeeee..........hhhhhh.hhhhhhhhhhhhhhh......eeee..........hhhhhhhh.....hhhhhhhhhhh........hhhhhh.hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rfv A   2 AMKRLLVTGAAGQLGRVMRERLAPMAEILRLADLSPLDPAGPNEECVQCDLADANAVNAMVAGCDGIVHLGGISVEKPFEQILQGNIIGLYNLYEAARAHGQPRIVFASSNHTIGYYPQTERLGPDVPARPDGLYGVSKCFGENLARMYFDKFGQETALVRIGSCTPEPNNYRMLSTWFSHDDFVSLIEAVFRAPVLGCPVVWGASANDAGWWDNSHLGFLGWKPKDNAEAFRRHITETTPPPDPNDALVRFQGGTFVDNPIFKQ 266
                                    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

Chain B from PDB  Type:PROTEIN  Length:265
 aligned with URODH_AGRFC | Q7CRQ0 from UniProtKB/Swiss-Prot  Length:265

    Alignment length:265
                             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     
          URODH_AGRFC     - -MKRLLVTGAAGQLGRVMRERLAPMAEILRLADLSPLDPAGPNEECVQCDLADANAVNAMVAGCDGIVHLGGISVEKPFEQILQGNIIGLYNLYEAARAHGQPRIVFASSNHTIGYYPQTERLGPDVPARPDGLYGVSKCFGENLARMYFDKFGQETALVRIGSCTPEPNNYRMLSTWFSHDDFVSLIEAVFRAPVLGCPVVWGASANDAGWWDNSHLGFLGWKPKDNAEAFRRHITETTPPPDPNDALVRFQGGTFVDNPIFKQ 264
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhh...eeeeeeee..........eeeee....hhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhh.................hhhhhhhhhhhhhhhhhhhhhh..eeeeee..........hhhhhh.hhhhhhhhhhhhhhh......eeee..........hhhhhhhh.....hhhhhhhhhhhhh......hhhhh..hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rfv B   2 AMKRLLVTGAAGQLGRVMRERLAPMAEILRLADLSPLDPAGPNEECVQCDLADANAVNAMVAGCDGIVHLGGISVEKPFEQILQGNIIGLYNLYEAARAHGQPRIVFASSNHTIGYYPQTERLGPDVPARPDGLYGVSKCFGENLARMYFDKFGQETALVRIGSCTPEPNNYRMLSTWFSHDDFVSLIEAVFRAPVLGCPVVWGASANDAGWWDNSHLGFLGWKPKDNAEAFRRHITETTPPPDPNDALVRFQGGTFVDNPIFKQ 266
                                    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

Chain C from PDB  Type:PROTEIN  Length:265
 aligned with URODH_AGRFC | Q7CRQ0 from UniProtKB/Swiss-Prot  Length:265

    Alignment length:265
                             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     
          URODH_AGRFC     - -MKRLLVTGAAGQLGRVMRERLAPMAEILRLADLSPLDPAGPNEECVQCDLADANAVNAMVAGCDGIVHLGGISVEKPFEQILQGNIIGLYNLYEAARAHGQPRIVFASSNHTIGYYPQTERLGPDVPARPDGLYGVSKCFGENLARMYFDKFGQETALVRIGSCTPEPNNYRMLSTWFSHDDFVSLIEAVFRAPVLGCPVVWGASANDAGWWDNSHLGFLGWKPKDNAEAFRRHITETTPPPDPNDALVRFQGGTFVDNPIFKQ 264
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhh...eeeeeeee..........eeeee....hhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhh.................hhhhhhhhhhhhhhhhhhhhhh..eeeeee..........hhhhhh.hhhhhhhhhhhhhhh......eeee..........hhhhhhhh.....hhhhhhhhhhhhh......hhhhhh.hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rfv C   2 AMKRLLVTGAAGQLGRVMRERLAPMAEILRLADLSPLDPAGPNEECVQCDLADANAVNAMVAGCDGIVHLGGISVEKPFEQILQGNIIGLYNLYEAARAHGQPRIVFASSNHTIGYYPQTERLGPDVPARPDGLYGVSKCFGENLARMYFDKFGQETALVRIGSCTPEPNNYRMLSTWFSHDDFVSLIEAVFRAPVLGCPVVWGASANDAGWWDNSHLGFLGWKPKDNAEAFRRHITETTPPPDPNDALVRFQGGTFVDNPIFKQ 266
                                    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

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 3RFV)

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (URODH_AGRFC | Q7CRQ0)

molecular function
	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:0050662	coenzyme binding	Interacting selectively and non-covalently with a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0050388	uronate dehydrogenase activity	Catalysis of the reaction: D-galacturonate + H(2)O + NAD(+) = galactarate + 2 H(+) + NADH.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3rfv)

Biological Unit
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	3rfv
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	1.1.1.203
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 14)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

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